PONE-D-24-31553AMMI Analysis of Elite Bread Wheat (Triticum aestivum L.) Selections for Genotype by Environment Interaction and Stability of Grain Yield in Southern EthiopiaPLOS ONE

Dear Dr. Gessese,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

Reviewer #3: Yes

Reviewer #4: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript is well designed and written in a fluent language. Since the manuscript using AMMI and GGE biplot on bread wheat genotypes across four locations, it has an international audience. The statistical analysis is performed on the data and clearly discussed with the figures.

Therefore, the manuscript is suitable to publish on the PLOS ONE journal

Reviewer #2: • The authors didnt shows the aim of the research in the abstract section.

• For citation format, authors must re-read the author guidelines.

• Inconsistent in the units used (grain yield (t/ha), 2.67 t ha-1, and 2.51 ton ha-1), check in all sections for all units.

• It would be interesting to conduct a correlation analysis or path analysis between environmental factors (temperature, rainfall, altitudes, and soil conditions) with yield and yield attributes.

• It needs to be explained that AMMI, ASV, YSI, and GGE Biplot are used to identify stability. And why use these analyses? There are many other stability analyses that can be used, such as combined stability analysis (parametric and non-parametric). If combined between Visual Analysis (AMMI and GGE biplots) with parametric and non-parametric, it will be very interesting and more precise (authors can read and cite some of these articles: https://doi.org/10.1007/s10681-019-2386-5 and https://doi.org/10.34044/j.anres.2022.56.4.10)

• There is no information on soil conditions at each location. Because soil fertility is one of the factors that affect crop yields.

• The subtitle "Mean Performance of the 11 selections for the 16 traits evaluated across locations" is confusing.

• Inconsistent subtitles, such as: "Analysis of variance" uses sequential numbers, but other subtitles do not use sequential numbers. In addition, the subtitles are also less descriptive of what will be discussed and are too general.

• In table 5, the numbers after the decimal point are inconsistent.

• There are several typos, such as "spikelets", in several sentences it is written as "spiklets"

• Inconsistent paragraph writing.

• It is necessary to add data for one more planting season in each location so that the influence of the genotypes by environment interactions is more visible.

• The discussion is not strong. How did the authors determine the best genotype (Stable and high yield) from all the analyses used?

• The use of the abbreviation of Genotype by environment interactions is inconsistent. In some parts it is written as GxL, but in other parts it is written as GxE

• The authors did not reveal the limits of genotype stability using AMMI and ASV. In AMMI Biplot, the radius of the ellipse should be displayed, which is one indicator of genotype stability.

• For mega environment analysis, the data used is still lacking.

• The authors do not disclose how they drew conclusions from all the analyses used.

• The conclusion section is not clear/ not concrete.

Reviewer #3: My corrections are attached in the manuscript. The major corrections are as follow,

The location is contributing more to the variation, so it is recommended to provide soil analysis data and weather parameters month wise during cropping season (as the crop grown in rainfed condition month wise rainfall data provide more insights), if available.

The disease score were mentioned as percentage in text in result section, but in table-4 the unit given as scale. If the scale converted as percent disease incidence provide the methodology with formula in material and method.

Provide details of scale along with category of resistance/susceptibility.

As, mentioned in methodology the DMRT analysis was performed for traits having significance for genotype and GEI, but the LR trait showed non significant in combined ANOVA, but the mean comparison was performed as visualized from table-4. Provide the reason.

The Table-6 is a repetitive of Table-4 and 7, better it should be removed.

The table-7 is numbered as table-73, correct it.

The figures were numbered in Italic, change to Arabian numerals.

The Conclusion and recommendation section is more elaborative, which is repetitive of result and discussion. For better reading make it crisp by highlighting significant result and it's future implementation.

Reviewer #4: The topic and analysis is sound. However, I consider the number of years studied in this article to be insufficient to make conclusions. I suggest that the authors should gather at least one more year of data to present the article.

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Reviewer #1: Yes: Ziya DUMLUPINAR

Reviewer #2: No

Reviewer #3: No

Reviewer #4: No

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Attachments

Attachment

Submitted filename: PONE-D-24-31553_reviewer1.pdf

Attachment

Submitted filename: liyew et al..docx

PONE-D-24-31553R1AMMI Analysis of Elite Bread Wheat (Triticum aestivum L.) Selections for Genotype by Environment Interaction and Stability of Grain Yield in Southern EthiopiaPLOS ONE

Dear Dr. Gessese,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 08 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: The authors have carefully addressed all the recommendations as suggested. However, a few recommendations need to be carried out before the manuscript (MS) is published.

The description of the testing environments given under Section 2.1 is too descriptive and deviates from the scope of the journal. Therefore, I suggest that the authors add a single paragraph explaining the key information about the sites, as the other climatic and soil parameters are provided in the table.

In Section 2.3, the section number is missing for the data collection subheading. Additionally, the traits listed under this subheading are in italics; please change them to regular font.

In the results under Sections 3.1 and 3.2, the traits can be mentioned in short form, with abbreviations explained in the materials section.

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: No

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[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

AMMI Analysis of Elite Bread Wheat (Triticum aestivum L.) Selections for Genotype by Environment Interaction and Stability of Grain Yield in Southern Ethiopia

PONE-D-24-31553R2

Dear Dr. Gessese,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: The authors have included all the recommended comments, hence the article can be accepted for publication

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: No

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