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How to write academic papers: a comprehensive guide.

BY SAMANTHA ANDERSON

The fact that the majority of students consider their academic papers as one of the most complex assignments does not seems surprising at all. Why is that so? Why are these assignments so complicated? There are a few main reasons. First of all, in order to provide a high-quality paper, one has to fulfill a whole list of subtasks, such as choosing the right topic, organizing the whole paper, finding relevant literature, conducting a research, etc… The actual writing is just one phase of the whole process. The problem with this phase is that it is not an easy task to provide the content that is concise and informative, but at the same time interesting and original. It seems that the writing talent is of great help in this process, but unfortunately, only a small percentage of students actually possess this kind of talent. Besides that, every academic term paper writing has to be done in accordance with a specific set of writing norms and rules (for example, APA or Chicago), so students should also get familiar with these.

The additional problem is that these obligations are very common, so they have a significant influence of the final grades. In the text below, a few tips and pieces of advice on how to provide a high-quality academic paper will be provided, so students should get familiar with these as they can be very beneficial for their future education.

Types of academic writing

Of course, there are different types of academic papers, depending on their content, research design, writing style, audience, etc… These are some of the most common types of academic papers.

            Research paper

This is one of the most common types of academic writing. This is a paper that requires the combination of creativity, research skill, and the knowledge of a particular topic. The creativity takes place at the beginning of the paper in which a student should elaborate the main idea of his research and explain why this domain is investigated. Although it is not always the case, these papers often include the actual research process, so a student has to collect his own data. This indicates that the research design has to be constructed. A research design contains information such as who will be the participants (i.e. the sample of a particular population), how the data will be collected, what instruments or questionnaire will be used, what kind of statistical analysis will be provided, etc… At the end, the results have to be interpreted and discussed.

            Essays

            Essays don’t include the process of collecting the data, but it does include the literature review, i.e. the process of collecting relevant information on a particular topic. Of course, one should only use academic and reliable sources of information (scientific books, articles, scientific papers, etc…). There are 4 main types of essays:

  • The expository essay (the elaboration and explanation of a particular topic or idea; for example, “The main postulates of the Roman law”)
  • The persuasive essay (the writer aims to defend a certain claim or a point of view; “Why smoking is harmful?”);
  • The analytical essay (the process of analyzing a certain domain, such as a work of art, some natural process, etc…; “The influence of Homer’s Iliad on poetry”)
  • The argumentative essay (elaborating why a certain point of view is more accurate than the other ones; “Why are non-physical forms of punishment more effective than the physical ones?”)

Academic proposal

This type of academic paper can be considered as a concise version of the scientific paper. It represents detailed and elaborated plan of the research. Another important thing to mention is that it is submitted before the actual research takes place.

Writing pitfalls

Although every student has his own style and specific writing issues, there are a few very common pitfalls.

Using complex expressions

A lot of students make mistake by thinking that they will make a positive impression by using complex expressions and complicated sentences. However, the truth is usually quite the opposite; this kind of elaboration can often represent the compensation for the lack of understanding a particular construct.

Forcing productivity

In the domain of writing, productivity is tightly connected to the creativity and inspiration, and the problem with these two is that they cannot be forced. Some students believe that they should finish their paper “in one breath”, so they force themselves to write even if they are tired. The best advice is to make a short break (preferably in a physically active manner) whenever a student feels that he is getting tired and losing his focus.

Writing in Second/Third person

Academic papers are almost always written in a third person. This way the content sounds more objective, as it can be seen in these examples.

Second person: You shouldn’t smoke because it is bad for you.

Third person: Smoking should be avoided, as it can cause serious physical consequences.

Citations and References

Every academic paper has to be written in accordance with a certain set of writing rules. The three of the most common ones are APA (American Psychological Association), MLA (Modern Language Association), and Chicago. Considering that there are minor differences between these citation styles, only one of them will be further elaborated, as it is very simple to find the examples of other two citation systems online.

APA is mostly used in psychology and education domain. Here are some examples:

In-text citation:

(Author, year of publication, page number); “People are not just on looking hosts of internal mechanisms orchestrated by environmental events” (Bandura, 2001, p.4)

Author, A. A. (Year of publication).  Title of work: Capital letter also for subtitle . Location: Publisher.; Amabile, T. M. (1983). The social psychology of creativity . New York: Springer-Verlag.

Author, A. (Publication Year). Article title. Periodical Title, Volume(Issue), pp.-pp.; Bruer, J. T. (1997). Education and the brain: A bridge too far. Educational researcher, 26 (8), 4-16.

Writing assignments are considered to be one of the most complex academic obligations for a good reason. In this text, some of the main domains were elaborated and a few pieces of advice were provided. With dedication and these tips in hand, it is almost certain that every student can ensure a high-quality academic paper of any kind.

About the author:

Samantha Anderson is a passionate teacher. She found her destiny in developing new educational approaches. Which she kindly shares on the blog. Her free time is dedicated to writing college essays for students in order to help them find the real purpose of it. according to Samantha’s lifestyle, rock climbing is the best thing for relaxation.

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Writing an Academic Paper: A Beginner’s Guide

Writing an Academic Paper: A Beginner’s Guide

Table of contents

write academic paper

Catherine Miller

An academic paper might be quite different from other writing you’ve done before. But never fear — with my experience of writing as an undergraduate, Master’s student, and teacher, I’m here to help you understand the ins and outs of writing an academic paper so you’ll ace your next assignment. 

Academic writing is done by scholars for an audience of other scholars. This means your audience is likely to be quite informed about your field of study, so you won’t need to start from the absolute basics. But, it also means your piece needs to be well-researched, with a clearly thought-out argument or informative literature review supported by academic sources. 

In this article, I’ll give you a step-by-step guide to putting together an academic paper that will get you a top grade. 

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Topic Selection

If you need to write an academic paper as part of your class assignment, you might have clear instructions on what the topic needs to be. This could be a question to answer, an argument statement to support or refute, or a general topic area to research which you can then develop your own specific paper title for. Make sure you double check the grading requirements and any other guidelines provided by your teacher or institution.

If you’ve got some freedom to come up with your own ideas, spending some time reading around your subject and brainstorming potential topics could be a good place to start.

Brainstorming Ideas

It’s wise to start by reading the recommended course material, especially the key texts. If you’re not sure what the best books and articles for additional reading might be, ask your professor for some recommendations. 

As you read, keep an eye out for ideas that might be ripe for exploration. If your paper is supposed to be an argument, look out for areas of the topic that seem to generate debate. 

It’s a good idea to make notes as you go, keeping track of potential citations and the information you’ll need to include in your bibliography. Organized notes can make all the difference when it comes to putting your finished paper together! You could do this using software like Notion , Evernote , or Google Keep , a spreadsheet, or even good old pen and paper.

Selecting a Focused Topic

Most academic papers will require you to come up with an argument, and a good place to start is narrowing down your thesis statement, i.e. the main point of your paper. This needs to be a defendable statement, so picking something for the sake of being controversial might leave you in a tricky position if there aren’t enough sources to back it up. Additionally, it needs to be something focused enough to explore in a few pages, rather than needing a whole book to explain. 

For example ‘ The economic situation of 1930s Germany was the key reason for Hitler’s rise to power.’ The thesis statement takes a clear position, can be defended, and isn’t too wide-ranging. 

Your own opinion on what you’ve read will be important, but you should also engage with the existing scholarship in the field. Whether you decide to stick with the consensus, or go against the grain, you will need to have a good understanding of what others have said.

Exploring the Background Information

Once you’ve reviewed any provided course materials and recommended reading, it’s important to recognize and address any glaring gaps in your knowledge. Are there any terms you don’t understand? Do you need to build an understanding of any particular events, people, or themes? Check the citations and bibliography of your readings to find and jump off to other works to build an understanding of how scholarship on the topic has progressed. 

Finding Scholarly Sources for Research

Depending on your subject area, you may need to find and use both primary and secondary sources for your research. Primary sources may include:

  • Newspaper articles
  • Historical documents
  • Eyewitness accounts or interviews
  • Documentary materials
  • Photographs
  • Novels, plays, and/or poems 
  • Pieces of art
  • Government reports
  • Lab data/reports

Secondary sources are usually other academic papers, critical works, or books that review a range of evidence and comment upon primary sources. These can include textbooks, biographies, literary criticism, etc., depending on your field of study. 

Your college library is a great place to start your research, especially if you need to use works that are not yet available digitally. However, many academic journals are now online, meaning you can find a wealth of other papers to read and reference within a few clicks. You should check which journals your college subscribes to, and you can search sites like JSTOR and Google Scholar .

Read the full article -  Best Research Tools of 2023

Outline Creation

Before you start writing, it’s a good idea to create a paper outline. This will help you fix your structure, clarify your points, and can ultimately make it quicker to write up the final piece.

Read the full article -  Creating an Outline with AI .

Creating an Overall Structure

The structure of an academic paper is likely to be more complex and developed than essays you may have written for school. You will need to make your thesis statement clear and support this with both evidence and analysis, as well as refuting other, competing ideas. Your work should reach a clear conclusion that leaves your reader in no doubt of your main argument. Nailing down your thesis statement, the key supporting points, and the main points you want to refute, should provide you with an overall structure for your academic paper.

Identifying and Summarizing Key Points

As you read around the topic, you should start to find repeated ideas that will become the main themes of your work. For example, if you are exploring how a theme is presented by a particular poet, you might find five or six ways the writer handles this idea. You will need to decide which one you find most persuasive by deciding which one has the most compelling evidence. This will become your thesis statement. The other ideas can be refuted as you develop your argument.

It’s a good idea to create a summary of each main idea you want to include by boiling it down into a few sentences at most. You can use software like Wordtune Read to help you. This AI (artificial intelligence) reader automatically summarizes longer documents to make it easier for you to condense the main ideas you will later re-expand. 

As you write out your plan, these summaries will form kernels of your developed paragraphs, saving you lots of time in writing the final piece.

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Essential Steps of the Writing Process

Writing up your academic paper might feel intimidating, but once you’ve got your structure plotted out, fleshing out the bones of the argument is the fun part. Make sure you leave enough time to write the paper and review it in plenty of time before the deadline, ideally taking some time away from the paper so you can come back to it with fresh ideas (which makes it easier to see any mistakes!).

Thesis Statement

Your thesis statement should come towards the start of your academic paper. This sets up the purpose of your paper, and establishes a trail of thought that your reader should be able to follow throughout the piece. It’s good practice to return to the thesis statement regularly throughout your work, and make sure you restate it in the conclusion (paraphrased if necessary to avoid robotic repetition). 

Before you begin writing the whole paper, work on your thesis statement by condensing the main argument of your paper into just one sentence. If you’re not sure if you have enough evidence for the argument you want to make by the time you finish your plan, you might need to revise your thesis statement before you write the whole paper. Trust me: it’s easier to change the thesis before you write all the paragraphs.

Read the full article -  How to Write a Thesis Statement with AI

Writing an Introduction

The introduction of an academic paper must make your argument clear, and should be concise and free of any fluff. You need to clearly lay out your argument, but should also set the scene for your work by summarizing the major scholarship, or history of the field, which most writers do first. You should also consider if the information you include in the introduction is definitely relevant to or necessary for the rest of the piece. For example, throwing in dates or definitions at this point may well be a distraction. Someone should be able to read just your introduction and already have a clear idea of your argument.

Additionally, your introduction needs to engage the audience by giving them a hint of the argument to come and suggesting why this topic is important. From a pile of 200+ papers, will your professor enjoy reading yours? A good introduction can help you to make a great first impression.

Read the full article - A Step-by-Step Guide to Writing Compelling Introductions

Body Paragraphs

Each paragraph of your paper should clearly support your thesis statement, or refute an alternative idea. Topic sentences (sentences that lay out the main point of each paragraph, before you go on to flesh out the detail) can be a good way to establish a clear thrust for each paragraph. However, it’s better to avoid formulaic or repetitive paragraph structures where you can. 

The key idea of each paragraph should be supported by evidence, which you will want to comment on, either to establish how you agree with it or to argue against it. Drawing connections between different pieces of evidence, or synthesizing and/or comparing ideas, can make your use of evidence more complex and nuanced, and therefore more effective.

Consider how the paragraphs flow into one another. Referencing the previous paragraph and setting up the purpose of the next can create a more coherent structure for your paper and therefore make it easier to follow. 

Drafting a Conclusion

The conclusion should bring the reader back to your thesis statement, and leave them in no doubt as to the strength of your argument. This is not a place to introduce new information or ideas at any length, although you may want to suggest further areas of study or research. 

Keep your conclusion concise, too. If possible, finishing with a memorable closing sentence can round off your paper with a flourish and leave a lasting impression on your audience. 

Don’t forget that revising your work is a crucial step! You should re-read your work a number of times to check if the structure and argument work well. You could try re-summarizing each paragraph, too, to make sure your points are clear. 

Once you are confident that the content of the paper is solid, it’s time to look at the technical construction of your phrases and sentences, which is where editing and proofreading come in. 

Editing and proofreading

Editing and proofreading are very important. The last thing you want to do is hand in a paper that’s difficult to read and follow because of technical errors. However, for many people, this is also an intimidating step.

One technique to try with your paper is to read it aloud. This can often highlight phrases or sentences that don’t work well or that don’t feel natural. You could also try reading your paper backwards, sentence by sentence. This forces your eye to stop skimming the page, which can lead to you missing mistakes. 

It’s not just technical features that may need editing. As you re-read, you might notice words and phrases that can be upgraded to make your ideas stronger, or to help you communicate in a more engaging way. Luckily, you don’t need to do this all yourself; a digital tool like Wordtune can help you improve your work by suggesting alternative ways to express your ideas. You can even direct it to make suggestions in a particular tone (for example, more or less formal). Wordtune will also check your work for spelling and grammar mistakes, which can also save you time and stress. 

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Including Citations

The evidence you use in your academic paper needs to be cited correctly. Check the guidelines your institution follows for citation, as there are a few different models out there. However, most models will share the following in common:

  • For each quotation from a source, provide the author’s name, date of publication, and page number (this can be in-text or as a footnote, depending on style guidelines). Some models also like you to provide the title of the text and the location of production.
  • Use quotation marks to indicate where you have taken text from another source (to avoid plagiarism) 
  • To include a bibliography at the end of your paper (a full list of works cited). This should only include the texts you have cited, and usually references the title of the academic journal or book, date of publication, volume number (if it’s a journal), page numbers (if referencing a chapter or article), publishing company and location of production.

Citing correctly is a crucial part of how to write an academic paper, but it can also be fiddly and time consuming. Keeping accurate and organized notes while you research can make this bit easier. 

Practice makes perfect

Learning how to write an academic paper is a process, so give yourself plenty of time to write your first one. As you progress in your studies, you will become more efficient and quicker at writing papers. And, don’t forget, you’re not alone! There are loads of resources out there to help you write an academic paper, including digital tools like Wordtune, online help guides, and support from your professor and institution, too. Before you know it, you’ll be turning in high quality, engaging academic papers that will help you ace your courses.

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Academic writing is an important aspect of higher education, as it helps to develop critical thinking, research skills, and the ability to communicate complex ideas effectively. However, for many people, writing an academic essay can be a daunting task. In this blog, we will take you through the process of writing an academic essay, step by step, so that you can approach your next writing assignment with confidence.

From understanding the assignment and researching the topic to developing an outline and revising your work, we will cover all of the key elements of the academic essay-writing process. We will also provide tips and tricks for overcoming common challenges and improving your writing skills. Whether you’re just starting out in your academic career, or you’re a seasoned pro looking to refine your writing skills, this blog has something to offer.

So, if you’re ready to take your academic writing to the next level, read on and discover how to write an academic essay that will impress your readers and help you achieve your goals.

Table of Contents

Writing an Academic Essay

1. introduction.

The introduction is one of the most important parts of an academic essay, as it sets the stage for what’s to come. The introduction should provide background information on the topic, establish the purpose of the essay, and clearly state your thesis. The purpose of the introduction is to engage your reader and make them want to continue reading.

writing an academic essay

Here are some key steps to writing a strong introduction:

1. Start with a hook

Begin your introduction with a hook that will grab the reader’s attention. This could be a quote, a statistic, or an interesting fact related to the topic.

2. Provide background information

After the hook, provide some background information on the topic to give context to the reader. This information should be relevant to the topic and help the reader understand why it’s important.

3. State your thesis

The thesis statement is a clear and concise statement of what you will argue in your essay. It should be placed near the end of the introduction and should reflect the focus of your essay.

4. Preview the main points

Preview the main points of your essay, so the reader knows what to expect. This will give your reader a roadmap for what is to come and will help you to stay focused as you write your essay.

5. Engage your reader

The introduction should engage your reader and make them want to continue reading. Avoid using too much technical language or jargon, and instead, focus on making your introduction accessible and interesting.

Writing a strong introduction to an academic essay is crucial for engaging your reader and setting the stage for what’s to come. By starting with a hook, providing background information, stating your thesis, previewing the main points, and engaging your reader, you will be well on your way to writing a strong academic essay.

2. Literature Review

The literature review is a critical component of an academic essay, as it provides a foundation for the rest of your research. The purpose of a literature review is to summarize and synthesize previous research on the topic and to identify gaps in the existing knowledge. The literature review should be more than just a list of articles and books, but rather an evaluation of the relevant literature.

writing an academic essay

Here are some key steps to writing a literature review :

1. Choose the right sources

Start by identifying relevant sources for your literature review. This may include academic journals, books, conference proceedings, and theses. Make sure to choose only the most relevant and up-to-date sources.

2. Read and take notes

Once you’ve identified your sources, it’s time to read and take notes. Use a system to keep track of the information and be sure to note the author, date, and key findings of each source.

3. Summarize the literature

In your literature review, you should summarize the key findings of each source, highlighting their relevance to your research. You should also synthesize the information, looking for patterns, similarities, and differences among the sources.

4. Evaluate the literature

A strong literature review should not just summarize the sources, but also evaluate them. This means examining their strengths and weaknesses and assessing their relevance to your research question .

5. Identify gaps in the literature

As you evaluate the sources, look for gaps in the existing knowledge and areas where further research is needed. This will help you to identify the significance of your research and justify the need for your study.

6. Organize your literature review

Once you’ve completed your evaluation, you should organize your literature review clearly and logically. This could be chronologically, thematically, or based on methodology.

By choosing the right sources, reading and taking notes, summarizing and evaluating the literature, identifying gaps, and organizing your review, you will be able to provide a thorough and well-supported foundation for the rest of your essay.

3. Methodology

The methodology section of an academic essay is where you describe the methods you used to conduct your research. This section is an opportunity to explain the steps you took to answer your research question and to justify why you chose these methods. The methodology should be detailed, precise, and transparent so that others can understand and replicate your study if necessary.

writing an academic essay

Here are some key steps to writing a strong methodology:

1. Define your research question

Before writing your methodology, you should have a clear understanding of your research question. This will guide the choice of methods you use and the information you collect.

2. Choose the right methods

The choice of methods should be guided by the research question. For example, if you’re conducting a survey, you would use a different method than if you were conducting a case study. Consider the strengths and limitations of each method, and choose the one that is best suited to your research question.

3. Explain your methods in detail

In your methodology, you should describe your methods in detail, so that others can understand how you conducted your research. This should include information on the sample size, how you collected the data, and any instruments or techniques you used.

4. Justify your methods

You should justify why you chose the methods you used and how they are appropriate for answering your research question. This might involve a discussion of the limitations of your methods and how they affect the results.

5. Address ethical considerations

If your research involved human subjects, you must address ethical considerations in your methodology. This might include information on informed consent, data confidentiality, and any potential risks to participants.

6. Be transparent

Your methodology should be transparent and honest so that others can understand and replicate your study if necessary. Be sure to report all of the methods you used, even if the results were not what you expected.

By defining your research question, choosing the right methods, explaining your methods in detail, justifying your methods, addressing ethical considerations, and being transparent, you will be able to provide a thorough and well-supported methodology for your essay.

The results section of an academic essay is where you present the findings of your research. This section should be clear, concise, and objective, and should present the data without any interpretation or discussion. The results should be organized logically and should include tables, figures, and other visual aids as necessary.

writing an academic essay

Here are some key steps to writing a strong results section:

1. Summarize the data

The first step in writing the results section is to summarize the data you collected. This might involve calculating means, standard deviations, and other descriptive statistics , depending on the type of data you collected.

2. Organize the results

This might involve presenting the results for each hypothesis, each research question, or each variable, depending on the nature of your study.

3. Use visual aids

Visual aids, such as tables and figures , can help to clarify and simplify the results. Make sure to label each visual aid clearly, and provide a caption that explains what the visual aid is showing.

4. Be objective

The results section should be objective, presenting the data without any interpretation or discussion. The interpretation of the results should be left to the discussion section.

5. Report results accurately

The results section should report the results accurately and precisely. This might involve rounding numbers to a specified number of decimal places, or using appropriate units of measurement.

In summary, by summarizing the data, organizing the results, using visual aids, being objective, and reporting the results accurately, you will be able to present your findings in a clear and compelling manner.

5. Discussion

The discussion section of an academic essay is where you interpret the results of your research and relate them to your research question and the broader literature. This section is an opportunity to conclude, make recommendations, and reflect on the strengths and limitations of your study. The discussion should be well-organized and should provide a clear and concise interpretation of the results.

writing an academic essay

Here are some key steps to writing a strong discussion section:

1. Interpret the results

The first step in writing the discussion section is to interpret the results of your study. This might involve comparing your results to previous research, explaining any unexpected results, and drawing conclusions about the implications of your findings.

2. Relate the results to your research question

The discussion should relate the results of your study to your research question, demonstrating how the results answer the question and providing insights into the topic.

3. Evaluate the strengths and limitations of your study

The discussion should include an evaluation of the strengths and limitations of your study, addressing any limitations that might affect the validity of the results, and suggesting areas for future research.

4. Draw conclusions

The discussion should conclude the results of the study, make recommendations based on the findings, and discuss the implications for future research.

5. Consider the broader context

The discussion should consider the broader context of the research, relating the findings to the broader literature and making connections to other related fields.

6. Write clearly and concisely

The discussion should be well-written and easy to understand, using clear and concise language. Avoid using technical jargon, and make sure to define any terms that may be unfamiliar to your reader.

6. Conclusion

The conclusion of an academic essay is the final section in which you summarize the key points of your argument and provide closure to your reader. This section should be concise and to the point, reiterating the main points of your essay and providing a final perspective on your topic. The conclusion should also reflect on the implications of your research, considering the broader context of your study and its contributions to the field.

writing an academic essay

Here are some key steps to writing a strong conclusion:

1. Summarize the key points

The first step in writing the conclusion is to summarize the key points of your essay. This might involve restating your research question, summarizing your findings, and reiterating your arguments.

2. Reflect on the implications of your research

The conclusion should reflect on the implications of your research, considering the broader context of your study and its contributions to the field. This might involve discussing the potential applications of your findings, considering any ethical implications, or discussing future directions for research.

3. Provide closure

The conclusion should provide closure to your reader, bringing your argument to a logical end and tying up any loose ends. This might involve suggesting a conclusion based on your research, or providing a final perspective on your topic.

4. Avoid introducing new information

The conclusion should avoid introducing new information or arguments that were not discussed in the body of your essay. This might confuse your reader and undermine the coherence of your argument.

5. Write concisely

The conclusion should be concise, using clear and concise language to summarize the key points of your essay. Avoid using technical jargon, and make sure to write in a way that is easy for your reader to understand.

By summarizing the key points, reflecting on the implications of your research, providing closure, avoiding introducing new information, and writing concisely, you will be able to provide a compelling conclusion to your argument.

7. References

The references section of an academic essay is a crucial component that provides a list of the sources you used in your research and writing. The purpose of the references section is to give credit to the authors whose work you have used, to provide evidence for your arguments, and to support the validity of your research.

writing an academic essay

Here are some key steps to writing a strong references section:

1. Follow a specific citation style

The first step in writing the references section is to follow a specific citation style. There are several citation styles used in academic writing, including APA , MLA , and Chicago , and it is important to choose the one that is appropriate for your discipline and the type of essay you are writing.

2. Cite all sources used in your essay

The references section should include a citation for all sources that you used in your essay, including books, journal articles, websites, and other types of sources.

3. Follow the format guidelines

The references section should be formatted according to the specific citation style that you have chosen. This might involve including information such as the author’s name, the title of the source, the publication date, and the page numbers for any direct quotes or paraphrased material.

4. Alphabetize the references

The references section should be alphabetized according to the author’s last name, or the first word of the title for sources without authors.

5. Check for accuracy

Before submitting your essay, make sure to check the references section for accuracy, verifying that all of the information is correct and that all of the sources are cited properly.

By following a specific citation style, citing all sources used in your essay, following the format guidelines, alphabetizing the references, and checking for accuracy, you will be able to provide a comprehensive and well-documented references section for your essay.

8. Appendices

The appendices section of an academic essay is an optional component that provides additional information that supports the main argument or research findings. This section might include materials such as graphs, tables, maps, images, or other types of data or supplementary information.

writing an academic essay

Here are some key steps to writing a strong appendices section:

1. Decide what to include

The first step in writing the appendices section is to decide what to include. This might involve evaluating the relevance of different types of information and determining which information is necessary to support your argument.

2. Label and organize the appendices

The appendices should be labeled and organized clearly and consistently, making it easy for the reader to understand the information being presented. This might involve including a title or description for each appendix, and numbering the appendices in a logical order.

3. Refer to the appendices in the main body of your essay

The appendices should be referred to in the main body of your essay, helping to connect the appendices to your argument. This might involve including a reference to the appendix in your text, or including a cross-reference to the appendix in your table of contents.

4. Use clear and concise language

The appendices should be written using clear and concise language, making it easy for the reader to understand the information being presented. Avoid using technical jargon, and make sure to write in a way that is accessible to your reader.

Before submitting your essay, make sure to check the appendices section for accuracy, verifying that all of the information is correct and that all of the tables, graphs, and other materials are properly labeled and organized.

By deciding what to include, labeling and organizing the appendices, referring to the appendices in the main body of your essay, using clear and concise language, and checking for accuracy, you will be able to provide a comprehensive and well-documented appendices section for your essay.

In Conclusion

Writing an academic essay is a complex and challenging task that requires careful planning, research, writing, and revision. From developing a strong thesis statement and researching the topic to writing the introduction, literature review, methodology, results, discussion, conclusion, and references, each step in the essay writing process requires attention to detail and a commitment to producing a high-quality essay.

By following the guidelines and tips outlined in this blog, you will be able to write a clear and well-structured essay that effectively communicates your argument, supports your claims with evidence, and meets the expectations of your reader.

In conclusion, writing an academic essay is a multi-step process that requires time, effort, and dedication. However, by breaking the process down into manageable steps, and by focusing on the key elements of writing an effective essay, you will be able to produce a high-quality essay that meets the expectations of your reader and contributes to your academic or professional success.

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Home » Academic Paper – Format, Example and Writing Guide

Academic Paper – Format, Example and Writing Guide

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Academic Paper

Academic Paper

Definition:

Academic paper is a written document that presents the findings of a research study or scholarly inquiry in a formal manner. It is typically written by researchers or scholars and is intended to communicate their research findings to their peers or the academic community at large.

Types of Academic Paper

There are several types of academic papers that are commonly assigned in academic settings, including:

  • Research papers : These are papers that involve the collection, analysis, and interpretation of data to answer a research question or test a hypothesis.
  • Review papers: These are papers that synthesize and analyze existing research on a particular topic to provide a comprehensive overview of the field.
  • Case studies: These are papers that examine a particular instance or example in-depth, often used in business or law settings.
  • Essays : These are papers that provide a well-organized argument or analysis of a topic, often used in literature or philosophy courses.
  • Lab reports : These are papers that document experiments conducted in a laboratory setting and include detailed observations, methods, results, and conclusions.
  • Thesis and dissertations : Thesis are long-form research papers that are typically required for advanced degrees, such as a Master’s or PhD.
  • White papers : These are papers that provide detailed information about a particular product, service, or issue, often used in marketing or policy settings.
  • Position papers : These are papers that present a particular point of view or stance on a controversial issue, often used in political or social settings.
  • Literature reviews : These are papers that critically evaluate and summarize the research literature on a particular topic, often used in social and health sciences.
  • Conference papers : These are papers presented at academic conferences, which typically focus on recent research and developments in a particular field.
  • Book reviews: These are papers that provide a critical analysis and evaluation of a book, often used in literature or history courses.
  • Personal statements : These are papers that are used in applications for academic programs or scholarships, in which the author describes their background, interests, and qualifications.
  • Reflection papers: These are papers in which the author reflects on their own experiences or observations related to a particular topic, often used in education or social work courses.
  • Policy papers : These are papers that provide recommendations or proposals for addressing a particular policy issue, often used in political science or public policy courses.
  • Technical reports : These are papers that provide detailed information about a technical project or process, often used in engineering or computer science settings.

Academic Paper Format

Academic papers typically follow a specific format, although it can vary depending on the discipline or journal. Here is a general outline of the components that are commonly included:

  • Title page : This should include the title of the paper, the author’s name, and their affiliation (e.g. university or organization).
  • Abstract : This is a brief summary of the paper, typically around 150-250 words. It should provide an overview of the research question, methods, results, and conclusions.
  • Introduction : This section should introduce the topic of the paper and provide some background information. It should also include a clear research question or hypothesis.
  • Literature review : This section should review the existing research on the topic and explain how the current study contributes to the field.
  • Methodology : This section should describe the methods used in the study, including the sample, measures, and procedures.
  • Results : This section should present the findings of the study, typically using tables and figures to display the data.
  • Discussion : This section should interpret the results and discuss their implications. It should also address the research question or hypothesis and explain how the findings contribute to the field.
  • Conclusion : This section should summarize the main findings and their implications, and suggest directions for future research.
  • References: This section should list all the sources cited in the paper, following a specific citation style (e.g. APA, MLA).

Example of Academic Paper

Example Sample of Academic Paper is as follows:

Title Page:

  • Running head: TITLE OF PAPER
  • Title of paper
  • Author’s name
  • Institutional affiliation
  • A brief summary of the paper’s main points, including the research question, methods, results, and conclusions
  • Should be no more than 250 words

Introduction:

  • Introduce the research question and provide background information
  • Discuss the significance of the research question and how it relates to previous research in the field
  • Provide a clear and concise thesis statement
  • Describe the research design, including the participants, procedures, and materials used
  • Explain how data was collected and analyzed
  • Present the findings of the study in a clear and organized manner
  • Use tables and figures to visually represent the data

Discussion :

  • Interpret the results and explain their significance
  • Discuss how the findings relate to the research question and previous research in the field
  • Identify limitations of the study and suggest directions for future research

References:

  • List all sources cited in the paper, formatted according to APA style guidelines.

When to Write Academic Paper

There are several occasions when you might want to write an academic paper, including:

  • Coursework : In many academic programs, you’ll be required to write papers as part of your coursework. This may include essays, research papers, case studies, or other types of academic writing.
  • Conference presentations: If you’re a researcher, you may want to present your work at academic conferences. Writing an academic paper can help you organize your thoughts and prepare for your presentation.
  • Journal publications: Publishing a paper in a peer-reviewed academic journal is an important way to share your research with the broader academic community. This can help you build your reputation as a scholar and may be required for promotion or tenure.
  • Grant proposals: When applying for research funding, you may need to submit a proposal that includes a research paper outlining your research question, methodology, and expected results.
  • Thesis or dissertation: If you’re pursuing a graduate degree, you’ll likely need to write a thesis or dissertation, which will require extensive research and academic writing.

Purpose of Academic Paper

Academic papers serve several purposes, including:

  • Contribution to knowledge : One of the primary purposes of academic papers is to contribute to the existing body of knowledge on a particular topic. By conducting research and presenting new findings, scholars and researchers can build upon previous work and expand our understanding of a subject.
  • Communication: Academic papers allow researchers to communicate their findings to a wider audience, including other scholars, students, and policymakers. Through publications, academic papers can reach a broader audience and have a greater impact on society.
  • Validation and peer review: Academic papers are subjected to rigorous peer review by other experts in the field. This process helps ensure the accuracy and validity of the research and helps maintain the quality of academic work.
  • Career advancement : Publishing academic papers is often a requirement for career advancement in academia. Researchers who publish frequently are more likely to receive grants, promotions, and tenure.
  • Preservation of knowledge : Academic papers are often archived and made available for future generations to study and learn from. They can provide a record of research and scholarship that can be used to build upon in the future.
  • Development of critical thinking skills : The process of writing an academic paper requires careful analysis, critical thinking, and problem-solving skills. By engaging in this process, researchers can develop their abilities to think deeply and systematically about complex topics.
  • Influence on policy: Academic papers can have a significant impact on policy decisions. Policymakers often rely on academic research to inform their decisions, and researchers who are able to communicate their findings effectively can have a real-world impact.
  • Advancement of science and technology : Many academic papers are focused on advancing science and technology. By publishing research on new technologies or breakthroughs in scientific understanding, researchers can help drive innovation and progress in these fields.
  • Education and training: Academic papers are often used as educational resources in universities and other academic settings. They can provide students with valuable insights into research methods, data analysis, and academic writing.
  • Building collaborations: Collaborations and partnerships can be built through academic papers. Researchers working on similar topics can connect through publications, leading to further research and collaboration opportunities.

Advantages of Academic Paper

Academic papers have several advantages, including:

  • Sharing knowledge : Academic papers are an effective way to share knowledge with other scholars and researchers in a particular field. Through publication, ideas and findings can be disseminated to a wider audience and contribute to the advancement of knowledge in a particular discipline.
  • Building credibility : Publishing academic papers can help researchers establish credibility and demonstrate expertise in their field. By contributing to the scholarly conversation, researchers can gain recognition and respect from their peers.
  • Facilitating collaboration: Academic papers can foster collaboration between researchers who share similar interests and can lead to new research partnerships and collaborations.
  • Providing feedback: Academic papers often go through a peer-review process, which allows for constructive feedback from other experts in the field. This feedback can help researchers refine their ideas, strengthen their arguments, and improve the quality of their work.
  • Career advancement: Publishing academic papers can be important for career advancement in academia. It is often a requirement for promotion and tenure, and can also help researchers secure funding for future research projects.
  • Preservation of knowledge : Academic papers are often archived and preserved, ensuring that the knowledge and findings they contain are accessible to future generations of researchers and scholars.

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  • November 30, 2022
  • Academic Advice

How To Write an Academic Essay: A Beginner’s Guide

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During college, you must participate in many writing assessments, one of the most important being academic essays. Unfortunately, only a few are well-informed about the process of academic writing. 

If you’re reading this, you probably want to learn how to write an academic essay. Follow our guide! Here we’ll introduce the concept of the academic essay, the five components of an academic essay, the format of an academic essay, and more.

Ready to master your academic essay writing? Let’s go!

What Is an Academic Essay?

An academic essay is writing created to initiate debate, defend an idea, or present a new point of view by supporting it with evidence. 

One of the most important components that differentiate it from typical essays you have written in high school is supporting ideas with evidence. If you claim that, for example, “divorces have a negative impact on young children,” you need to find sources that support your argument to make it more convincing.

Interpreting facts is another essential element of a successful academic piece of writing. Academic essays should be written in a formal tone, with a set structure, and have a critical, based, and objective viewpoint. You should be able to understand and transmit different points of view to your readers in a simple but formal manner. 

Are you still trying to figure out what steps you should take to start writing? Keep scrolling!  

How To Write an Academic Essay

write academic paper

Writing an academic essay can initially seem intimidating, especially if you are unfamiliar with the rules and requirements. 

The time and effort spent on the writing task might differ depending on the topic, word limit, deadline, and other factors. However, the key steps, including preparing for the writing, creating a thesis statement, introduction, conclusion, and editing process, must be included in every academic writing style. 

By following the detailed list of actions below, you can start and finish your essay in no time.

Prepare to write your essay

Before going into the technical part of the writing process, one piece of advice you should keep in mind is planning. Planning is as important as the writing process. If you plan correctly, you will have sufficient time to perform every step successfully. Failure to plan will lead to a messy essay and, worst-case scenario, an unfinished writing piece. 

Understand your assignment

First and foremost, before you take any action regarding writing your essay, you must ensure you have clearly understood every tiny detail that your instructor has provided you—this step will determine your academic essay’s effectiveness. But why is that? Understanding the assignment in detail will leave no space for any irrelevant information that would lead to wasted time and, ultimately, a lower grade. 

Develop your essay topic

If your instructor doesn’t give you a specific topic, you should spend some time finding a topic that fits the requirements. Finding a topic sounds easy, but finding the right one requires more than just a simple google search.

So, ensure you develop an original topic, as it adds more value to your academic writing. However, ensure that there is enough evidence from other sources to help you back up your arguments. You can do this by researching similar topics from trusted sources.

Do your research and take notes

Once you determine the topic, go on and do some research. This part takes a lot of effort since there are countless sources online, and obviously, you have to choose some of the best. 

Depending on your topic, there might be cases where online sources are not available, and you’ll also have to visit local libraries. Whatever the case, you need to take notes and highlight the components you want to include in your essay. 

A quick tip: Go back to your topic often to avoid getting swayed or influenced by other less relevant ideas. 

Come up with a clear thesis statement

An excellent academic essay contains a strong thesis statement. A strong thesis statement successfully narrows your topic into a specific area of investigation. It should also intrigue your readers and initiate debate. 

A good thesis statement is:

  • NOT a question  
  • NOT a personal opinion

Create a structure

After gathering all the necessary information, you can begin outlining your main ideas. The primary academic essay structure is classified into the following 

  • Introduction

Failure to maintain these three components in your academic essay will result in a poorly written assignment. Luckily, you can easily avoid that by following our guide.

Writing the introduction

what-is-the-format-of-academic-essay

Your essay will be divided into paragraphs of equal importance, but the introductory part should always stand out. You must make your introduction as presentable as possible and get the reader’s attention. Work on it as if you were to get graded only by the evaluation of that first paragraph. 

The purpose of the introduction is to demonstrate that your thoughts and ideas are logical and coherent. Also, depending on the word limit, you can use more than one paragraph.  

Hook the reader

All forms of writing benefit from an attractive hook. If you have no idea of how to hook the reader, you can go the safe way and choose a recent fact or statistic. Statistics will give your essay credibility, surprise the readers, and make them want to keep reading.  

Give background on the topic

Now that you have the reader’s attention, you should strive to expand the essay’s key points but to a limit since the introduction is only one part of the whole essay. You should generally explain what gaps from previous sources you will cover and what others have covered so far. 

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Present your thesis statement

When introducing your thesis statement, you can present it as a statement of fact or controversial. If you decide to give a statement fact, it will be challenging to keep your audience engaged since facts can be easily proven. But presenting it more controversially will keep your audience awake and can even result in a better grade overall.

Writing the body of your essay

how-do-you-write-an-effective-academic-essay

The body part of your essay is where you’ll expand all of your ideas presented in the introduction. It’s essential to stay consistent and not include irrelevant information. Since it is the longest part of your essay, you can easily get lost, and to prevent that, it would be best to map an internal outline specific to each paragraph. This way, you know what to include and where. 

Paragraph structure

Each paragraph should follow a specific structure. It should begin with an introductory sentence that tells the reader the main ideas you will discuss in the paragraph. It’s advisable to point back to your thesis statement to identify the relationship between it and the existing idea. Also, ensure that each paragraph demonstrates new ideas.  

Length of the body paragraphs

Depending on the topic and the arguments you’ve gathered, it’s advisable not to exceed 200 words per paragraph in academic writing. If your paragraphs are too long and contain unnecessary wording, it will become difficult for the reader to follow your point. So keep them clear and concise.

Writing the conclusion

Congratulation, now you’ve made it to the last paragraph of your essay. The conclusion’s primary purpose is to summarize the ideas presented throughout your essay. Writing a good conclusion should take little time since you know what the essay contains. However, be aware of what points you should or shouldn’t include.

What to include in your conclusion 

A strong conclusion needs to have an introductory sentence. In some cases, if your instructor approves, it can include other areas that need to be investigated in the future. But at its core, it should only remind the reader about the main arguments discussed.

What not to include in your conclusion 

You should at all times refrain from including new ideas. Since the essay ends with the conclusion, don’t go into details or support new points. Doing that will confuse the reader and result in a poor grade. 

Editing your essay

how-to-write-an-academic-essay

Without a doubt, editing is just as important as writing. No matter how careful you are during writing, there’s a high possibility that there will be some slip-ups. These can range from spelling mistakes to grammar, punctuation, and so on. We suggest you spend time doing other things and return to the essay again. This will help you notice errors that you otherwise wouldn’t. 

Tips for Writing a Great College Essay

Now that you have a clear idea of the process of writing an academic essay, we have a few more tips: 

  • Always cite your sources
  • Gather enough sources to support your thesis statement
  • Keep your sentences short and comprehensive
  • Start the research as early as possible 
  • Do not skip revising 

The Bottom Line

Writing an academic essay is a complex task. But with the right tools, guidance, and willingness to learn from your mistakes, you will master academic writing in no time. Make sure to follow each of the abovementioned steps and practice as much as possible. And don’t forget to edit!

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  • how to write an academic paper
  • How to Write Good Academic Papers: Easy Guide for Beginners

How to Write Good Academic Papers: Easy Guide for Beginners

How to Write Academic Paper: Main Points to Consider

General principles, essential steps of the writing process, thesis statement, introduction, body paragraphs, editing and proofreading.

Have no idea how start an engaging introduction paragraph in your history essay? Need advice on how to write good academic paper  - you are not alone. Academic writing is an important skill for the success in higher education and in any career field but many university students find their written assignments too challenging and often consider them to be a form of a medieval torture.

Why is it so? The problem is that a lot of high school graduates enter colleges and universities having no idea how to complete grammatically correct sentences that make sense, to say nothing about writing a college-level academic paper because no one taught them how to do it right and present a clear, logical and convincing argument.

If you struggle with similar issues, read this article where you will find a complete guide on how to write good academic papers. We will provide you with all necessary information. You can order a well-written model essay on our website to have a better understanding of the general rules of academic writing and the proper paper structure and format.  

Many young people have difficulties with academic paper writing. This type of writing is specific and differs a lot from what you were asked to produce in high school because it involves a lot of reading, doing in-depth research of scholarly literature, planning, revising, making changes in content and structure, rewriting, editing, proofreading, and formatting. Don’t be scared. Writing is a skill that any student can learn and master. We hope that this short guide will explain everything you need to succeed.

What is an academic paper ? This type of writing can be defined in many ways and your instructors can give different names to these assignments – essay, term paper, analysis essay but all of them have the same purpose and are based on the same principles.

The goal of completing written assignments is to show that you have a profound knowledge of a specific topic and to share your own thoughts about a scientific question or an issue that may be of interest to your audience – students, your professor, and other scholars. You have to demonstrate your critical thinking skills.

Take into account 8 key principle of academic writing.

  • Your papers must have a clear purpose (inform, analyze, synthesize or persuade) and answer your topic question.
  • Your papers must present your original point of view.
  • Your writing must have a single focus – all paragraphs have to include relevant evidence (facts, expert opinions, quotations, examples) to support your thesis statement.
  • You must follow a standard organizational pattern. Every academic text must include the following parts: an introduction, the main body, and a conclusion. Some papers may require an abstract .
  • As an author, you need to provide clear, logical, and simple explanations to your reader.
  • You should refer to a number of scholarly sources. You need to integrate source materials into your discussion. Take care to include all sources (books, articles from a scientific journal, publications on online resources) that you cite, introduce, analyze or explain on a reference list in the bibliography page.
  • To ensure academic integrity, all college essays should be formatted in accordance with the requirements of one of the specific citation styles – APA, MLA, Harvard, Chicago that determine the rules for in-text citations, paper sections, format, reference list.
  • You need to use your own words. Don’t try to be too formal or you may sound boring to your readers. Use natural language, common for conversations.

Writing an academic paper can be done step-by-step. If you are a beginner, you can follow these steps that have worked for millions of college students; they can save you a lot of time.

  • Select an interesting topic. If you lack ideas, you may search the internet using Google, look through your lecture notes, and consider your course readings or current news.
  • Do research and record sources’ information. Keep in mind that you may need to continue research as you discover thesis, make an outline, write and revise the document.
  • Formulate a strong thesis statement that you will argue.
  • Plan your essay and make a basic outline. Take notes from your sources and add details to your outline and make sure that you have supporting evidence for your points.
  • Write the first draft of your essay. You can start from any part and you shouldn’t worry about grammar, punctuation and spelling as you construct your sentences. You will fix it later.
  • Revise your first draft and improve the content, logic, and the flow. Make transitions between your ideas. Make changes to improve the content and rewrite your draft. You may need to do it more than once.
  • Edit and proofread your final draft to ensure that your essay is flawless.

These are basic steps. When you gain experience, you may think about a different order that can work best for you. Find that this process complicated? Buy a professionally written sample to analyze it and see how your essay should look like!

Let’s discuss the major steps of the writing process.

A thesis statement determines the main argument of your essay. A good thesis statement expresses the main idea of your essay, presents your own point of view, and gives an answer to your research question. The success of your entire project depends on your thesis and you need to do your best to ensure that it is debatable, specific, and concise. Try to write your thesis early. It will help you stay focused when you do research and take notes.

Introductions and conclusions are very important. The introduction introduces your argument to your reader and convinces them why they should care about reading your paper. Your task is to engage your audience. Wondering how to do it? Check this useful article on our blog that discusses engaging strategies for starting an essay .

Start your introduction with attention grabber and provide background information about the significance of your topic, introduce a subject, and give some definitions of the key terms. End your introduction with a thesis statement.

Start each body paragraph with a topic sentence; don’t begin a paragraph with a fact. The topic sentence should present the main idea of the paragraph and express your point of view. In the next sentences, you should support the topic sentence with additional supporting ideas, specific details, interesting facts, statistics, clear explanations, relevant examples. All supporting sentences should be logical. You should make sure they are connected with connection words to help your reader follow your argument.

Finish every paragraph with a concluding sentence. It should be your own idea and not a source citation. The last sentence in a paragraph should review the key points you have discussed in it, emphasize your main idea or your thesis statement, and prepare your audience to the points that you are going to discuss in the next paragraph.

This part of your paper is the most important. Actually, readers remember the first and the last parts of what they read; a conclusion is your last chance to make an impression and show the significance of your findings. How can you achieve that? When writing a conclusion, you need to provide connections to the previous ideas, briefly summarize your findings or restate the thesis. You shouldn’t include any new information. Finish your essay with a strong concluding statement that your readers will remember.  

No one can write a perfect first draft. It’s impossible - revising is critical if you want to impress your professor and get a high grade for your work. You should start revising the content at least a week before your paper is due. You can use another strategy as well - revise individual paragraphs as you write them. Be ready that you may need to write more than one draft or revise your paper several times.

Read your paper and make changes to fix it and make impeccable. You can do it in a number of ways.

  • Eliminate irrelevant ideas and unnecessary information
  • Add new explanations, details, points to ensure additional support for your argument
  • Rewrite paragraphs and sentences to present your ideas better
  • Re-organize paragraphs and sentences to make your paper logical

Do you like your essay’s content? If you do, it’s time to edit it and add finishing touches. The goal of editing is making your writing clearer, more precise to ensure that your readers will be able to understand it.

How should you do it? You may ask someone to read your essay and request their feedback. You can read your college paper aloud yourself to hear the lack of clarity, repetition, wordiness, grammar mistakes and correct them. Use English dictionaries and grammar books.

You should use the following editing strategies to make your essay as best as it can be.

  • Fix sentences with the passive voice
  • Improve word choice by replacing long words with shorter ones
  • Improve sentence structure and word order – correct run-ons and fragments
  • Fix the logic, flow, and connections between ideas
  • Rewrite long sentences and make them concise; eliminate unnecessary sentences in paragraphs if they don’t convey new messages
  • Fix repetition and use thesaurus to find synonyms

When you finish editing, proofread your essay and fix minor errors, careless mistakes, typos. Check punctuation and spelling. Use the printed copy to notice mistakes you may overlook on a computer screen. Start proofreading with the last sentence and go backward; in this way, you will focus on spelling and grammar and not on the content.

We have discussed how to write academic paper. Let’s talk about another important aspect of your future essay – citations. To avoid plagiarism, you must give credit to other people whose ideas you use in your own work.

You have the right to express your opinions. You have the right to use ideas of people to support your argument and draw conclusions, but it’s your responsibility to inform your audience which ideas in your essay are not yours and which are your own. With proper citations, you demonstrate that you understand the significance of other people’s research, findings, and ideas in developing your own argument.

How to cite your sources? You should include in-text citations in accordance with the guidelines of the citation style recommended by your instructor. You are required to include a list of the sources you have cited at the end of your paper. Don’t cite works that are not in your bibliography.

Follow these guidelines and useful tips to create great papers and impress your professor. Need interesting topic ideas for your projects? Check other articles on our blog.

Writing academically on a college level is a hard work that requires a lot of time and effort. You can’t become a confident writer in a few days if you just read grammar and style guides no matter how full and detailed they are. You have to practice a lot. It means working for many hours every day.

If you are not sure that you can cope with your complicated assignment on your own, you can pay to get professional help in any subject from experts on our site.  Our writers can provide you with quality sample papers on different topics that will be perfect in content and style. They are sure to be free of errors. You can use paid custom papers as good templates you can follow when creating your own works and understand how to write good academic papers. In this way, you can easily improve your analytical, critical and writing skills and become a successful student who gets high grades.   

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Content Writing How to Write an Academic Paper – Tips with Examples

write academic paper

  • 1) What is An Academic Paper?
  • 2.1) Share research findings with others
  • 2.2) Establish credibility and expertise
  • 2.3) Contribute to the academic community
  • 2.4) Build Academic career
  • 2.5) Improve writing and critical thinking skills
  • 3.1) Choose a Topic
  • 3.2) Conduct Research
  • 3.3) Create an Outline
  • 3.4) Write a Thesis Statement
  • 3.5) Write the Introduction
  • 3.6) Write the Body
  • 3.7) Write the Conclusion
  • 3.8) Add References and Citations
  • 3.9) Edit and Revise
  • 4.1) APA style:
  • 4.2) MLA style:
  • 4.3) Chicago style:
  • 4.4) Harvard style:
  • 5.1) Choose the appropriate citation style:
  • 5.2) Use a citation management tool:
  • 5.3) Include in-text citations:
  • 5.4) Include a reference list or bibliography:
  • 5.5) Double-check your citations:
  • 6.1) Title page:
  • 6.2) Abstract:
  • 6.3) Introduction:
  • 6.4) Literature review:
  • 6.5) Methodology:
  • 6.6) Results:
  • 6.7) Discussion:
  • 6.8) Conclusion:
  • 6.9) References:
  • 6.10) Appendices:
  • 7.1) Do’s of Academic Writing:
  • 7.2) Don’ts of Academic Writing
  • 8.1) Research help:
  • 8.2) Organizing information:
  • 8.3) Brainstorming ideas:
  • 9) How to Write an Academic Paper – Use this Outline
  • 10) Conclusion:

Academic writing is challenging for many students. But with the right approach, you can create a well-structured and compelling paper to showcase your knowledge and research. In this blog post, we will discuss steps on how to write an academic paper with useful academic writing tips.

What is An Academic Paper?

An academic paper is a piece of writing that presents research, analysis, or a new idea on a specific topic. These papers are usually written by scholars, researchers, or students as part of their academic work and are often published in academic journals or presented at conferences.

Academic papers follow a specific format and structure, including an introduction that explains the purpose of the paper, a literature review that summarizes previous research on the topic, a methodology section that outlines how the research was conducted, a results section that presents the findings, and a conclusion that summarizes the main points and offers implications for further research.

The language used in academic papers is typically formal and technical, and the writing is often dense and complex. However, the purpose of academic papers is to communicate new ideas or research findings to a specific audience of scholars and researchers, so the language used is precise and focused on the topic at hand.

What is the Importance of Writing an Academic Paper?

Most academic paper pros write academic papers to:

Share research findings with others

Writing an academic paper is an effective way to share your research findings with others in your field. By publishing your work in academic journals or presenting it at conferences, you can contribute to the body of knowledge in your area of study.

Establish credibility and expertise

Publishing an academic paper establishes your credibility and expertise in your field. It demonstrates that you have conducted research and analysis and have a deep understanding of the subject matter.

Contribute to the academic community

Academic papers contribute to the academic community by advancing knowledge and understanding in a particular field. By publishing your work, you are helping to shape and inform future research and study in your area of expertise.

Build Academic career

Publishing academic papers helps you build your career in academia or other fields. It can lead to opportunities for further research, collaborations with other scholars, and job offers in your area of expertise.

Improve writing and critical thinking skills

Writing an academic paper requires a high level of writing and critical thinking skills. By writing academic papers, you can improve these skills and become a better communicator and researcher.

How to Write an Academic Paper – Step by Step Guide

Choose a topic.

Choosing a topic for your academic paper is the first step in writing an effective paper. The topic should be relevant to your field of study and should be interesting and engaging.

Conduct Research

Conducting research is an essential part of writing an academic paper. Research involves gathering information and data from credible sources such as academic journals, books, and reputable websites.

Create an Outline

Creating an outline helps you organize your thoughts and ideas in a logical and structured manner. It provides a roadmap for your paper and helps you stay on track.

Write a Thesis Statement

A thesis statement is the main argument or point that you will be making in your academic paper. It should be clear and concise, and it should be included in your introduction.

Write the Introduction

The introduction is the first section of your paper, and it should provide a brief overview of your topic and the purpose of your paper. It should also include your thesis statement.

Write the Body

The body of your paper should provide detailed information and analysis on your topic. It should be organized into sections and paragraphs, with each section addressing a specific point related to your thesis statement.

Write the Conclusion

The conclusion is the final section of your paper, and it should summarize your main points and restate your thesis statement in a new way. It should also provide some final thoughts and implications for future research.

Add References and Citations

Adding references and citations is an important aspect of academic writing, as it allows you to give credit to the sources you have used and also helps to strengthen the credibility of your arguments.

Edit and Revise

Editing and revising are important steps in writing an effective academic paper. You should read through your paper carefully, checking for errors in grammar, punctuation, and spelling. You should also make sure that your paper is well-organized and flows logically.

How to Write an Academic Paper References and Citations – Different Styles

Here are some popular styles of academic writing references and citations:

APA style: 

The American Psychological Association (APA) style is a widely adopted style for research work in the social sciences. In-text citations in APA style include the author’s last name and the year of publication, such as (Smith, 2019). The reference list at the end of the paper should include the author’s last name, first initial, year of publication, title of the article, title of the journal, volume number, and page numbers, in that order.

MLA style: 

The Modern Language Association (MLA) style is commonly used in the humanities. In-text citations in MLA style include the author’s last name and the page number, such as (Smith 23). The cited page at the end of the paper should include the author’s last name, first name, title of the book or article, title of the journal or publisher, year of publication, and page numbers, in that order.

Chicago style: 

The Chicago style is commonly used in history, social sciences, and some humanities. In-text citations in Chicago style include the author’s last name, year of publication, and page number, such as (Smith 2019, 23). The bibliography at the end of the paper should include the author’s last name, first name, title of the book or article, title of the journal or publisher, year of publication, and page numbers, in that order.

Harvard style: 

The Harvard style is commonly used in the sciences and social sciences. In-text citations in Harvard style include the author’s last name and year of publication, such as (Smith 2019). The reference list at the end of the paper should include the author’s last name, first initial, year of publication, title of the article, title of the journal, volume number, and page numbers, in that order.

Things to Keep in Mind When Adding References and Citations

Here are some points to keep in mind when adding references and citations in an academic paper:

Choose the appropriate citation style: 

Different academic disciplines use different citation styles, so it is important to choose the appropriate style for your paper. Common citation styles include APA, MLA, Chicago, and Harvard. Each style has its own set of rules for formatting citations, so be sure to familiarize yourself with the guidelines before you begin.

Use a citation management tool: 

Citation management tools, such as Mendeley, Zotero, or EndNote, can be helpful in organizing and formatting your references and citations. These tools allow you to easily import and store references from different sources, and they can generate citations and bibliographies in the appropriate style.

Include in-text citations: 

In-text citations are used to indicate where you have used information from a source within your paper. They usually include the author’s last name and the year of publication, and they can be formatted differently depending on the citation style you are using.

Include a reference list or bibliography: 

A reference list or bibliography should be included at the end of your paper, and it should include all of the sources you have cited in your paper. This list should be formatted according to the citation style you are using.

Double-check your citations: 

It is important to double-check your citations to ensure that they are accurate and consistent with the guidelines of your chosen citation style. You should also make sure that you have cited all of the sources you have used in your paper.

What is the Format of an Academic Paper?

The format of an academic paper varies depending on the specific requirements of the assignment, institution, or academic discipline. However, there are some general guidelines followed in academic writing. Here are the basic elements of an academic paper format:

Title page: 

This includes the title of the paper, the author’s name, the name of the institution, and the date of submission.

This is a brief summary of the main points of the paper, typically no more than 250 words. It should provide an overview of the research question, methodology, and results.

Introduction: 

This section provides background information on the topic, outlines the research question or problem, and sets out the objectives or hypotheses of the paper.

Literature review: 

This section provides an overview of the existing research on the topic, highlighting key studies and theories relevant to the research question.

Methodology: 

This section outlines the research methods and techniques used in the study, including the data collection and analysis procedures.

Results: 

This section presents the findings of the research, typically using tables, charts, or graphs to display the data.

Discussion: 

This section interprets the results of the research and discusses their implications, relating the findings back to the research question and objectives.

Conclusion: 

This section summarizes the main findings of the study, highlights the implications and limitations of the research, and suggests directions for future research.

References: 

This is a list of all the sources cited in the paper, typically presented in alphabetical order according to the chosen citation style.

Appendices: 

This section may include any additional material that is relevant to the study but not included in the main text, such as survey questionnaires or raw data.

Do’s and Don’ts of Writing an Academic Paper

Here are some do’s and don’ts of how to write an academic paper:

here are some do’s and don’ts of writing an academic paper explained in an expressive language:

Do’s of Academic Writing:

  • Do conduct thorough research: Conducting thorough research is essential to ensure that you have enough information to support your arguments and ideas.
  • Do use credible sources: Use credible sources such as academic journals, books, and reputable websites to support your arguments.
  • Do write in a formal tone: Academic papers should be written in a formal tone, using clear and concise language.
  • Do proofread your work: Proofreading your work helps to eliminate errors in grammar, punctuation, and spelling.
  • Do follow the proper format and structure: Follow the proper format and structure for your particular field of study, including the appropriate citation style.
  • Do present your arguments clearly and logically: Your arguments should be presented clearly and logically to ensure that your readers can follow your thought process.

Don’ts of Academic Writing

  • Don’t plagiarize: Plagiarism is a serious offense and can result in severe consequences, including failing the course or even expulsion from school.
  • Don’t use informal language: Avoid using slang, contractions, and other informal language in your academic paper.
  • Don’t overuse quotes: Overusing quotes can make it seem like you are not providing original thought and can detract from the strength of your arguments.
  • Don’t write in a disorganized manner: Writing in a disorganized manner can make it difficult for your readers to follow your thought process and can weaken the impact of your arguments.
  • Don’t ignore the importance of editing and revising: Editing and revising are crucial steps in the writing process and can help to improve the quality and effectiveness of your academic paper.
  • Don’t rely solely on one source: Relying solely on one source can limit the depth and breadth of your research and can weaken the credibility of your arguments.

Can You Use AI For Academic Writing?

Here are some benefits of using an AI writing tool for academic writing:

Research help: 

AI-powered research tools can assist in finding relevant sources related to your topic. These tools use natural language processing (NLP) algorithms to identify key concepts in your query and search for articles that match those concepts.

Organizing information: 

AI-powered tools can assist in organizing research notes, ideas, and outlines. For example, some tools use a “networked thought” approach that allows you to create links between different ideas and concepts. Others allow you to store and organize your references and citations.

Brainstorming ideas: 

AI-powered tools can assist in generating new ideas and insights. For example, some tools use machine learning algorithms to help you cluster similar ideas together and generate new insights from your brainstorming sessions.

AI is a useful tool for academic writing research and organization, but it should not replace critical thinking, analysis, and original thought. It is always important to double-check the accuracy and relevance of the information you find using AI tools. Use AI while following ethical standards and responsibly.

How to Write an Academic Paper – Use this Outline

I. Introduction

A. Background information

B. Brief overview of the research problem

C. Thesis statement

II. Literature Review

A. Overview of research done previously on the topic

B. Gaps in the literature that your research will address

C. Theoretical framework that informs your research

III. Methodology

A. Research design

B. Data collection methods

C. Data analysis methods

IV. Results

A. Presentation of data and findings

B. Analysis of the data and findings

C. Discussion of how the results support or refute the thesis statement

V. Discussion

A. Interpretation of the results

B. Implications for future research

C. Limitations of the study

VI. Conclusion

A. Summary of the main points

B. Significance of the research

C. Recommendations for future research

VII. References

A. List of sources cited in the paper

You can produce a high-quality academic paper that meets the standards of your institution by following these tips. Remember that an academic paper should be of high quality as it demonstrates your expertise in your chosen field.

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  • Open access
  • Published: 19 February 2024

A corpus-based comparison of linguistic markers of stance and genre in the academic writing of novice and advanced engineering learners

  • Siu Wing Yee Barbara 1 ,
  • Muhammad Afzaal   ORCID: orcid.org/0000-0003-4649-781X 2 &
  • Hessah Saleh Aldayel 3  

Humanities and Social Sciences Communications volume  11 , Article number:  284 ( 2024 ) Cite this article

221 Accesses

Metrics details

  • Language and linguistics

Stance-taking in academic writing plays a crucial role in enabling tertiary academic writers to express their positions about their topics and other voices. Based on a corpus linguistic analysis of academic reports by civil and environmental engineering (CEE) undergraduate students and student papers in the Michigan Corpus of Upper-Level Student Papers (MICUSP), this article investigates the use of stance markers in the genres of persuasive and argumentative writing as well as analytical explanatory writing. This study compares the stance markers used by L2 engineering students (Hong Kong University) and native engineering students (U.S. University) to investigate the genre-specific lexical stance patterns used by academic writers. This study found that stance within the CEE reports and MICUSP was expressed through approximative hedges and boosters, code glosses, and adversative and contrast connections, pointing to a specific developmental trajectory as academic writers. Non-native engineering students were found to use a significantly smaller number of approximative, self-mention, and evidential verb hedges. In addition, they tend to use a more significant number of modal hedges compared to native English speakers. The CEE students’ reports also tended to be characterized by the underuse of boosters, contrastive connectors, emphasis, and counter-expectancy markers. However, the study found no significant difference in the use of exemplification markers between the CEE and MICUSP. The findings of this study support the construction of the academic stance as a process of delimiting one’s perspective. This is achieved by deploying selected stance features to account for other scholarly perspectives.

Introduction

In academic writing, linguistic devices are strategically deployed by writers to communicate with their readers (Jin, 2015 ). In technical terms, such attempts to interact with readers may be understood as ‘stance’ (Alghazo et al., 2021a ). ‘Stance’ is defined here as ‘the speaker’s or writer’s feeling, attitude, perspective, or position as enacted in discourse’ (Strauss and Feiz, 2013 ). In an academic context, this allows academic writers to take charge of their work by expressing knowledge-based evaluations of the topics within their writing to convince their readers of their authorial position (Jiang and Hyland, 2015 ). In the realm of academia, writing assumes a formal and enduring style of communication, where individuals from diverse linguistic backgrounds employ stance to share knowledge and actively contribute to the advancement of scientific knowledge, (Alghazo et al., 2021a ; Abusalim et al., 2022 ).

As part of their studies, undergraduate and graduate engineering students undertake various types of scholarly writing, with academic reports comprising one of the most common writing tasks assigned to them. A vital imperative of an effective academic report is the need for students to formulate and present their position or stance towards the topic of scholarly voices within the field. Numerous scholars have identified stance as playing a pivotal role in academic writing research, particularly in linguistics-based studies (Hunston and Thompson, 2001 ; Hyland, 2005b , 2012 ; Silver, 2003 ; Afzaal et al., 2021 , 2022 ; Strange, 2023 ; Keisling, 2011 ; Lu, 2023 ; Alghazo et al., 2023 ). In light of this context, the current study undertakes a comparative analysis of stance markers employed by L2 engineering students and native engineering students with the aim of investigating genre-specific lexical stance patterns utilized by academic writers. Consequently, this research concentrates on undergraduate students pursuing civil engineering, specifically those who have submitted their final-year projects and hold the potential to publish their reports in high-caliber academic journals.

Over the past two decades, various linguistic features have been examined to gauge how writers express stance (Hunston and Thompson, 2001 ), namely: appraisal (Martin and White, 2005 ), evidentiality (Chafe, 1986 ), metadiscourse features (Hyland, 2005a ; Vande Kopple, 1985 ), and positioning (Harré and Van Langenhove, 1999 ; Aull and Landcaster, 2014 ). As this body of research shows, the importance of posture is evident in academic writing across early and upper-level English second language (L2) writing and published academic writing (Hyland and Jiang, 2018 ). Stance-taking and stance-support are considered to be defining acts in the argumentative or expository essay, a text type often used as an assessment tool in academic settings (Chandrasegaran and Kong, 2006 ). Furthermore, stance is viewed as part of an expert writer’s tacit genre knowledge awareness, which can help student writers succeed in college-level writing (Soliday, 2011 , p. 37).

In academic writing, stance is considered vital because it expresses the communicator’s “attitudes, feelings, judgments, or commitment concerning the propositional content of a message” (Biber, 1999 , p. 23). Biber ( 2006 ) elaborates that stance expressions “convey many different kinds of personal feelings and assessments, including attitudes [towards] certain information, how certain they are about its veracity, and how they obtained access to it and what perspective they are taking”. Stance can be achieved through “grammatical devices and lexical words, which express epistemic knowledge (e.g., might, suggest, probably, possibly, likely) and authors’ attitudes towards propositions (e.g., unfortunately, surprisingly)” (Biber et al., 1999 in Shen and Tao, 2021 , p. 2). As a linguistic mechanism, stance is studied from the perspectives of evidentiality, affect, attitude, attitude, evaluation, appraisal, and meta-discourse (Shen and Tao, 2021 ). Drawing upon these linguistic mechanisms, writers can convey their position and feelings about the proposition within their discourse and establish an effective interpersonal relationship with their readers (Kiesling et al., 2018 ; Shen and Tao, 2021 ; Zhang and Zhang, 2023 ).

Metadiscursive cues for facilitating “social negotiations embedded in discourse” are prominent in all “university registers” (Biber, 2006 in Aull, 2019 , p. 268). However, they are particularly significant in scholarly discourse in which “stance is constantly adjusted in interaction with the construed readership” (Wharton, 2012 , p. 262). Drawing upon Hyland ( 2012 ) and Soliday ( 2011 ), Aull ( 2019 ) observes that for learners entering tertiary education programs, linguistic mechanisms for expressing stance tend to be “tacit”. Hence, it is difficult for novice academic writers to comprehend scholarly writing as a discourse that acknowledges, creates, and navigates social relations through the use of stance devices, thus enabling them to evaluate propositions and address alternative perspectives. This is something that is unlikely to be unattainable if the text lacks the use of stance. Under such circumstances, the text is likely to reflect impersonality.

Although stance markers are present in all university registers, they tend to be more prominent in scholarly writing, wherein stance experiences ongoing modification while interacting with an imagined audience (Wharton, 2012 , p. 262). Changing one’s stance is contingent upon disciplinary preferences and broader academic practices (Afzaal & Du, 2023 ; Hyland and Tse, 2004 ). Using stance norms is also important because it directly impacts the grades achieved by native speakers and English language learners who write for school (Lee and Deakin, 2016 ).

Research interests in linguistic stance markers within undergraduate writing have been growing as students who are new to higher education tend to be unaware of these linguistic devices (Hyland, 2012 ). In addition, studying Stance in the writings of L2 writers is also necessary because they employ fewer linguistic resources to alter epistemic commitment when compared with L1 writers (Hyland and Milton, 1997 ). The academic writing of L2 writers differs noticeably, indicating that undergraduates are still learning to apply these linguistic markers. Compared with seasoned scholarly writing, the written output of undergraduate learners tends to make more extensive use of boosters and significantly limited use of hedges (Hyland, 2012 ).

Against this backdrop, the present paper compares the stance markers used by L2 engineering students (from the Hong Kong Polytechnic University) and native engineering students (U.S. University) to investigate the genre-specific lexical stance patterns used by academic writers. Therefore, this study focuses on undergraduate students studying civil engineering who have submitted their final-year projects and have the potential to publish their reports in top-quality academic journals.

Understanding how to identify what constitutes valuable stance patterns in student writing is another difficulty the students face. For instance, a valuable stance pattern may depend on the purpose of writing, ranging as it may from laying out the facts to persuading the readers. For the most part, undergraduate student writing does not resemble published academic writing in terms of level and genre. Students are far more likely to respond to assignments rather than produce writing for scholarly journals. For instance, the writing of undergraduates studying language, philosophy, and education reflects a greater tendency towards the expression of opinions as well as mental processes in the form of lexical verbs and phrases compared with the writing of graduate-level engineering students (Hyland and Jiang, 2018 ). In research comparing authorial attitude expressed via stance adverbs in abstracts within Chinese and American doctoral engineering dissertations, Bao ( 2022 ) found that the Chinese writers tended to deploy more boosters (a category of epistemic stance adverbs) and to use stance adverbs for the expression of affect rather than evaluation. It was observed that the language used to express thoughts and mental processes tends to be more prevalent in reports and research documents than in the assignment genre within the advanced writing corpus (Hardy and Friginal, 2016 ; Rhee, 2023 ). Hitherto, stance research on student writing has confined itself to common genres. While Charles ( 2007 ) has investigated theses and Hyland and Tse ( 2004 ) have focused on abstracts, Hyland ( 2012 ) has explored dissertations, and Aull et al. ( 2019 ) have turned their attention to argumentative essays.

The present paper undertakes a corpus-based comparative analysis of stance expressions in a corpus of final-year projects of engineering students (L2) and an L1 engineering academic writing corpus. As researchers have yet to explore the MICUSP assignment category from this perspective, the present study’s focus represents an attempt to address this gap.

Stance in academic writing

There has been considerable research into using hedges and boosters in academic writing. According to Hyland and Jiang ( 2016 ), these markers demonstrate that “the writer has expressed commitment to the veracity of the propositions he or she offers and the prospective influence on the reader”. Epistemic position markers such as “perhaps”, “maybe”, or “might” allow the creation of a dialogic space. They downplay the degree of confidence ascribed to an accompanying claim, thus allowing for the potential of other ways of thinking and divergence in opinion. On the other hand, boosters such as “unquestionably” sequester the dialogic space by allowing no room for dissent. Existing literature suggests that hedges and boosters enable authors to introduce more indirectness and politeness in academic prose (Hyland, 1998 ; Li and Wharton, 2012 ; Vande Kopple, 2002 ). Based on their studies of hedges and boosters, researchers such as Aull ( 2015 ) and Aull and Lancaster ( 2014 ) observe that successful academic writing is characterized by carefully calibrated epistemic commitment achieved through the strategic deployment of boosters and more liberal use of hedges.

Additionally, according to the studies mentioned above, students transitioning from secondary to postsecondary writing are not always aware of this expectation. Aull et al. ( 2017 ) and Hyland ( 2012 ) pointed out that learners transitioning to postsecondary writing are not always familiar with the notion of epistemic commitment or how to achieve it. Secondary and postsecondary writing is characterized by greater certainty and generality, even though teachers appear to prioritize writing with lower levels of certainty and generality. For instance, while the deployment of hedges in late secondary essays was associated with higher ratings of writing quality (Uccelli et al., 2013), Brown and Aull ( 2017 ) reported “emphatic generality” to be evident in low-attainment writing and “elaborated specificity” to be evident in high-attainment writing in advanced placement (AP) English. Research shows a predominant use of hedges in A-awarded argumentative essays (in contrast with B-graded essays) written by Chinese writers of English and native writers of English in their first year of college (Lee and Deakin, 2016 ). According to Thompson ( 2001 ), interactional techniques include questions or views potentially belonging to the reader (Aull and Lancaster, 2014 ). Interactional resources are modeled more generally as functioning either as “stance” or “engagement” devices in Hyland’s more lexically focused approach (see, for example, Hyland, 2005a , 2005b ). Hyland ( 2005 ) introduces the model of interactional metadiscourse features; within the context of this model, “interactional macro functions” are served by stance and engagement (Hyland, 2005b , p. 176).

Novice and advanced academic writers

Aull and Lancaster ( 2014 ) identified a greater use of hedges and limited generality compared to writing done by novice undergraduate learners (Aull and Lancaster, 2014 ). Investigating instructor evaluations of advanced undergraduate prose, Aull and Lancaster ( 2014 ) notes that while the writing teachers support the strategic use of boosters, they show a preference for student writers demonstrating critical neutrality from the claims. While research suggests that academic writers mould their writing in response to the discursive practices prevalent in their disciplinary field (Hunston, 1994), advanced academic prose, irrespective of the discipline within which it is produced, integrates characteristics that are obstructive rather than supportive of the writer’s argument (Mei, 2007 ). For instance, while observing that clausal features that explicated ideas and relationships supported strongly critical claims in undergraduate argumentative writing, Staples et al. (2016) found that in more explanatory genres, the student academic writers tended to deploy passive voice and complex phrases to distance themselves from critical statements. Therefore, this study focuses on comparing novice and advanced academic writers.

This study investigates stance-taking/interactional strategies deployed by L2 writers compared to native English writers in their report writing. The linguistic aspects of text-based analytical writing asking students to assess a nonfiction article’s theme, make claims about the author’s message, provide evidence to support the claim, and analyze the author’s craft remain unexplored. It is essential to explore these because understanding these aspects enables student writers to express their position and stance toward a topic, author, or issue more effectively. Writing in this style differs from the more common source-based, argumentative style. The present study is significant as it contributes to the existing literature by focusing on the idea that academic argumentation “involves articulating a viewpoint on matters that matter to a discipline” (Hyland, 2012 , p. 134) which can be improved through attention to stance in undergraduate writing. Therefore, the study addresses the following research questions.

The following research questions framed our investigation:

RQ1) What stance-taking/interactional strategies were deployed by L2 writers compared to native English writers in their report writing?

RQ2) What are the key patterns in stance markers deployed by writers in assignments from the CEE and MICUSP corpora?

RQ3) What are the implications of these patterns for the development of L2 writers in the argumentative genre?

The study investigated the stance-taking/interactional strategies used by the L2 writers in relation to upper-level writers in English in an L1 university setting. Therefore, MICUSP is used as the expert corpus, whereas CEE is used as the L2 corpus. A detailed description of the corpora is given in the next section.

The MICUSP corpus

The MICUSP is an online corpus of 829 upper-level student writing documented at the English Language Institute at the University of Michigan (see Romer and O’Donnell, 2011 ). It comprises the writings of ‘highly advanced student writers whose written assignments have been awarded the grade ‘A’ (Ädel and Römer, 2012 , p. 3). This online corpus is freely available to the public. The writing in MICUSP represents a very high standard of upper-level student writing because of the competitiveness of the University of Michigan (UM) undergraduate and post-graduate programs and the high ranking of UM itself, which was ranked as the 28th best undergraduate school in the country in the 2018 US News and World Report rankings (Romer and O’Donnell, 2011 ). Each post-graduate-level UM program included in this research is likewise very selective, placing amongst the top 15 in the country. These programs range from psychology and education to engineering and political science. The study focused on the essays written by civil and environmental engineering departments uploaded to the official corpus of the MICUSP. The upper-level writing in civil and environmental engineering was included to compare the final year reports of Hong Kong Polytechnic University undergraduates.

We extracted 155 Upper-Level Student Papers from the Michigan Corpus of (MICUSP) for our analysis. The MICUSP contains A-graded papers written by native students in the final year of undergraduate education or the first three years of graduate school, thus offering insights into ‘successful university writing models in terms of their linguistic composition, format, and style”’(Hardy and Römer, 2013 ).

The CEE corpus

The Polytechnic University corpus of civil and environmental engineering (CEE) was based on the final year reports submitted by undergraduates studying in the civil and environmental engineering department at the Hong Kong Polytechnic University. This study’s unit of analysis comprised 97 final-year reports written by L2 undergraduates at the Hong Kong Polytechnic University in Hong Kong. Students write final-year project arguments using evidence from expository texts and take their time reading, drafting, writing, and revising them. The CEE corpus comprises a significant collection of writing completed by students transitioning to the next level of their education. The writing was in the form of an argumentative response to readings that were not discipline-specific and included time for the stages of the writing process. The length of the reports in the corpus varies. The average word count of the reports in the entire sample is 8362.69, and the total number of tokens in the CEE corpus are 811,181 (Table 1 ).

Analysis procedure

The research employs a mixed-method approach to analyze the data, encompassing both quantitative and qualitative methodologies. Initially, the study employs quantitative analysis, statistical analysis, and corpus-based analysis using Sketch Engine. Texts in the CEE and MICUSP were uploaded to Sketch Engine (Kilgarriff et al., 2014 ) and annotated with TreeTagger Tag Set (Santorini, 1990 ). The targeted searches of stance markers corresponding to each functional category were adopted from Aull and Lancaster’s ( 2014 ) analysis, which was compiled based on a large strand of relevant literature. In addition, several studies have also utilized Python to extract stance features from political discourse and narratives, as well as for the acquisition of discourse markers. This approach is exemplified in the works of Aminu and Chiluwa ( 2023 ) and Polat ( 2011 ). Corpus query language was written to extract stance markers. Then, each concordance line was manually scrutinized to confirm whether the retrieved item was used as a particular stance marker. For example, we first used the query language [lemma = “particularly”] to extract concordances containing the word particularly and then manually eliminated those in which mainly was used as an adverb, instead of a code gloss, for example, particularly complicated . Subsequently, it transitions to qualitative analysis to delve deeper into the data and gain a comprehensive understanding of the research phenomena. The mean and standard deviation of stance markers used in each corpus are summarized in Table 2 .

This study compares the use of stance markers in reports written by non-native civil engineering students (CEE corpus) with reports produced by native English academic writers (MICUSP corpus). Both hedging and boosting assist authors in expressing a greater or lesser level of commitment to their claims; the phenomenon is examined in our analysis. Hedging is typically realized through appearance-based evidential verbs ( seems, appears ), self-mention phrases ( we believe, from our perspective ), modal verbs of probability ( may, might, and could ), and approximative adverbs ( approximately, about ). In contrast, boosting refers to efforts made to increase epistemic commitment. This is typically accomplished by exaggerating or intensifying adverbs, such as completely and definitely which boost authors’ expressions of stance. Boosting is a form of embellishment (Biber et al., 1999 ; Hyland, 2005b ; Quirk et al., 1985 ).

The proportion of each metadiscourse category

Considering that the MICUSP has different sizes, the frequencies of stance markers used in each corpus are normalized to a common base, i.e., per 10,000 words. Figure 1 compares the normalized frequencies of metadiscourse in reports written by the CEE students and MICUSP writers. The most striking observation to emerge from the data comparison is that these metadiscourse categories are employed in loosely similar proportions in the CEE and MICUSP corpus. Hedges are used most frequently by native and non-native university students, with boosters coming in second place and contrastive connectors in third place. Moreover, the least frequent use is code glosses. Although Biber ( 2006 ) divides epistemic adverbs into four different categories, namely certainty, attitude, and style, these categories are not mutually exclusive. Our results indicated that civil engineering students used fewer phrases of clarity for expressions of likelihood. For example, a claim that is described as either extraordinarily likely or certainly unlikely is a boosted assertion along these lines.

figure 1

Frequency Distribution of Metadiscourse Features in the CEE (Black) and MICUSP (Grey).

Figure 1 indicates that both native and non-native undergraduates used hedges more frequently than other categories of stance markers. The result highlights a general trend that writers, especially advanced language users, tend to open dialogic space using hedges in their writings (Aull, 2019 ). Moreover, the result suggests that boosters are the second most frequently used stance markers in both CEE and MICUSP. The finding is consistent with that of Hyland ( 2005 ) and Lancaster ( 2016 ), who found that advanced language users appear to employ hedges to open dialogic space while using boosters to close dialogic space to achieve more measures and less blunt tone of scholarly writing. Table 3 presents the normalized frequencies of stance makers used in the CEE and MICUSP. A chi-square test of independence was performed via SPSS to examine the relationship between native university students and non-native undergraduates in their use of metadiscourse features. Moreover, Fisher’s exact test was conducted for additional information about the significance value.

As shown in Table 3 , statistical analysis reveals that the use of modal hedges in the MICUSP was significantly less (62.42) than in the writings within the CEE corpus (81.65). However, native college students used a significantly greater number of approximative hedges (49.26), self-mention hedges (1.92), and evidential verb hedges (20.76) than non-native university students (respectively, 32.24, 0.12, and 13.46). In addition, the use of boosters in the MICUSP was greater (114) than evidenced in the writings within the CEE corpus (87.49).

The use of code glosses presents mixed results. Essays written by native college students were found to make significantly more frequent use of emphasis (3.30) and counter-expectancy markers (0.55) and less frequent use of elucidation markers (5.92). Moreover, there was no significant difference between the CEE (17.65) and MICUSP (16.19) concerning the use of exemplification markers. In terms of contrastive connectors, the frequency of contrastive connectors in the MICUSP (72.16) is significantly higher than in the essays written by the CEE students (34.14).

Further analysis of the most frequently used stance words or phrases by native and non-native university students shows more similarities than differences between the corpora from MICUSP and CEE. Table 4 presents the frequently used stance markers in the CEE and MICUSP in the order of their frequencies. For example, the most frequently used evidential verb hedges and self-mention hedges in the two corpora are identical.

Elucidation and exemplifying: use of code glosses

The analysis of the results focuses on code glosses because these are linguistic resources that “assist readers in grasping the acceptable interpretations of components in texts” (Vande Kopple, 1985 , p. 84). Many different code glosses, like approximative hedges, are used to express meanings with greater precision. Furthermore, by indicating that a proposition requires careful elaboration or clarification, code glosses can implicitly elevate the status of material as deserving readers’ attention.

One clear difference between types of code glosses is the distinction between elucidation and exemplification techniques (Hyland, 2007 ). As illustrated in examples 1 and 2 below, extracted from the CEE corpus, the former category comprises moves for explaining, paraphrasing, or specifying a point (made by the writer or someone else), whereas the latter includes moves to further illustrate a point with examples.

Elucidation : The microplastics cannot be treated by a normal wastewater treatment process because it is too small to screen and settle. In other words, microbead finally will discharge to the river or ocean directly and causing plastic resin pellet pollution. (FYP-CEE)
Exemplification: Sources of microplastics in the oceans of the world. Microbead can be defined as a 5 micrometre (μm) to 1 mm plastic fragments or beads made of synthetic polymers. For instance, polyethene, polylactic acid and polypropylene (Rochman, 2015 ). It can usually be existed in various exfoliating personal care and cosmetic products, including body wash, face wash and cosmetics instead of natural ingredients, including oatmeal, walnut husks, and pumice (FYP-CEE).

According to our findings, the CEE used more elucidation than the MICUSP students. Figure 1 also shows that CEE writers use other categories such as counter expectancy of code glosses less frequently than MICUSP writers. While there is a slight increase in the use of exemplification between CEE and MICUSP writers, the differences are minor. The CEE students, like the MICUSP students, include many examples in their argumentation, denoted by such as, for example , and other wordings.

Expressing concession and contrast

Our analysis of frequently occurring adversative/contrast connectors such as however, but , and nevertheless revealed the need to differentiate between two related functional categories: concessive/counter connectors on the one hand and contrast connectors on the other (see, e.g., Halliday and Hasan, 1976 ; Izutsu, 2008 ). Stance features appear in bold and are discussed below each passage. For example, example 3 comes from a research report written by an undergraduate student in civil engineering in the CEE corpus. Fu and Wang ( 2022 ) suggest that interpreted and spontaneous speeches tend to follow distinct hedging patterns in terms of preferred linguistic choices. In addition, hedges can assist researchers in defending their positions while also assisting them in applying plausibility and clarity to their assertions (e.g., Lakoff, 1972 ; Hyland, 2000 , 2005 ).

Concessive/counter : The supply of fresh water supplies declines, wastewater reuse after treatment is gaining recognition around the world. However, it is also important to remember the social and cultural disparities that in various parts of the world, particularly those in which wastewater reuse for food production or some other domestic usage is not yet suitable (FYP-CEE).
Contrast : People use these personal care and cosmetic products every day so that the microbeads flow to the wastewater treatment plant with wastewater. The microplastics cannot be treated by a normal wastewater treatment process because it is too small to screen and settle. In contrast, microbead finally will discharge to the river or ocean directly and causing plastic resin pellet pollution (FYP-CEE).

Concessive/counter connectors, such as those used in Examples 3 and 4, seek to establish an assertion as being contrary to the imagined reader’s anticipation, which falls under the functional category of counter expectancy (e.g., Martin and White, 2005 ). However, there is one more distinction to be made within this category. Whereas ‘however’ follows an earlier conceded element in example 3 (Gladwell is correct), it works in example 4 to signal a counter to an earlier conditional statement. If there is a concession element in the first sentence, it is not stated explicitly (e.g., through signals like certainly, of course, obviously, or is correct). Because these two meanings are related—the element being countered is projected as a possible view—we classified them as concessive/counters. However, contrast expressions such as in contrast and on the other hand , as seen in example 3, work to distinguish between two opposing ideas or views rather than to contradict an earlier statement’s expectation.

In the third example, the author presents both his or her own analytical technique as well as an alternate strategy, emphasizing the distinction between the two by employing a contrastive phrase. In these descriptions, the student allots roughly the same amount of textual space to each strategy, and they place an emphasis on processes (rather than, for example, human actors) and the assumptions that support each strategy.

The need for water in the residential, farming, manufacturing, and urban sectors grows as the human population grows. Whereas the effect of effluent reuse on human health and environmental risk are the two main issues. The effluent reuse should be approached cautiously and only with close analysis of the possible consequences and risks (FYP-CEE).
It became evident shortly after installation that the membranes were fouling. Because the water in Dundee is supplied from Lake Eerie, Enviroquip assumed that there should be no problems with mineral deposits in the Dundee plant. Therefore, in order to solve the fouling problem, the plant began flushing the membranes with a 1% sodium hypochlorite solution. Due to the frequent recurrence of the problem, the plant has used the cleaning solution every two months since the membranes were installed. Recently, the membrane racks were removed for cleaning, at which point mineral deposits were observed on the membrane surfaces. This means that the plant will also have to add flushes of 1% citric acid. However, it is possible that the fouling problems will be resolved by using the proper chemicals because the problem was related to mineral deposits rather than to biomass. As a result of the membrane fouling, the plant is forced to treat a lower quantity of water than it is capable of treating, making the current plant maximum capacity 3.3 MGD instead of the 4.0 MGD possible with the new raw wastewater pumps. Additionally, Enviroquip suggested that they lower the Mixed Liquor Suspended Solids (MLSS), which means that they are wasting a higher volume, and therefore producing more sludge. (FYP- MICUSP Corpus)
Common problems of prairie re-creation and restoration may be further complicated by managing LIHD systems for biofuel production. For example, degraded fields can be so dominated by persistent invasive species such as spotted knapweed (Centuarea maculosa), Kentucky bluegrass (Poa pratensis), and orchard grass (Dactylis glomerata) that increasing native diversity is nearly impossible. Many sub-dominant prairie species, important for overall diversity, have conservative establishment characteristics that limit their ability to compete with invasives. However, the greatest biomass, and thus the most energy, is available after the summer growing season (FYP-MICUSP Corpus)

When compared to the CEE corpus, the MICUSP students use more reformulation strategies, almost around half as often as noted in the examples from the experienced student writers. The bulk of these resources implement a certain kind of reformulation move, referred to as a particular reformulation move, which is perhaps the most significant point to substantiate their work.

Discussions

The study analyzed selected assignments from the CEE Corpus and the MICUSP to identify overlapping patterns in the CEE and the MICUSP corpora. Textual signals that signify reformulation, on the other hand, appear to be equally appreciated in both genre groups. In addition, the study suggests that second language (L2) writers need to be familiar with academic writing rules and the formal code. It is essential for students to understand what linguistic options they have and why and when these options are appropriate. A multi-faceted pedagogical approach may be necessary for teachers to help L2 students develop their language resources and repertoires. The findings presented in the “Results” section also resonate with previous research on boosters and hedges, which suggests that in general, and across all academic fields, skilled academic writers use more hedges than boosters (Hyland, 2005b ; Hyland and Milton, 1997 ; Piqué-Angordans et al., 2002 ). This approach should include exposing students to a variety of materials and activities that are representative of academic writing and align with its conventions, as well as providing explicit instruction that focuses students on syntactic structures and lexical use, as well as strategy instruction that shows how language is used to construct meaning (Maamuujav and Olson, 2018 ). Teachers can assist students in understanding how writers make meaning from and with texts and how linguistic choices are influenced by socially established genre conventions through this approach. Investigating paper categories in the MICUSP, Hardy and Friginal ( 2016 ) found that while more objective genres like reports or research papers featured a greater number of passive voice constructions, argumentative writing was more dialogic, reflecting the linguistic devices of the conversation (e.g., pronouns and adverbs). Students’ performance, academic writing, and metadiscourse markers have been studied extensively. These studies have investigated the ways L2 students write, adjust degrees of doubt and certainty (Hyland and Milton, 1997 ), engage and recruit readers into the discourse, intrude interpersonally in the text through sentence beginnings or themes (Ebeling and Wickens, 2012 ). Research based on secondary and early undergraduate writing has studied the connections between corpus patterns and the genre of assignments. For example, keyword analysis by Aull et al., ( 2017 ) revealed notable divergences between argumentative and explanatory writing in a composition module.

Overall, our investigation of stance markers or metadiscoursal features across all three levels revealed that there appeared to be a clear developmental trajectory in terms of frequency for three categories: hedges, boosters, code glosses, and connectors. These results align with Alharbi’s ( 2023 ) findings, indicating that Arabic writers prioritize the substance of their writing over captivating their audience. Notably, the Arabic corpus demonstrates a significant utilization of self-mentions, with a frequency of 4.2 occurrences per 1000 words. In addition, the most apparent discrepancies were seen between CEE students in more advanced writing corpus MICUSP. As a result of this, the response to our first question is that the CEE students have underused stance markers such as hedges, code glosses, and contrast expressions. In contrast, their more advanced peers and native English learners within MICUSP tend to draw on these linguistic resources more frequently. Moreover, as compared to second language learners of Arab countries extensively employ literary techniques like repetition and emphasis in their scientific writing.

The study found that metadiscoursal resources (e.g., hedges/boosters, code glosses, and adversative/contrast connectors) appeared with greater frequency in the MICUSP corpus (advanced writers) than in the CEE corpus (novice writers). Final-year students studying civil and environmental engineering programs used fewer metadiscourse markers than native English writers whose writings were part of the MICUSP. Specifically, the CEE students tended to underuse approximative hedges, code glosses, concessions, and contrast expressions, while the MICUSP academic writers made more frequent use of these.

These results help to identify the areas where learners might need further support with their academic writing. This highlights indicators that help language teachers to arrange workshops and engage students in writing practice to improve their academic writing skills. Our study is limited to the students enrolled in environmental and engineering school of the Hong Kong Polytechnic University, but future studies may find it valuable to study the reports from other schools because stance analysis is key to preparing student writers effectively for meeting the writing requirements in a variety of genres and disciplines.

These findings have pedagogical implications’ making clear to the reader that these findings have meaning in the real world. For instance, accommodating perspectives, negotiating stance, rebutting alternatives, and persuading the readers can be done more effectively if L2 writers learn to use contrastive connectors within argumentative essays more strategically. The students may also learn about deploying hedging more effectively to contribute to the overall impact of academic writing. Further, corpus-based studies such as this one are vital for identifying variations in stance patterns across writing proficiency levels and study majors.

Data availability

All data generated or analyzed during this study are included in this published article in the supplementary files.

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Introduction, materials and methods, acknowledgments, author contributions, supplementary data, data availability, dive curated terms, molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato.

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Xiaobiao Zhu, Airu Chen and Nathaniel M Butler contributed equally.

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Xiaobiao Zhu, Airu Chen, Nathaniel M Butler, Zixian Zeng, Haoyang Xin, Lixia Wang, Zhaoyan Lv, Dani Eshel, David S Douches, Jiming Jiang, Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato, The Plant Cell , 2024;, koae050, https://doi.org/10.1093/plcell/koae050

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Potato ( Solanum tuberosum ) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene ( VInv ) and cause reducing sugar accumulation. This process, referred to as “cold-induced sweetening,” is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200 bp enhancer, VInv In2En, located in its second intron. We identified several DNA motifs in VInv In2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInv In2En function as a transcriptional enhancer. We developed VInv In2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInv In2En sequence is highly conserved among distantly related Solanum species, including tomato ( Solanum lycopersicum ) and other non-tuber-bearing species. We conclude that the VInv gene and the VInv In2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.

Potato ( Solanum tuberosum ) is the third most important food crop in the world in terms of human consumption ( Devaux et al . 2020 ). In addition, French fries and potato chips are among the most consumed snacks, especially in developed countries. Unlike the grain crops, storage is one of the most important issues related to the potato industry because tubers must be stored at cold temperatures to prevent sprouting and diseases. Unfortunately, cold storage triggers the breakdown of starch and accumulation of reducing sugars, which is referred to as “cold-induced sweetening” (CIS) ( Dale and Bradshaw 2003 ), a costly and nagging problem for the potato processing industry ( Sowokinos 2001 ). The reducing sugars in tubers will react with free amino acids via a nonenzymatic, Maillard-type reaction during high-temperature processing. This reaction results in products with dark color and bitter taste and produces acrylamide, a potential carcinogen ( Mottram et al . 2002 ; Stadler et al . 2002 ). Reducing sugars are the primary determinants for the acrylamide content in fried potato products ( Amrein et al . 2003 ; Becalski et al . 2004 ; Zhu et al . 2016 ). Thus, developing methods to minimize reducing sugars in cold-stored tubers has been an important research focus to reduce acrylamide in fried potato products.

CIS was reported to be associated with numerous genetic loci based on genetic mapping ( Menendez et al . 2002 ; Li et al . 2008 ; Braun et al . 2017 ), genome-wide association studies (GWAS) ( Byrne et al . 2020 ), and comparative proteomics studies between CIS-resistant and CIS-susceptible potato cultivars ( Fischer et al . 2013 ). This can be explained by the fact that CIS is likely linked to numerous enzymes that function in central carbohydrate metabolism in potato tubers ( Sowokinos 2001 ). The vacuolar invertase gene ( VInv ) received a major attention on its potential role in CIS. Partial control of CIS was accomplished by manipulating the activity of the VINV protein ( Greiner et al . 1999 ; Agarwal et al . 2003 ) or the transcription of the VInv gene ( Zrenner et al . 1996 ; Zhang et al . 2008 ). Silencing of VInv using RNAi resulted in nearly full control of CIS in at least some potato cultivars ( Bhaskar et al . 2010 ; Ye et al . 2010 ). Interestingly, VInv gene transcription in tubers is maintained at a minimal level under room temperature. VInv is dramatically upregulated during cold storage in CIS-susceptible potato cultivars ( Zrenner et al . 1996 ; Bagnaresi et al . 2008 ; Bhaskar et al . 2010 ), causing rapid accumulation of reducing sugars. Silencing of the VInv gene has been proven to be an effective approach to control CIS in many potato cultivars ( Bhaskar et al . 2010 ; Ye et al . 2010 ; Liu et al . 2011 ; Wu et al . 2011 ; Clasen et al . 2016 ; Ly et al . 2023 ). Concordantly, overexpression of StInvInh2 , which encodes a vacuolar invertase inhibitor, can also reduce potato CIS ( Liu et al . 2013 ; Mckenzie et al . 2013 ).

Interestingly, the upregulation of VInv in cold-stored tubers is not controlled by its promoter ( Ou et al . 2013 ). The VInv promoter is required to respond to sugars, indole-3-acetic acid (IAA), and gibberellic acid (GA 3 ) but not to cold temperatures ( Ou et al . 2013 ). Here, we report the discovery of a 200 bp transcriptional enhancer, VInv In2En, located in the second intron of VInv . This enhancer is responsible for the cold-induced expression of the VInv gene. We identified several DNA motifs that bind transcription factors (TFs) involved in plant response to cold stress. Mutation of these motifs abolished the function of VInv In2En. We developed VInv In2En deletion lines in both diploid and tetraploid potato lines using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated genome editing. VInv transcription was significantly reduced in the deletion lines during cold storage. Interestingly, the VInv In2En sequence was found to be highly conserved among distantly related plant species, revealing an evolutionary trajectory of the VInv gene in response to cold stress in the tuber-bearing Solanum species.

Discovery of a cold-responsive intronic enhancer within VInv gene

Genomic regions containing active cis -regulatory elements (CREs), such as promoters and transcriptional enhancers, can be identified as DNase I hypersensitive sites (DHSs) ( Zhang et al . 2012 ; Jiang 2015 ; Zhao et al . 2018 ). We previously developed genome-wide DHS maps in DM1-3 potato using chromatin isolated from tuber tissue ( Zeng et al . 2019 ). DM1-3 is a homozygous diploid clone and was developed from chromosome doubling of a monoploid derived from an S. tuberosum Phureja Group clone ( Mribu and Veilleux 1990 ; Paz and Veilleux 1999 ) and has been fully sequenced (2 n = 2 x = 24) ( The Potato Genome Sequencing Consortium 2011 ; Pham et al . 2020 ). We detected a 475 bp DHS within the second intron of VInv ( Fig. 1A ), suggesting that this intron may play a role in the regulation of the expression of VInv . We have recently demonstrated the enhancer function of several intronic DHSs in Arabidopsis ( Arabidopsis thaliana ) ( Meng et al . 2021 ).

Discovery of a cold-responsive intronic enhancer in VInv gene. A) DHSs associated with VInv gene. DHS map was developed from tuber tissue of DM1-3 potato. Two DHSs, 1 at the 5′ of the gene and 1 in the second intron, were detected. B) GUS reporter gene assays of the second intron of VInv gene in ‘Katahdin’ potato. Constructs using a minimal 35S promoter (m35S) and a full-length 35S promoter were used as negative and positive controls. Tubers from transgenic ‘Katahdin’ lines developed using the intronic construct (VInvIn2) and a reverse construct (VInvIn2R) showed minimal GUS signals under room temperature (22 °C). Strong GUS signals were detected from tubers after 4 wks of cold storage under 4 °C. The scale bar represents 2 cm.

Discovery of a cold-responsive intronic enhancer in VInv gene. A) DHSs associated with VInv gene. DHS map was developed from tuber tissue of DM1-3 potato. Two DHSs, 1 at the 5′ of the gene and 1 in the second intron, were detected. B) GUS reporter gene assays of the second intron of VInv gene in ‘Katahdin’ potato. Constructs using a minimal 35S promoter (m35S) and a full-length 35S promoter were used as negative and positive controls. Tubers from transgenic ‘Katahdin’ lines developed using the intronic construct ( VInv In2) and a reverse construct ( VInv In2R) showed minimal GUS signals under room temperature (22 °C). Strong GUS signals were detected from tubers after 4 wks of cold storage under 4 °C. The scale bar represents 2 cm.

To confirm its cis -regulatory function, we cloned the entire VInv second intron (1,327 bp) from RH potato, which is a heterozygous diploid clone ( van Os et al . 2006 ) and has recently been fully sequenced ( Zhou et al . 2020 ). RH is susceptible to CIS ( Supplementary Fig. S1 ). The intron was cloned into the pKGWFS 7.0 vector containing a minimal 35S promoter (−50 to −2 bp) (m35S) and the β-glucuronidase (GUS) reporter gene ( Zhu et al . 2015 ). ‘Katahdin,’ a CIS-susceptible tetraploid cultivar ( Bhaskar et al . 2010 ), was used for transformation. We developed 20 transgenic ‘Katahdin’ lines from the intron construct ( VInv In2) and 20 lines from a reverse construct ( VInv In2R) in which the sequence orientation of the cloned intron is reversed. We detected minimal GUS signals in transgenic tubers stored at room temperature (22 °C). In contrast, substantially enhanced GUS signals were detected in the transgenic tubers after 4 wks of cold storage (4 °C) ( Fig. 1B ). These results indicate that intron 2 of VInv contains an enhancer that is responsible for its cold-induced expression.

Dissection of intronic enhancer via reporter gene assays in A. thaliana

Since the entire intron 2 from RH potato was used for GUS reporter assays, the precise size and position of the predicted enhancer within intron 2 could not be determined. We attempted to fine-map the enhancer using reporter gene assay in A. thaliana . We first examined the GUS signal profiles of transgenic A. thaliana plants using the VInv In2 and VInv In2R constructs. Consistent and strong GUS signals were detected in stems and petioles in transgenic plants derived from both constructs. In addition, relatively weak and sporadic GUS signals were also detected in roots ( Fig. 2B ). The VInv gene is expressed at relatively high levels in several nontuber tissues of potato, including both petiole and stem ( The Potato Genome Sequencing Consortium 2011 ; Zhou et al . 2020 ). Thus, the GUS signal patterns observed in the transgenic A. thaliana plants correspond well with the VInv expression patterns in potato tissues.

Identification of transcriptional enhancers in intron 2 of VInv gene. A) A diagram illustrating the sizes and positions of 10 subfragments derived from intron 2 of the VInv gene. The 1,327 bp intron was divided into 10 fragments (#1 to #10) using 5 breaks (b1 to b5). B) GUS reporter gene assays of intron 2 in A. thaliana. Constructs with minimal 35S promoter (m35S) and a full-length 35S promoter (35S) were used as negative and positive controls. C)  GUS expression patterns of representative A. thaliana transgenic seedlings derived from each of the 10 constructs consisting of a fragment ligated with the m35S promoter and the GUS reporter gene. D) A diagram illustrating the sizes and positions of the 13 fragments derived from the DNA fragment #11. A dashed red line marks the middle point of the 600 bp segment #11. “+” and “−” indicate the derived transgenic seedlings showing positive and negative GUS signals, respectively. E) GUS staining of 20 A. thaliana transgenic seedlings derived from constructs #11, #17, #19, and #21, respectively. F) GUS reporter gene assay of the 200 bp VInvIn2En enhancer in ‘Katahdin’ potato. Tubers from 3 independent transgenic lines showed minimal GUS signals under 22 °C but strong signals from tubers after 4 wks of cold storage under 4 °C. All numbers above bars/lines in A) and D) indicate base pairs. The scale bar represents 2 mm in B, C) and 1 cm in E, F). Fragment numbers highlighted in red color in A), C), D), and E) indicate representative constructs with full enhancer function.

Identification of transcriptional enhancers in intron 2 of VInv gene. A) A diagram illustrating the sizes and positions of 10 subfragments derived from intron 2 of the VInv gene. The 1,327 bp intron was divided into 10 fragments (#1 to #10) using 5 breaks (b1 to b5). B) GUS reporter gene assays of intron 2 in A. thaliana . Constructs with minimal 35S promoter (m35S) and a full-length 35S promoter (35S) were used as negative and positive controls. C)   GUS expression patterns of representative A. thaliana transgenic seedlings derived from each of the 10 constructs consisting of a fragment ligated with the m35S promoter and the GUS reporter gene. D) A diagram illustrating the sizes and positions of the 13 fragments derived from the DNA fragment #11. A dashed red line marks the middle point of the 600 bp segment #11. “+” and “−” indicate the derived transgenic seedlings showing positive and negative GUS signals, respectively. E) GUS staining of 20 A. thaliana transgenic seedlings derived from constructs #11, #17, #19, and #21, respectively. F) GUS reporter gene assay of the 200 bp VInv In2En enhancer in ‘Katahdin’ potato. Tubers from 3 independent transgenic lines showed minimal GUS signals under 22 °C but strong signals from tubers after 4 wks of cold storage under 4 °C. All numbers above bars/lines in A) and D) indicate base pairs. The scale bar represents 2 mm in B , C) and 1 cm in E , F) . Fragment numbers highlighted in red color in A) , C) , D) , and E) indicate representative constructs with full enhancer function.

We next divided the 1,327 bp intron 2 into 10 DNA fragments (#1 to #10) using 5 breaks (b1 to b5; Fig. 2A ). Each fragment was ligated to the m35S promoter and cloned into the pKGWFS 7.0 vector. Transgenic plants derived from DNA fragments #1, #2, #9, and #10 showed strong GUS signals in stems and petioles, which were similar to the transgenic plants developed from the VInv In2 and VInv In2R constructs. Similar but weaker signals were detected from transgenic plants derived from fragment #8 ( Fig. 2C ). These results indicated that the enhancer driving GUS expression in stems and petioles is located between b2 and b4, which was named fragment #11 ( Fig. 2D ).

We next further divided the 600 bp fragment #11 into 13 subfragments (#12 to #24; Fig. 2D ) for GUS reporter assays. Transgenic plants derived from construct #21 (200 bp) showed strong GUS signals in stems and petioles. In contrast, transgenic plants derived from constructs #17 and #19 did not show GUS signals ( Fig. 2E ). Thus, the core enhancer in intron 2 was mapped within the 200 bp #21 sequence and was named as VInv In2En thereafter. VInv In2En spans 678 to 877 bp in the intron and is located within the 475 bp DHS, which spans 597 to 1,071 bp in the intron ( Fig. 1A ).

To confirm the function of VInv In2En in potato, we developed transgenic lines using a VInv In2En-m35S-GUS construct in ‘Katahdin’ potato. We detected minimal GUS signals in tubers stored at room temperature (22 °C) but strong GUS signals in cold-stored tubers (4 °C) from 3 independent transgenic lines ( Fig. 2F ). Thus, the VInv In2En sequence retains the same function as the entire intron 2 in potato ( Fig. 1B ).

Identification of DNA motifs related to VInv In2En function

We speculated that VInv In2En contains DNA motifs bound by TFs involved in plant response to cold stress. We identified putative DNA motifs related to a total of 15 TFs in the intron 2 sequence of RH ( Zhou et al . 2020 ). These motifs were consistently detected by 2 independent programs using both CIS-BP ( Weirauch et al . 2014 ) and PlantPAN 3.0 ( Chow et al . 2019 ). Interestingly, 10 of these 15 TFs were previously reported to be associated with responses to cold stress in 1 or multiple plant species ( Fig. 3A ), including AT-hook ( Dahro et al . 2022 ), C2H2 ZF ( He et al . 2019 ), MADS-box ( Chen et al . 2019 ), NAC/NAM ( Li et al . 2016 ), bHLH ( Xie et al . 2012 ), CBF/NF-Y ( Zhou et al . 2022 ; Zhang et al . 2023 ), bZIP ( Liu et al . 2018 ; Li et al . 2022b ), B3 ( Verma and Bhatia 2019 ), TCP ( Li et al . 2022a ), and GATA ( Zhang et al . 2021 ).

Distribution and function of DNA motifs in intron 2 and the VInvIn2En enhancer. A) Distribution of DNA motifs related to TFs involved in response to cold stress. Each vertical bar represents a potential TF-binding site. A red horizontal bar marks the position of the 200 bp enhancer. Vertical blue bars indicate that the binding sites of a relevant TF are enriched or exclusively located within the 200 bp enhancer. Vertical green bars indicate that the binding sites of a relevant TF are not enriched within the enhancer. B) Transgenic assays of VInvIn2En with mutated DNA motifs related to 5 different TFs. Red-colored nucleotides indicate the replaced sequence(s) in each construct. No GUS signals were detected in any transgenic A. thaliana plants derived from the 3 constructs with mutated motifs related to CBF/NF-Y, TCP, and GATA.

Distribution and function of DNA motifs in intron 2 and the VInv In2En enhancer. A) Distribution of DNA motifs related to TFs involved in response to cold stress. Each vertical bar represents a potential TF-binding site. A red horizontal bar marks the position of the 200 bp enhancer. Vertical blue bars indicate that the binding sites of a relevant TF are enriched or exclusively located within the 200 bp enhancer. Vertical green bars indicate that the binding sites of a relevant TF are not enriched within the enhancer. B) Transgenic assays of VInv In2En with mutated DNA motifs related to 5 different TFs. Red-colored nucleotides indicate the replaced sequence(s) in each construct. No GUS signals were detected in any transgenic A. thaliana plants derived from the 3 constructs with mutated motifs related to CBF/NF-Y, TCP, and GATA.

Several TF motifs were enriched in the 200 bp VInv In2En, including bHLH and CBF/NF-Y. In addition, motifs related to TCP and GATA were found only in the 200 bp enhancer region ( Fig. 3A ). We designed mutated versions of VInv In2En to test the function of the DNA motifs related to B3, bHLH, CBF/NF-Y, TCP, and GATA. In each construct, the target motif(s) were mutated by replacing 1 to 3 nucleotide(s) within the sequence ( Fig. 3B , Supplementary Table S1 ). Transgenic A. thaliana plants using VInv In2En with a mutated B3 motif showed similar GUS signal patterns as those from wild-type (WT) VInv In2En. Reduced GUS signals were detected from transgenic plants using VInv In2En with 2 mutated bHLH motifs. In contrast, we did not detect any GUS signals from transgenic plants derived from the 3 constructs with mutated motifs related to CBF/NF-Y, TCP, and GATA. Most strikingly, a single-nucleotide mutation within the GATA motif resulted in a complete loss of function of the VInv In2En enhancer ( Fig. 3B ). These results indicated that CBF/NF-Y, TCP, and GATA all play important roles for VInv In2En driving GUS expression in stems and petioles.

To seek additional functional evidence of the 3 DNA motifs identified in VInv In2En, we conducted a yeast 1-hybrid (Y1H) assay using triple copies of the VInv In2En sequence as a bait (see Materials and methods ). A total of 387 yeast colonies were obtained by screening a cDNA library developed from cold-treated tuber tissues from RH potato. All 387 clones were fully sequenced. The sequences were used for BLAST search in the DM1-3 potato cDNA (v6.1) database using Spud DB BLASTn program ( http://spuddb.uga.edu/blast.shtml ). All of the best matched cDNA sequences with an E -value < 1e −5 and a minimum sequence identity of 82% were kept for further analyses. A total of 33 unique cDNA sequences were obtained after filtering out repeated cDNA sequences. The candidate proteins related to these 33 cDNAs were used for further validation using point-to-point Y1H assay (see Materials and methods ). Five proteins, including StNF-YC1 and StNF-YC9 ( Fig. 4 ), were validated as positive interacting proteins binding to VInv In2En. The StNF-YC1 and StNF-YC9 proteins share 86% and 73% sequence similarity with AtNF-YC1 and AtNF-YC9 of A. thaliana , respectively. These results validated the predicted role of CBF/NF-Y family TFs in the regulation of CIS mediated by the VInv In2En enhancer.

Identification of StNF-YC1 and StNF-YC9 proteins that bind to VInvIn2En using Y1H assay. Triple copies of the VInvIn2En sequence (VInvIn2En*3) were synthesized to develop the bait plasmid pVInvIn2En*3-AbAi. The pGADT7 vector was used as negative control, and a combination of 2 constructs (p53-AbAi and pGADT7-Rec-p53) was used as positive control.

Identification of StNF-YC1 and StNF-YC9 proteins that bind to VInv In2En using Y1H assay. Triple copies of the VInv In2En sequence ( VInv In2En*3) were synthesized to develop the bait plasmid p VInv In2En*3-AbAi. The pGADT7 vector was used as negative control, and a combination of 2 constructs (p53-AbAi and pGADT7-Rec-p53) was used as positive control.

Genome editing of VInv In2En in diploid potato

The in vivo function of a predicted enhancer can be validated by mutation or deletion using genome editing ( Meng et al . 2021 ; Zhao et al . 2022 ; Fang et al . 2023 ). We attempted to develop VInv In2En deletion lines in potato to validate its in vivo function. We first conducted CRISPR/Cas experiments using a self-compatible diploid clone DMF5-73-1. This clone was self-pollinated for 5 generations from a self-compatible diploid hybrid DM1-3 × M6 ( Endelman and Jansky 2016 ). DMF5-73-1 is amenable to Agrobacterium -mediated transformation ( Butler et al . 2020 ). Five sgRNAs flanking VInv In2En (1a, 2a, 3a, 1b, and 2b) and a single sgRNA (3b) targeting VInv In2En ( Fig. 5A , Supplementary Table S2 ) were designed and assembled into a single construct ( Supplementary Fig. S2 ). Primary transformants were generated using a hairy root-based procedure to create stable CRISPR/Cas mutants in the first generation (T0) ( Butler et al . 2020 ). T0 events carrying targeted deletions were self-pollinated, and the progeny were screened for homozygous mutations (T1). We identified 3 homozygous T1 deletion lines ( Fig. 5B ). Two lines, 13-1-3 and 13-2-1, were derived from the same hairy root culture. Sequencing analysis showed that deletion line 2-2-8 lost 369 bp, including the entire 200 bp VInv In2En. Lines 13-1-3 and 13-2-1 lost 394 bp, including the first 122 bp of VInv In2En ( Supplementary Fig. S3 ), which spans the GATA and the 3 CBF/NF-Y motifs.

Functional validation of the VInvIn2En enhancer using genome editing. A) A diagram illustrating the positions of all sgRNAs within and outside of intron 2 of VInv gene. The red bar marks the 200 bp enhancer VInvIn2En. Red arrows indicate the position of sgRNAs R1, R2, R3, and R4. Blue arrows indicate the position of sgRNAs 1a, 2a, 3a, 1b, 2b, and 3b. B) Gel electrophoresis of PCR products amplified from the 3 homozygous CRISPR/Cas9 deletion lines (2-2-8, 13-1-3, and 13-2-1) developed from the WT DMF5-73-1. C) RT-qPCR-based transcription analysis of VInv gene in cold-stored potato tissues from the 3 homozygous deletion lines (2-2-8, 13-1-3, and 13-2-1). All 3 lines showed significant reduction of VInv expression relative to the Actin97 reference gene. The y axis represents the relative expression level normalized by setting VInv expression in cold-stored tubers of the WT DMF5-73-1 to 1. Data are presented as mean ± sd from 3 biological replicates and were tested by the Student t test (*P < 0.05). D) Chipping of tubers from deletion line 13-1-3 and from the WT DMF5-73-1. Note: (i) the dark color toward 1 end of each chip is caused by the “jelly end” problem (2 examples are indicated by arrows) associated with both 13-1-3 and WT. (ii) 13-1-3 is a selfed progeny of a T0 DMF5-73-1 (heterozygous) transgenic line. Thus, the tubers from the 2 lines show different shapes. Three tubers from each line were used for chipping, and 2 chips from each tuber were included in the illustration. E) Gel electrophoresis of PCR products amplified from the genomic DNA of 3 T0 CRISPR/Cas9 lines (KV78, KV87, and KV108) developed from tetraploid potato cultivar ‘Katahdin.’ Red arrows indicate fragments resulted from deletions within VInvIn2En. F) Sequencing of PCR products amplified from cDNAs of the 3 CRISPR/Cas9 lines. Normal splicing between exons 1 and 3 was detected in all 3 lines. G) RT-qPCR-based analysis of VInv expression relative to the Actin97 gene of the 3 CRISPR/Cas lines. Expression was analyzed using tubers after 2 wks of storage at 22 °C and 4 °C, respectively. The y axis represents the relative expression level normalized by setting VInv expression in 22 °C-stored tubers of the WT ‘Katahdin’ to 1. Data are presented as mean ± sd from 3 biological replicates and were tested by using PROC GLM ANOVA. Different lower case letters represent statistically significant differences at P = 0.05.

Functional validation of the VInv In2En enhancer using genome editing. A) A diagram illustrating the positions of all sgRNAs within and outside of intron 2 of VInv gene. The red bar marks the 200 bp enhancer VInv In2En. Red arrows indicate the position of sgRNAs R1, R2, R3, and R4. Blue arrows indicate the position of sgRNAs 1a, 2a, 3a, 1b, 2b, and 3b. B) Gel electrophoresis of PCR products amplified from the 3 homozygous CRISPR/Cas9 deletion lines (2-2-8, 13-1-3, and 13-2-1) developed from the WT DMF5-73-1. C) RT-qPCR-based transcription analysis of VInv gene in cold-stored potato tissues from the 3 homozygous deletion lines (2-2-8, 13-1-3, and 13-2-1). All 3 lines showed significant reduction of VInv expression relative to the Actin97 reference gene. The y axis represents the relative expression level normalized by setting VInv expression in cold-stored tubers of the WT DMF5-73-1 to 1. Data are presented as mean ± sd from 3 biological replicates and were tested by the Student t test (* P < 0.05). D) Chipping of tubers from deletion line 13-1-3 and from the WT DMF5-73-1. Note: (i) the dark color toward 1 end of each chip is caused by the “jelly end” problem (2 examples are indicated by arrows) associated with both 13-1-3 and WT. (ii) 13-1-3 is a selfed progeny of a T0 DMF5-73-1 (heterozygous) transgenic line. Thus, the tubers from the 2 lines show different shapes. Three tubers from each line were used for chipping, and 2 chips from each tuber were included in the illustration. E) Gel electrophoresis of PCR products amplified from the genomic DNA of 3 T0 CRISPR/Cas9 lines (KV78, KV87, and KV108) developed from tetraploid potato cultivar ‘Katahdin.’ Red arrows indicate fragments resulted from deletions within VInv In2En. F) Sequencing of PCR products amplified from cDNAs of the 3 CRISPR/Cas9 lines. Normal splicing between exons 1 and 3 was detected in all 3 lines. G) RT-qPCR-based analysis of VInv expression relative to the Actin97 gene of the 3 CRISPR/Cas lines. Expression was analyzed using tubers after 2 wks of storage at 22 °C and 4 °C, respectively. The y axis represents the relative expression level normalized by setting VInv expression in 22 °C-stored tubers of the WT ‘Katahdin’ to 1. Data are presented as mean ± sd from 3 biological replicates and were tested by using PROC GLM ANOVA. Different lower case letters represent statistically significant differences at P = 0.05.

DMF5-73-1 is not susceptible to CIS and expresses a weak CIS phenotype. Tubers harvested from the 3 deletion lines were stored at 12.8 °C for 6 wks followed by at 6.7 °C for 9 additional wks, a storage procedure used to maximize the CIS phenotype. Tuber tissues were then sampled for RNA extraction and RT-qPCR analysis. We found that the expression of VInv gene was reduced by 54% for 2-2-8, 45% for 13-1-3, and 41% for 13-2-1, respectively, compared with the WT DMF5-73-1 ( Fig. 5C ). However, it was challenging to perform chipping analysis from the deletion lines because all 3 lines have small tubers and are associated with the “jelly end” defect derived from the parental clone DM1-3 ( Endelman and Jansky 2016 ) ( Fig. 5D ). Nevertheless, potato chips processed from cold-stored tubers of line 13-1-3 showed a lighter color compared with those processed from WT DMF5-73-1 ( Fig. 5D ).

Genome editing of VInv In2En in tetraploid potato

DMF5-73-1 is ideal for CRISPR/Cas experiments due to its self-compatibility that allows for identification of homozygous deletions. However, DMF5-73-1 is not an ideal line to accurately evaluate the impact of VInv In2En on CIS since it is resistant to CIS and has poor tuber traits. In addition, DMF5-73-1 retains a significant level of heterozygosity. Hence, the homozygous deletion lines developed from this clone are phenotypically different from the parental DMF5-73-1 ( Fig. 5D ). We next attempted to conduct CRISPR/Cas experiments in ‘Katahdin,’ a tetraploid potato cultivar that is highly susceptible to CIS ( Bhaskar et al . 2010 ). We first amplified and sequenced intron 2 of VInv from ‘Katahdin.’ We identified 3 haplotypes: A (2 copies), B, and C. These haplotypes are differentiated by SNPs and small indels, including those within the VInv In2En region ( Supplementary Fig. S4 ). We designed 4 sgRNAs, including R1 outside of VInv In2En and R2, R3, and R4 inside the VInv In2En boundary ( Fig. 5A , Supplementary Fig. S4 and Table S2 ). The 4 sgRNAs were assembled into a single construct for CRISPR/Cas experiments ( Supplementary Fig. S5 ).

We identified 3 different T0 CRISPR/Cas9 lines, KV78, KV87, and KV108. PCR amplifications using primers VInv -Edit-F/R that span the 4 sgRNAs ( Supplementary Fig. S4 and Table S3 ) produced additional smaller bands as well as the WT band ( Fig. 5E ), suggesting that all 3 T0 lines contain both intact and deleted intron 2, possibly derived from different lineages of cells. We then isolated and mixed all DNA fragments visible on the agarose gel, including the WT band, from all 3 lines. The mixed DNA fragments were cloned, and a minimum of 60 randomly selected clones from each line were fully sequenced. Sequence analysis confirmed that each of the 3 T0 lines contained different types of deletions within VInv In2En, ranging from 3 to 124 bp deletions within VInv In2En associated with haplotype A and 1 to 15 bp deletions within VInv In2En associated with haplotype B ( Supplementary Fig. S6 ). However, no deletions were detected in VInv In2En associated with haplotype C, probably due to the SNPs located in the PAM sequences downstream of sgRNAs R2 and R3. Based on the number of individual sequences related to VInv In2En, 67.7% of the haplotype A sequences from KV78 contained a deletion ranging from 4 to 97 bp; 64.7% of the haplotype A sequences from KV87 contained a deletion of 3 to 64 bp; 59.3% of the haplotype A sequences from KV108 contained a 4 to 124 bp deletion ( Supplementary Fig. S6 ).

We amplified the cDNAs of VInv from the 3 CRISPR/Cas lines using primers Splicing-F/R spanning exons 1 to 3 ( Supplementary Table S3 ). Sequencing of the PCR products showed that the transcripts from the 3 CRISPR/Cas lines were identical to those from WT ‘Katahdin’ ( Fig. 5F ). Thus, the deletions occurred in VInv In2En did not affect the splicing of the VInv gene. We next analyzed the expression of the VInv gene in the 3 CRISPR/Cas lines using RNAs isolated from tubers stored for 2 wks under 22 °C and 4 °C, respectively. A similar and minimal level of VInv expression was observed in 22 °C-stored tubers from WT ‘Katahdin’ and all 3 CRISPR/Case lines. In contrast, the expression level of VInv in 4 °C-stored tubers of the 3 CRISPR/Cas lines was only 6.6%, 16.4%, and 27.3%, respectively, of the WT ‘Katahdin’ ( Fig. 5G , Supplementary Table S4 ). Potato chipping was performed using tubers stored under 22 °C and 4 °C, respectively. Potato chips processed from tubers stored under 22 °C showed a similar color from all 3 lines as well as WT ‘Katahdin’ ( Supplementary Fig. S7 ). After the 4 wks of storage of the tubers under 4 °C, chips from KV78, KV87, and KV108 all showed a lighter color than those from ‘Katahdin’ ( Supplementary Fig. S7 ).

Collectively, these results showed that although the deletions associated with VInv In2En of ‘Katahdin’ are in heterozygous and mosaic conditions in the 3 T0 CRISPR/Cas lines, the deletions resulted in a significant reduction of VInv expression under cold storage condition, confirming the cold-responsive function of VInv In2En in ‘Katahdin.’

Evolution of VInv gene and VInv In2En enhancer

We computationally extracted the DNA sequence of VInv gene from a total of 28 sequenced Solanaceous species. Sequences from several distantly related species, including A. thaliana , cucumber ( Cucumis sativus ), and soybean ( Glycine max ), were used as outgroups in evolutionary analysis. The VINV protein of potato shared 92% to 99% sequence similarity with those from tomato and wild Solanum species ( Supplementary Fig. S8 ). In addition, the structure of the VInv genes is also highly conserved among different species ( Fig. 6 ). The distinct small exon 2 (9 bp) was detected in all Solanaceous species, as well as in several distantly related plant species. In addition, a large intron 2 was identified following the small exon 2 in all species ( Fig. 6 ), with sizes ranging from 780 bp to 2,997 bp ( Supplementary Table S5 ).

Composition of introns and exons of VInv genes from different plant species. A total of 28 Solanaceous species and 8 distantly related dicot species were selected for the analysis. The distinctly small exon 2 (9 bp) was detected in all Solanaceous species, as well as in 5 distantly related plant species. In addition, a large intron 2 (ranging from 780 to 2,997 bp) following the small exon 2 was identified in most plant species.

Composition of introns and exons of VInv genes from different plant species. A total of 28 Solanaceous species and 8 distantly related dicot species were selected for the analysis. The distinctly small exon 2 (9 bp) was detected in all Solanaceous species, as well as in 5 distantly related plant species. In addition, a large intron 2 (ranging from 780 to 2,997 bp) following the small exon 2 was identified in most plant species.

The 1,327 bp intron 2 sequence from RH ( Zhou et al . 2020 ) was used to align intron 2 sequences from other Solanaceous species. Homologous sequences were detected in the same intron of the VInv gene from all Solanum species, as well as from several distantly related species, including eggplant ( Solanum melongena ) and pepper ( Capsicum annuum ) ( Supplementary Table S5 ). We next aligned the 200 bp VInv In2En sequence from RH to intron 2 sequences from different species. Surprisingly, the VInv In2En sequences were more conserved than intron 2 sequences among the species analyzed ( Supplementary Table S5 ). Furthermore, the DNA motifs related to CBF/NF-Y, TCP, and GATA were detected in the VInv In2En sequences from distantly related Solanum species ( Supplementary Table S5 ). Therefore, VInv In2En represents a conserved enhancer sequence in Solanum species.

We extracted the VInv In2En sequence from several different potato genotypes to further exploit its sequence polymorphism ( Supplementary Fig. S9 ), including diploid potato clones M6 ( Jansky et al . 2014 ) and H28-7 ( Bhaskar et al . 2010 ), which are resistant to CIS. SNPs and small indels were observed throughout the VInv In2En sequence in comparison between CIS-resistant (H28-7 and M6) and CIS-susceptible (RH) genotypes, including SNPs located in the CBF/NF-Y, GATA, and TCP motifs ( Supplementary Fig. S9 ). Thus, sequence polymorphism of VInv In2En may contribute to the level of CIS resistance of different potato genotypes.

Invertases hydrolyze sucrose into glucose and fructose, thereby playing important roles in metabolism and development in plants ( Ruan et al . 2010 ). Different plant invertases have been found to be specific to the cell wall, vacuole, or cytosol, respectively. Both cell wall and vacuolar invertases are also known to contribute to defense responses to abiotic and biotic stresses ( Wan et al . 2018 ). Vacuolar invertases play essential roles in cell expansion and sugar accumulation, which are related to plant growth and development ( Ruan et al . 2010 ; Wan et al . 2018 ). Therefore, silencing of the vacuolar invertase gene can cause major developmental defects in plants. For example, silencing of the vacuolar invertase gene in tomato ( Solanum lycopersicum ) resulted in substantially smaller fruits ( Klann et al . 1996 ). Major developmental defects were also reported in silencing of the vacuolar invertase gene in several other species, including carrot ( Daucus carota ) ( Tang et al . 1999 ), muskmelon ( Cucumis melo ) ( Yu et al . 2008 ), cotton ( Gossypium hirsutum ) ( Wang et al . 2014 ; Wang and Ruan 2016 ), and rice ( Oryza sativa ) ( Lee et al . 2019 ; Deng et al . 2020 ).

VInv ( Pain-1 ) is the only vacuolar invertase gene identified in the potato genome ( Bhaskar et al . 2010 ; Draffehn et al . 2010 ). Interestingly, silencing of the VInv gene by RNAi in potato did not cause unambiguous defects in growth and development ( Bhaskar et al . 2010 ). The potato RNAi lines did not show yield loss in field-based yield trials ( Bhaskar et al . 2010 ). These results suggest that the VInv gene may not play a similar developmental role in potato as compared with other plant species. Although VInv is expressed in nontuber tissues, the expression of VInv is not upregulated by cold stress in several nontuber tissues, including petiole, stem, and root (X.B. Zhu, unpublished data). Similarly, the GUS signals in the transgenic A. thaliana plants derived from VInv In2 and VInv In2En constructs were not enhanced by cold stress. We hypothesize that the VInv gene has adapted for a distinct role in the tuber-bearing species in response to cold stress. A high level of VInv expression at cold temperatures would generate more sugars in tuber cells, which in turn would affect the osmotic pressure and increase the freezing tolerance of tuber cells that contain a high percentage of water.

The VInv In2En sequence is conserved among distantly related Solanum species, including tomato and several other non-tuber-bearing species ( Supplementary Table S5 and Fig. S9 ). Thus, VInv In2En emerged before the divergence between tuber-bearing and non-tuber-bearing species. We speculate that VInv In2En contains unidentified sequence motif(s) that are responsible for its tuber-specific function. We previously showed that the CIS-resistant diploid potato germplasm line H28-7 exhibits a very low level of VInv expression in cold-stored tubers ( Bhaskar et al . 2010 ). Interestingly, we detected a SNP in each of the 2 CBF/NF-Y motifs in VInv In2E between H28-7 and RH ( Supplementary Fig. S9 ). These results suggest that variation of the VInv In2En sequence is likely the key factor for the resistance of the CIS-resistant germplasm. In contrast, an identical VInv In2En sequence was observed in DM1-3 and RH potatoes ( Supplementary Fig. S9 ), which have different levels of resistance to CIS. Thus, the VInv -mediated cold tolerance is likely associated with additional factors depending on species or genotypes within a species. This hypothesis is supported by previous reports demonstrating an invertase inhibitor, StInvInh2, which specifically suppresses the activity of the VINV protein ( Liu et al . 2010 ; Brummell et al . 2011 ). A combination of VInv In2En-mediated cold-induced expression of VInv and posttranscriptional regulation of VINV protein provides a multilayer of defense system for potato to adapt to different environments and/or stress conditions.

Several TFs, including CBF/NF-Y, TCP, and GATA, may play a role in VInv In2En-mediated regulation of VInv under cold conditions, since mutations of the predicted binding sites of these TFs abolished the function of VInv In2En as a transcriptional enhancer in A. thaliana ( Fig. 3 ). CBF/NF-Y, TCP, and GATA are large TF families in plants and include 41, 31, and 49 genes, respectively, in the potato genome ( Wang et al . 2019 ; Li et al . 2021 ; Yu et al . 2022 ). Although there are no reports yet on cold response associated with these TFs in potato, specific members from the CBF/NF-Y, TCP, and GATA families have been documented for playing a role in cold temperature response in other plant species. For example, a GATA-family TF in rice, OsGATA16, was induced by cold treatment and can improve cold tolerance by repressing some cold-related genes ( Zhang et al . 2021 ). A TCP1 TF in Chrysanthemum morifolium , DgTCP1, was induced by cold temperature and can regulate peroxidase activity and reduce ROS accumulation ( Li et al . 2022a ). It is interesting to note the presence of 3 CBF/NF-Y binding sites in close vicinity within VInv In2En. The NF-Y TFs have been documented to confer response to various types of abiotic stresses, including drought, salt, nutrient, and temperature ( Zhang et al . 2023 ). Thus, it will be essential to validate the functions of these TF-binding sites in potato and to identify a specific member(s) from these TF families that are responsible for the function of VInv In2En.

Enhancer validation using transgenic assays in potato

An intronic DHS within intron 2 of VInv gene was identified from the DHS data published previously ( Zeng et al . 2019 ). The entire intron 2 from the VInv gene of RH potato ( S. tuberosum ) was used for enhancer validation using a GUS reporter system ( Zhu et al . 2015 ). The forward ( VInv In2) and reverse ( VInv In2R) sequences of intron 2 were amplified from genomic DNA of RH potato using PCR with primers VIT-F6/R6 and VIT-F8/R8 ( Supplementary Table S3 ), respectively, and were ligated to a minimal 35S promoter (−50 to −2 bp) (m35S) through the Eco RI cloning site. The ligated PCR products were cloned into the pENTR/D directional TOPO cloning vector (Invitrogen) and then transferred into the pKGWFS 7.0 vector containing the GUS reporter using the LR Clonase recombination method ( Zhu et al . 2015 ). Constructs were transferred into Agrobacterium tumefaciens strain GV3101 (pMP90), followed by transformation to potato variety ‘Katahdin’ using methods described previously ( Bhaskar et al. 2008 ; Bhaskar et al. 2010 ).

Transgenic ‘Katahdin’ lines derived from the forward or reverse construct were obtained and screened using PCR with the kanamycin gene-specific primers Kan-F/R and the construct-specific primers ( Supplementary Table S3 ). All transgenic lines with 3 replicates for each line were grown in greenhouses using photoperiod of 16 h daylight at 22 °C and 8 h darkness at 16 °C (50% to 70% humidity) and light intensity of 500  μ mol/m 2 /s (natural light combined with light of high-pressure sodium lamps) until leaves became senesced naturally. Tubers harvested from each line were divided into 2 groups: stored in dark at 22 °C (50% to 70% humidity) or 4 °C (60% to 70% humidity) for 4 wks, respectively. Tuber slices prepared by slicing longitudinal sections 2 mm thick from the center of individual tubers were examined for GUS activity. Tuber slices were placed in a plastic plate (70 × 15 mm) and soaked in GUS staining solution (100 m m sodium phosphate, pH 7.0, 10 m m EDTA, 0.1% [ v / v ] Triton X-100, 0.5 m m potassium ferrocyanide, 0.5 m m potassium ferricyanide, and 0.05% [w/v] X-Gluc), with vacuum infiltration for 30 min and incubation in dark at 37 °C overnight. Tuber slices were washed in 80% ( v / v ) ethanol several times. Images of tuber slices were captured using an EPSON Perfection 4180 scanner.

Enhancer dissection using transgenic assays in A. thaliana

Seeds of Arabidopsis ( A. thaliana ) accession Col-0 were germinated in half-strength MS (0.5× MS) medium, and the seedlings were transplanted in potting soil and grown in plant growth chambers with 16/8 h light/dark cycles at 23 °C and light intensity of 150  μ mol/m 2 /s (white fluorescent lamps) until flowering. The VInv In2 and VInv In2R constructs were initially used to transform A. thaliana accession Col-0 using the floral dip method ( Clough and Bent 1998 ). Transgenic seedlings were screened on solid 0.5× MS medium containing kanamycin (50  μ g/mL) and were grown in an illumination incubator with the same light–dark condition described above and were examined for GUS activity according to published protocols ( Zhu et al . 2015 ).

To map the position of the enhancer within intron 2 of VInv , we divided intron 2 into 10 DNA fragments (#1 to #10) using 5 breaks (b1 to b5) for transgenic assays. The stem/petiole-specific enhancer (within DNA fragment #11) was further divided into 14 (#11 to #24) subfragments. All target DNA fragments together with the m35S were synthesized from GenScript Inc. and cloned into the pKGWFS 7.0 vector containing the m35S and the GUS reporter gene ( Zhu et al . 2015 ). Images of transgenic A. thaliana seedlings were captured using the EPSON Perfection 4180 scanner to record the GUS signals.

Analysis of TF-binding motifs

TF-binding motifs and their corresponding TFs within intron 2 of VInv were identified using 2 independent programs of CIS-BP ( Weirauch et al . 2014 ) and PlantPAN 3.0 ( Chow et al . 2019 ) with default parameters. DNA motifs consistently detected by both programs were used for further analysis. Motifs reported to be associated with cold response in 1 or multiple plant species were mapped to intron 2 of VInv using TBtools ( Chen et al . 2020 ).

Development of CRISPR/Cas deletion lines

A self-compatible diploid potato clone DMF5-73-1 was developed from a cross between S. tuberosum Gp. Phureja DM 1-3 516 R44 (DM1-3) and Solanum chacoense (M6) ( Endelman and Jansky 2016 ) and has been self-pollinated for 5 generations. WT and CRISPR/Cas lines were propagated in vitro on MS medium (MS basal salts plus vitamins, 3% sucrose, 0.7% plant agar, pH 5.8) ( Murashige and Skoog 1962 ). In vitro plants were maintained in growth chambers with 16 h light/8 h dark photoperiod at 22 °C and average light intensity of 200  μ mol/m 2 /s (white fluorescent lamps) Pro .

The Csy4-based CRISPR/Cas9 system ( Cermak et al . 2017 ) was used to develop VInv In2En deletion lines in DMF5-73-1. In brief, 5 sgRNAs flanking VInv In2En (1a, 2a, 3a, 1b, and 2b) and a single sgRNA (3b) targeting VInv In2En ( Supplementary Table S2 ) were designed using program of CRISPR-P v2.0 ( Liu et al . 2017 ). The 6 gRNAs were linked by Csy4 binding sites and then cloned into the Csy4 multiplexing vector ( Supplementary Fig. S3 ) based on published methods ( Cermak et al . 2017 ). The construct was delivered into A. tumefaciens GV3101 (pMP90) and was used to conduct hairy root-based Agrobacterium transformation ( Butler et al . 2020 ). T0 CRISPR/Cas lines showing the expected smaller PCR products were further confirmed by Sanger sequencing using VInv -mut-F1/R1 primers ( Supplementary Table S3 ). Several T0 lines with large deletion of VInv In2En were grown under greenhouse conditions as described above, followed by subsequent self-pollination to obtain homozygous T1 deletion lines.

A tetraploid potato cultivar ‘Katahdin’ was used to develop deletion lines using the U3/U6-based CRISPR/Cas9 system ( Hu et al . 2019 ). Four sgRNAs, including R1 outside of VInv In2En and R2, R3, and R4 inside the VInv In2En ( Supplementary Table S2 ), were designed using CRISPR-P v2.0 ( Liu et al . 2017 ). The sgRNAs were assembled into 4 expression cassettes ( ProAtU3b:gRNA1 , ProAtU3d:gRNA2 , ProAtU6-29:gRNA3 , and ProAtU6-29:gRNA4 ), which were cloned into the pHNCas9 vector by using the Golden Gate cloning strategy ( Ma et al. 2015 ; Xie et al. 2015 ; Ma et al. 2016 ; Hu et al. 2019 ). The construct pHNCas9:: VInv In2En was introduced into A. tumefaciens GV3101 (pMP90) and was used to transform ‘Katahdin’ according to published protocols ( Bhaskar et al . 2008 ). Positive transformants were screened using PCR with primers Kan -F3/R3, Cas -F1/R1, and VInv -Edit-F/R ( Supplementary Table S3 ). Transgenic lines containing additional smaller bands (2% agarose gel) were further confirmed by Sanger sequencing. PCR products were purified by using QIAquick PCR Purification Kit (Qiagen) and were cloned into Escherichia coli using pMD 19-T vector (TaKaRa). A minimum of 60 randomly selected positive colonies derived from each deletion line were fully sequenced. Statistical analysis of different types of deletions was conducted on each of the ‘Katahdin’ CRISPR/Cas deletion lines containing 3 haplotypes, A (2 copies), B, and C.

Greenhouse trials, tuber sample preparation, and chipping analysis

Each of 10 seed tubers of RH potato was planted in potting soil under normal greenhouse conditions as described above. Standard cultivation and management practices were followed throughout the growing period. Tubers were harvested 120 d after seedling emergence when leaves senesced naturally. Tubers harvested from 2 pots were combined together as 1 biological replicate. Tubers of 5 biological replicates were stored in dark at 22 °C (50% to 70% humidity) for 10 d and then divided into 2 groups. Each group was stored in dark at 22 °C (50% to 70% humidity) or 4 °C (60% to 70% humidity) for 0, 2, 4, 8, and 16 wks, respectively.

Three T0 CRISPR/Cas deletion lines (3 plants for each line) developed from ‘Katahdin’ were grown under normal greenhouse conditions as described above. Tubers harvested from the same line were combined together and stored under dark at 22 °C for 10 d and then divided into 2 groups for 22 °C (50% to 70% humidity) or 4 °C (60% to 70% humidity) treatments, and each group of tubers with 3 replicates was treated for 2 and 4 wks, respectively.

Tuber samples of 1.5-mm-thick slices (1 to 3 slices for each tuber) prepared from the apical to basal end of the tuber were taken for chipping analysis. The remaining tuber samples were frozen in liquid nitrogen and used for analysis of VInv expression. Tuber slices were fried in cottonseed oil at 191 °C for 2 min or until the cessation of bubbles. Chip color of cold-stored tubers is compared with that of the corresponding controls.

VInv transcription and splicing assays

RNAs were extracted from tuber tissues using Plant RNA Isolation Mini Kit (Agilent) following the manufacturer's instructions and were reverse transcribed to cDNAs using Invitrogen SuperScript III Reverse Transcriptase Kit (Invitrogen) with oligo(dT) 20 primer. VInv transcripts were quantified by RT-qPCR using the SYBR Advantage qPCR Premix (Clontech) with the specific primers for VInv and the reference gene Actin97 described previously ( Zhu et al. 2014 ; Zhu et al. 2016 ). RT-qPCR was performed on the CFX96 Touch Real-Time PCR Detection System (Bio-Rad) with a program of 30 s at 95 °C, 40 cycles of 10 s at 95 °C, 20 s at 60 °C for VInv and Actin97 , and 30 s at 72 °C, followed by a plate read. Next is 2 s at 50 °C to 95 °C with 0.2 °C steps for melting curve, followed by a final extension step of 10 min at 72 °C. Relative expression levels of VInv gene were calculated using Gene Expression Macro software version 1.1 (Bio-Rad Laboratories). Data for each treatment are presented as se of the means of the 3 biological replicates. For RT-qPCR data of 3 ‘Katahdin’ CRISPR/Cas9 lines and the WT, ANOVA was carried out using PROC GLM in the Statistical Analysis System version 9.1 (SAS v9.1) (SAS Institute Inc., Cary, NC) ( Supplementary Table S4 ).

To examine whether VInv In2En deletions affect VInv gene splicing, we prepared cDNAs from tuber tissues of the 3 ‘Katahdin’ CRISPR/Cas lines. Exon 1 to exon 3 of VInv was amplified using primers Splicing-F/R ( Supplementary Table S3 ; amplicon size: 612 bp). The RT-PCR products were purified by using QIAquick PCR Purification Kit (Qiagen) and then used for Sanger sequencing.

Triple copies of the VInv In2En sequence ( VInv In2En*3) were synthesized and used to develop a bait plasmid p VInv In2En*3-AbAi. The bait plasmid was used to screen the cDNA library, developed from cold-treated tuber tissues of RH potato, according to methods described in the Matchmaker Gold Yeast One-Hybrid Library Screening System User Manual (Clontech, http://www.takarabio.com/ ). Yeast ( Saccharomyces cerevisiae ) colonies were cultured on plates containing SD/-Leu/AbA 200 ng/mL medium at 30 °C for 3 to 5 d, and those >2 mm in diameter were analyzed by PCR amplification and Sanger sequencing using primers pGADT7-F/R ( Supplementary Table S3 ). The resulted sequences from the 387 yeast colonies were used for BLAST search in the DM1-3 potato cDNA (v6.1) database by using Spud DB BLASTn program with default parameters ( http://spuddb.uga.edu/blast.shtml ). We identified the best matched cDNA sequence for each of the 387 sequences. The cDNA sequences with an E -value < 1e −5 and a minimum sequence identity of 82% were kept for further analyses. We identified a total of 33 unique cDNA sequences after filtering out repetitive cDNA sequences.

To further validate the interactions between the candidate proteins and the VInv In2En enhancer, point-to-point Y1H assay was performed. Full-length CDSs of the candidate proteins related to the 33 identified cDNAs were inserted into the prey vector pGADT7 by using HB-infusion Cloning Kit (HANBIO, https://www.hanbio.net/en/company.shtml/ ). The prey plasmids were subsequently transformed into the bait yeast strain Y1HGold[p VInv In2En*3-AbAi] by using the Yeastmaker Yeast Transformation System 2 (Clontech, http://www.takarabio.com/ ). The yeast colonies were transferred to plates containing SD/-Leu/AbA 200 ng/mL medium and then allowed to grow at 30 °C for 3 d.

Analysis of VInv evolution

A total of 28 Solanaceous species ( https://solgenomics.net/ ) ( Tang et al . 2022 ) and several other dicot species ( Supplementary Table S5 ), including A. thaliana , cucumber ( C. sativus ), and soybean ( G. max ), were selected for evolutionary analysis of the VInv gene. Information on evolutionary timescale of life for all 31 species were collected from the TimeTree 5 database ( http://www.timetree.org/ ) ( Kumar et al . 2022 ) and visualized in MEGA X software ( Kumar et al . 2018 ).

Protein sequences of VInv gene from the 31 different plant species were extracted and aligned to that from RH potato using the National Center for Biotechnology Information (NCBI) BLASTp program ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ). The intron and exon composition of the VInv gene from 31 plant species was analyzed using the online tool GSDS 2.0 ( Hu et al . 2015 ). The 1,327 bp intron 2 and the 200 bp VInv In2En sequences from RH were used to align intron 2 sequences from other 30 species to identify homologous sequences using the program of NCBI BLASTn.

Accession numbers

Sequence data from this article can be found in the GenBank/EMBL libraries under the following accession numbers: Soltu.DM.03G015280 ( VInv ), Soltu.DM.01G024340 (StNF-YC9), and Soltu.DM.06G027230 (StNF-YC1). All mutants and transgenic lines are described in Supplementary Table S6 .

This research project was initiated at the University of Wisconsin-Madison and continued by Zhu lab at Anhui Agricultural University and Jiang lab at Michigan State University. We are grateful to Dr. Hainan Zhao (China Agricultural University) for assistance on evolutionary analysis of VInv gene and to Dr. Nan Hu (Anyang Institute of Technology) for providing the U3/U6-based CRISPR/Cas9 genome editing system (the pHNCas9 binary vector).

J.J. conceived the research. X.Z., A.C., N.M.B., and J.J. designed the experiments. X.Z., A.C., N.M.B., Z.Z., H.X., L.W., and Z.L. conducted the experiments. X.Z., D.E., D.S.D., and J.J. analyzed the data. X.Z. and J.J. wrote the manuscript.

The following materials are available in the online version of this article.

Supplementary Figure S1 .   VInv expression and its impact on chip color of RH potato.

Supplementary Figure S2 . Binary vector for delivering CRISPR/Cas9 components targeting VInv In2En in diploid potato DMF5-73-1.

Supplementary Figure S3 . Genotyping of homozygous CRISPR/Cas deletion lines developed from DMF5-73-1.

Supplementary Figure S4 . Three haplotypes associated with the middle portion of intron 2 of VInv gene from tetraploid potato ‘Katahdin.’

Supplementary Figure S5 . Binary vector for delivering CRISPR/Cas9 components targeting VInv In2En in ‘Katahdin.’

Supplementary Figure S6 . Deletions within VInv In2En of ‘Katahdin.’

Supplementary Figure S7 . Potato chips processed from the 3 CRISPR/Cas9 deletion lines and WT ‘Katahdin.’

Supplementary Figure S8 . Evolution of the VINV protein and enhancer VInv In2En.

Supplementary Figure S9 . Alignment of the VInv In2En sequence from tomato and 4 different diploid potato genotypes.

Supplementary Table S1 . Sequences and mutated nucleotides within the 200 bp VInv In2En.

Supplementary Table S2 . List of sgRNAs used in all CRISPR/Cas experiments.

Supplementary Table S3 . List of primers for GUS reporter, CRISPR/Cas-based genome editing, splicing, and Y1H.

Supplementary Table S4 . ANOVA for RT-qPCR data from the ‘Katahdin’ CRISPR/Cas9 lines.

Supplementary Table S5 . Sequence analysis of intron 2 and enhancer VInvIn2En from different plant species.

Supplementary Table S6 . Mutants and transgenic lines.

Research was supported by grant 31771857 from the National Natural Science Foundation of China, grant 1808085MC65 from the Anhui Provincial Natural Science Foundation, grant 2021H276 from the Scientific Research Fund for Candidates of Anhui Provincial Academic and Technical Leaders, and grant 22532002 from the Anhui Province Vegetable Industry Technology System Fund to X.Z., by USDA-NIFA-SCRI grant 2011-51181-30629 to J.J., by grants IS-5038-17C and IS-5317-20C from BARD (the United States—Israel Binational Agricultural Research and Development Fund) to D.E. and J.J., and by AgBioResearch at Michigan State University (Hatch grant MICL02571) and MSU startup fund to J.J.

All materials, including constructs, are available upon request.

The following phenotypic, genotypic, and functional terms are of significance to the work described in this paper:

DHS Gramene: AT5G05920

DHS Araport: AT5G05920

TCP1 Gramene: AT1G67260

TCP1 Araport: AT1G67260

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Xie   XB , Li   S , Zhang   RF , Zhao   J , Chen   YC , Zhao   Q , Yao   YX , You   CX , Zhang   XS , Hao   YJ . The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples . Plant Cell Environ . 2012 : 35 ( 11 ): 1884 – 1897 . https://doi.org/10.1111/j.1365-3040.2012.02523.x

Ye   J , Shakya   R , Shrestha   P , Rommens   CM . Tuber-specific silencing of the acid invertase gene substantially lowers the acrylamide forming potential of potato . J. Agric Food Chem . 2010 : 58 ( 23 ): 12162 – 12167 . https://doi.org/10.1021/jf1032262

Yu   RM , Chang   YN , Chen   HZ , Feng   JL , Wang   HJ , Tian   T , Song   YJ , Gao   G . Genome-wide identification of the GATA gene family in potato ( Solanum tuberosum L.) and expression analysis . J Plant Biochem Biotechnol . 2022 : 31 ( 1 ): 37 – 48 . https://doi.org/10.1007/s13562-021-00652-6

Yu   XY , Wang   XF , Zhang   WQ , Qian   TT , Tang   GM , Guo   YK , Zheng   CC . Antisense suppression of an acid invertase gene ( MAI1 ) in muskmelon alters plant growth and fruit development . J Exp Bot . 2008 : 59 ( 11 ): 2969 – 2977 . https://doi.org/10.1093/jxb/ern158

Zeng   ZX , Zhang   WL , Marand   AP , Zhu   B , Buell   CR , Jiang   JM . Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato . Genome Biol . 2019 : 20 ( 1 ): 123 . https://doi.org/10.1186/s13059-019-1731-2

Zhang   C , Xie   C-H , Song   B-T , Liu   X , Liu   J . RNAi effects on regulation of endogenous acid invertase activity in potato ( Solanum tuberosum L . ) tubers . Chinese J Agri Biotech . 2008 : 5 ( 2 ): 107 – 112 . https://doi.org/10.1017/S1479236208002192

Zhang   H , Liu   SJ , Ren   TM , Niu   MX , Liu   X , Liu   C , Wang   HL , Yin   WL , Xia   XL . Crucial abiotic stress regulatory network of NF-Y transcription factor in plants . Int J Mol Sci . 2023 : 24 ( 5 ): 4426 . https://doi.org/10.3390/ijms24054426

Zhang   H , Wu   T , Li   Z , Huang   K , Kim   NE , Ma   ZM , Kwon   SW , Jiang   WZ , Du   XL . OsGATA16, a GATA transcription factor, confers cold tolerance by repressing OsWRKY45-1 at the seedling stage in rice . Rice (N Y) . 2021 : 14 ( 1 ): 42 . https://doi.org/10.1186/s12284-021-00485-w

Zhang   WL , Zhang   T , Wu   YF , Jiang   JM . Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis . Plant Cell . 2012 : 24 ( 7 ): 2719 – 2731 . https://doi.org/10.1105/tpc.112.098061

Zhao   HN , Yang   MY , Bishop   J , Teng   YH , Cao   YX , Beall   BD , Li   SL , Liu   TX , Fang   QX , Fang   C , et al.    Identification and functional validation of super-enhancers in Arabidopsis thaliana . Proc Natl Acad Sci U S A . 2022 : 119 ( 48 ): e2215328119 . https://doi.org/10.1073/pnas.2215328119

Zhao   HN , Zhang   WL , Chen   LF , Wang   L , Marand   AP , Wu   YF , Jiang   JM . Proliferation of regulatory DNA elements derived from transposable elements in the maize genome . Plant Physiol . 2018 : 176 ( 4 ): 2789 – 2803 . https://doi.org/10.1104/pp.17.01467

Zhou   H , Zeng   RF , Liu   TJ , Ai   XY , Ren   MK , Zhou   JJ , Hu   CG , Zhang   JZ . Drought and low temperature-induced NF-YA1 activates FT expression to promote citrus flowering . Plant Cell Environ . 2022 : 45 ( 12 ): 3505 – 3522 . https://doi.org/10.1111/pce.14442

Zhou   Q , Tang   D , Huang   W , Yang   ZM , Zhang   Y , Hamilton   JP , Visser   RGF , Bachem   CWB , Buell   CR , Zhang   ZH , et al.    Haplotype-resolved genome analyses of a heterozygous diploid potato . Nat Genet . 2020 : 52 ( 10 ): 1018 – 1023 . https://doi.org/10.1038/s41588-020-0699-x

Zhu   B , Zhang   WL , Zhang   T , Liu   B , Jiang   JM . Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures . Plant Cell . 2015 : 27 ( 9 ): 2415 – 2426 . https://doi.org/10.1105/tpc.15.00537

Zhu   XB , Gong   HL , He   QY , Zeng   ZX , Busse   JS , Jin   WW , Bethke   PC , Jiang   JM . Silencing of vacuolar invertase and asparagine synthetase genes and its impact on acrylamide formation of fried potato products . Plant Biotechnol J . 2016 : 14 ( 2 ): 709 – 718 . https://doi.org/10.1111/pbi.12421

Zhu   XB , Richael   C , Chamberlain   P , Busse   JS , Bussan   AJ , Jiang   JM , Bethke   PC . Vacuolar invertase gene silencing in potato ( Solanum tuberosum L.) improves processing quality by decreasing the frequency of sugar-end defects . PLoS One   2014 : 9 ( 4 ): e93381 . https://doi.org/10.1371/journal.pone.0093381

Zrenner   R , Schuler   K , Sonnewald   U . Soluble acid invertase determines the hexose-to-sucrose ratio in cold-stored potato tubers . Planta   1996 : 198 ( 2 ): 246 – 252 . https://doi.org/10.1007/BF00206250

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Title: assisting in writing wikipedia-like articles from scratch with large language models.

Abstract: We study how to apply large language models to write grounded and organized long-form articles from scratch, with comparable breadth and depth to Wikipedia pages. This underexplored problem poses new challenges at the pre-writing stage, including how to research the topic and prepare an outline prior to writing. We propose STORM, a writing system for the Synthesis of Topic Outlines through Retrieval and Multi-perspective Question Asking. STORM models the pre-writing stage by (1) discovering diverse perspectives in researching the given topic, (2) simulating conversations where writers carrying different perspectives pose questions to a topic expert grounded on trusted Internet sources, (3) curating the collected information to create an outline. For evaluation, we curate FreshWiki, a dataset of recent high-quality Wikipedia articles, and formulate outline assessments to evaluate the pre-writing stage. We further gather feedback from experienced Wikipedia editors. Compared to articles generated by an outline-driven retrieval-augmented baseline, more of STORM's articles are deemed to be organized (by a 25% absolute increase) and broad in coverage (by 10%). The expert feedback also helps identify new challenges for generating grounded long articles, such as source bias transfer and over-association of unrelated facts.

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College student put on academic probation for using Grammarly: ‘AI violation’

A college junior has told The Post how she was put on academic probation after college anti-plagiarism software accused her of using AI to write a paper — which she strongly denies.

Marley Stevens, 21, a human services and delivery and administration major at the University of North Georgia Dahlonega Campus told The Post she used Grammarly, a web browser attachment that corrects spelling and punctuation, to proofread a criminal justice paper she submitted in October. 

But the junior automatically failed the assignment after it was flagged for artificial intelligence use by anti-plagiarism software TurnItIn.com — leading to losing a scholarship, and this month being put on academic probation after a disciplinary hearing.

The anti-plagiarism software is installed on the system students at the college use to submit papers.

Now Stevens is warning college students around the country to beware of getting wrongly accused of cheating by an anti-AI dragnet. 

“I worked really hard on this,” Stevens told The Post of the two-page paper on rehabilitation and re-entry rates in the criminal justice system.

Stevens thought she was being hacked when her criminal justice professor, Robert Ellison, emailed her saying her paper had a “positive response for AI” and that he had reported her to the student academic integrity committee. 

“He gave me a zero and called me a cheater,” she said. “I was shocked – at first I thought he’d sent the email to the wrong person.”

Stevens, who said she maintained a 3.0 GPA before the allegation, said she had the free version of Grammarly installed in her web browser to fix spelling and punctuation errors, not to create or edit content.

Ellison told her in an email that “the entire paper except for the last couple of sentences” had been flagged as AI-generated and said he confirmed this “through another app.” 

Stevens explained her use of Grammarly for spellchecking could be the culprit and stressed, it’s “not like ChatGPT.” She asked to redo the paper, pleading “I don’t want to fail the class.” 

Stevens said she and other students have used Grammarly on other homework assignments without penalty, noting that she’s had professors who have urged them to install the extension.

But Ellison stopped answering, she told The Post, and last week at a hearing with the dean of student integrity she was put on academic probation for “cheating.”

A week after meeting with the dean of student integrity, Stevens said, the office sent out a campus-wide email advising students to “Please be aware that some online tools used to assist students with grammar, punctuation, sentence structure, utilize generative artificial intelligence (AI); which can be flagged by TurnItIn.” 

Grammarly told The Post its “suggestions for spelling, grammatical correctness, clarity, concision, and tone are not powered by generative AI,” and warned that some tools can “mistakenly” flag its use as AI-generated content.

The Post has reached out to TurnItIn.com. The University of North Georgia said that it could not comment on Stevens’ fail because of federal privacy laws.

“Our faculty members communicate specific guidelines regarding the use of AI for various classes, and those guidelines are included in the class syllabi,” a spokesperson said. “The inappropriate use of AI is also addressed in our Student Code of Conduct.” 

Stevens works two jobs in retail and assists a friend who works as a flight instructor to help pay for school and said she considered transferring to another college, but says it would be more expensive to do so.

She has highlighted her case on TikTok and on Wednesday was asked by Grammarly to share more information about what happened.

“People have asked me what advice I have for other college students – my advice is ask every professor you have about Grammarly and AI,” she told The Post.

“Email them so you have it in writing take a screen shot and save it so if something like this does come up.”

College student put on academic probation for using Grammarly: ‘AI violation’

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Writing a Research Paper Introduction | Step-by-Step Guide

Published on September 24, 2022 by Jack Caulfield . Revised on March 27, 2023.

Writing a Research Paper Introduction

The introduction to a research paper is where you set up your topic and approach for the reader. It has several key goals:

  • Present your topic and get the reader interested
  • Provide background or summarize existing research
  • Position your own approach
  • Detail your specific research problem and problem statement
  • Give an overview of the paper’s structure

The introduction looks slightly different depending on whether your paper presents the results of original empirical research or constructs an argument by engaging with a variety of sources.

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Table of contents

Step 1: introduce your topic, step 2: describe the background, step 3: establish your research problem, step 4: specify your objective(s), step 5: map out your paper, research paper introduction examples, frequently asked questions about the research paper introduction.

The first job of the introduction is to tell the reader what your topic is and why it’s interesting or important. This is generally accomplished with a strong opening hook.

The hook is a striking opening sentence that clearly conveys the relevance of your topic. Think of an interesting fact or statistic, a strong statement, a question, or a brief anecdote that will get the reader wondering about your topic.

For example, the following could be an effective hook for an argumentative paper about the environmental impact of cattle farming:

A more empirical paper investigating the relationship of Instagram use with body image issues in adolescent girls might use the following hook:

Don’t feel that your hook necessarily has to be deeply impressive or creative. Clarity and relevance are still more important than catchiness. The key thing is to guide the reader into your topic and situate your ideas.

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This part of the introduction differs depending on what approach your paper is taking.

In a more argumentative paper, you’ll explore some general background here. In a more empirical paper, this is the place to review previous research and establish how yours fits in.

Argumentative paper: Background information

After you’ve caught your reader’s attention, specify a bit more, providing context and narrowing down your topic.

Provide only the most relevant background information. The introduction isn’t the place to get too in-depth; if more background is essential to your paper, it can appear in the body .

Empirical paper: Describing previous research

For a paper describing original research, you’ll instead provide an overview of the most relevant research that has already been conducted. This is a sort of miniature literature review —a sketch of the current state of research into your topic, boiled down to a few sentences.

This should be informed by genuine engagement with the literature. Your search can be less extensive than in a full literature review, but a clear sense of the relevant research is crucial to inform your own work.

Begin by establishing the kinds of research that have been done, and end with limitations or gaps in the research that you intend to respond to.

The next step is to clarify how your own research fits in and what problem it addresses.

Argumentative paper: Emphasize importance

In an argumentative research paper, you can simply state the problem you intend to discuss, and what is original or important about your argument.

Empirical paper: Relate to the literature

In an empirical research paper, try to lead into the problem on the basis of your discussion of the literature. Think in terms of these questions:

  • What research gap is your work intended to fill?
  • What limitations in previous work does it address?
  • What contribution to knowledge does it make?

You can make the connection between your problem and the existing research using phrases like the following.

Now you’ll get into the specifics of what you intend to find out or express in your research paper.

The way you frame your research objectives varies. An argumentative paper presents a thesis statement, while an empirical paper generally poses a research question (sometimes with a hypothesis as to the answer).

Argumentative paper: Thesis statement

The thesis statement expresses the position that the rest of the paper will present evidence and arguments for. It can be presented in one or two sentences, and should state your position clearly and directly, without providing specific arguments for it at this point.

Empirical paper: Research question and hypothesis

The research question is the question you want to answer in an empirical research paper.

Present your research question clearly and directly, with a minimum of discussion at this point. The rest of the paper will be taken up with discussing and investigating this question; here you just need to express it.

A research question can be framed either directly or indirectly.

  • This study set out to answer the following question: What effects does daily use of Instagram have on the prevalence of body image issues among adolescent girls?
  • We investigated the effects of daily Instagram use on the prevalence of body image issues among adolescent girls.

If your research involved testing hypotheses , these should be stated along with your research question. They are usually presented in the past tense, since the hypothesis will already have been tested by the time you are writing up your paper.

For example, the following hypothesis might respond to the research question above:

The final part of the introduction is often dedicated to a brief overview of the rest of the paper.

In a paper structured using the standard scientific “introduction, methods, results, discussion” format, this isn’t always necessary. But if your paper is structured in a less predictable way, it’s important to describe the shape of it for the reader.

If included, the overview should be concise, direct, and written in the present tense.

  • This paper will first discuss several examples of survey-based research into adolescent social media use, then will go on to …
  • This paper first discusses several examples of survey-based research into adolescent social media use, then goes on to …

Full examples of research paper introductions are shown in the tabs below: one for an argumentative paper, the other for an empirical paper.

  • Argumentative paper
  • Empirical paper

Are cows responsible for climate change? A recent study (RIVM, 2019) shows that cattle farmers account for two thirds of agricultural nitrogen emissions in the Netherlands. These emissions result from nitrogen in manure, which can degrade into ammonia and enter the atmosphere. The study’s calculations show that agriculture is the main source of nitrogen pollution, accounting for 46% of the country’s total emissions. By comparison, road traffic and households are responsible for 6.1% each, the industrial sector for 1%. While efforts are being made to mitigate these emissions, policymakers are reluctant to reckon with the scale of the problem. The approach presented here is a radical one, but commensurate with the issue. This paper argues that the Dutch government must stimulate and subsidize livestock farmers, especially cattle farmers, to transition to sustainable vegetable farming. It first establishes the inadequacy of current mitigation measures, then discusses the various advantages of the results proposed, and finally addresses potential objections to the plan on economic grounds.

The rise of social media has been accompanied by a sharp increase in the prevalence of body image issues among women and girls. This correlation has received significant academic attention: Various empirical studies have been conducted into Facebook usage among adolescent girls (Tiggermann & Slater, 2013; Meier & Gray, 2014). These studies have consistently found that the visual and interactive aspects of the platform have the greatest influence on body image issues. Despite this, highly visual social media (HVSM) such as Instagram have yet to be robustly researched. This paper sets out to address this research gap. We investigated the effects of daily Instagram use on the prevalence of body image issues among adolescent girls. It was hypothesized that daily Instagram use would be associated with an increase in body image concerns and a decrease in self-esteem ratings.

The introduction of a research paper includes several key elements:

  • A hook to catch the reader’s interest
  • Relevant background on the topic
  • Details of your research problem

and your problem statement

  • A thesis statement or research question
  • Sometimes an overview of the paper

Don’t feel that you have to write the introduction first. The introduction is often one of the last parts of the research paper you’ll write, along with the conclusion.

This is because it can be easier to introduce your paper once you’ve already written the body ; you may not have the clearest idea of your arguments until you’ve written them, and things can change during the writing process .

The way you present your research problem in your introduction varies depending on the nature of your research paper . A research paper that presents a sustained argument will usually encapsulate this argument in a thesis statement .

A research paper designed to present the results of empirical research tends to present a research question that it seeks to answer. It may also include a hypothesis —a prediction that will be confirmed or disproved by your research.

Cite this Scribbr article

If you want to cite this source, you can copy and paste the citation or click the “Cite this Scribbr article” button to automatically add the citation to our free Citation Generator.

Caulfield, J. (2023, March 27). Writing a Research Paper Introduction | Step-by-Step Guide. Scribbr. Retrieved February 28, 2024, from https://www.scribbr.com/research-paper/research-paper-introduction/

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