PONE-D-20-27285

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

PLOS ONE

Dear Dr. Kisten,

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Kind regards,

Aimin Zhang, Ph.D.

Academic Editor

PLOS ONE

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[Funding for the research undertaken in this manuscript were sourced from the following funders:

1.    South African Winter Cereal Trust

https://www.wintercerealtrust.co.za

Grant WCT/W/2018/06 - Awarded to VT

PhD bursary - Awarded to LK

2.    National Research Foundation - Research and Technology Fund

https://www.nrf.ac.za

Grant RTF1505 2911 8466 - Awarded to VT

3.    National Research Foundation - Professional Development Programme

https://www.nrf.ac.za

Block Grant PDP160318160924 - Awarded to VT via Jasper Rees

PhD bursary - Awarded to LK

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.].   

We note that one or more of the authors are employed by a commercial company: LongReach Plant Breeders Management Pty Ltd

1. Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form.

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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: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: Yes

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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: 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 represents a breakthrough contribution to the plant resistance literature for RWA, using an excellent merger of well-known conventional breeding with wheat genomics.

The Manhattan plots of SNP markers associated with RWA resistance completely explodes the idea that RWA resistance genes are dominant traits and reinforces the central theme of the manuscript – that QTLs explain resistance and that QTL-based resistance is strongly influenced by the pedigrees of resistant genotypes.

By combing mapped-based linkage mapping with genomic association mapping results, the authors have demonstrated that an allelic gene cluster is present on chromosome 1DS, but at the same time clearly demonstrated the shortcomings of mapped-based linkage.

The identification of new regions and MTAs on chromosomes 5A and 6B associated with resistance to South African biotypes is a seminal development in the understanding of the complexity of RWA resistance in wheat.

Finally, the identification of plant DR genes with putative function in RWA resistance represents an additional major step in understanding arthropod resistance genes.

At the end of the discussion, the authors may wish to consider adding plant level examples of the effect of temperature and light on expression of resistance i.e. Hessian fly resistance gene sensitivity to temperature (Chen et al. 2014. J. Econ. Entomol. 107:1266) and wheat stem sawfly resistance gene sensitivity to light intensity (Varella et al. 2016 Plant Breed.135: 546).

Minor grammar edits were included in the reviewer attachment.

Reviewer #2: In this study，authors perform a characterization of RWA resistance phenotypes of 32 wheat lines using four South African RWA biotypes and a total of 181 samples were genotyped using the Illumina 9K SNP wheat chip. A GWAS study using 7598 polymorphic SNPs identified 27 marker trait associations (MTA) with an average linkage disequilibrium of 0.38 at 10 Mbp. Twenty putative genes were annotated using the IWGSC RefSeq, three of which are linked to plant defence responses. Technically the strategy seems sound, but I found some processes were not rigorous.

1. Representative samples are required for GWAS analysis. Only 32 samples are used in this paper. The author should elaborate on why these samples are used and how these samples can obtain accurate results of correlation analysis.

2. The relationship between the 32 phenotyped samples and the 181 genotyped samples was not clearly described.

3. Fig. 3A shows that LD has two peaks. Generally, LD is gradually attenuated, what is the reason for forming the double peak of LD?

4. 66

5. Page 16, line 1 an average.

6. Page 5, line 145-147 too long sentence. please split it.

7. Fig. 1 and Fig. 4 is too blurry to be clearly distinguished, please give a higher resolution image.

8. Fig. 21 line 8, ti should be to

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-20-27285_reviewer.pdf

PONE-D-20-27285R1

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

PLOS ONE

Dear Dr. Kisten,

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 Jan 11 2021 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Aimin Zhang, Ph.D.

Academic Editor

PLOS ONE

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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: (No Response)

Reviewer #4: All comments have been addressed

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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

Reviewer #4: Yes

**********

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

Reviewer #3: Yes

Reviewer #4: 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

Reviewer #4: 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

Reviewer #4: 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: Dear authors,

I have some suggestions or corrections in the revised manuscript.

1. In page 6, line 137-139, Table 1 was stated that there are 25 genotypes containing Dn4 genes. However, there are 24 genotypes carrying the Dn4 gene in table 1. Also, the sum of the specified numbers of genotypes makes 33 in the same lines.

2. In page 14, line 4-5, the sentence

“Three of the MTRWA92 breeding lines (91, 120 and 160), contained the 195 bp fragment, while the remaining nine lines (93, 114, 115, 121, 145, 149, 150, 155, 158) had the 175 bp fragment.”

MTRWA92-160 line does not contain the 195 bp fragment in Table 2.

3. In page 14, line 11-12, the sentence

“The 125 bp fragment was amplified in PI372129, Halt, 12 BondCL, Yumar and all of the 18 FAWWON-SA 64 plants. ”

Also, Corwa genotype contains the 125 bp fragment according to Table2.

4. In page 18, line 10-11,

“MTRWA92-161 was resistant to RWASA1, RWASA3 and RWASA4 and showed a moderate resistance to RWASA2.”

This information was given two sentences before in the same paragraph, in that;

“Genotypes MTRWA92- 161 and MTRWA92-93 were moderately resistant to RWASA2 and showed a high level of resistance to RWASA1, RWASA3 and RWASA4.”

Best regards

Reviewer #4: It is suggested that some description in the discussion for the resistance level to of the test wheat lines to the other wheat aphids, because the several wheat aphids species usually concur at the same.

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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

Reviewer #4: No

[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.

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

PONE-D-20-27285R2

Dear Dr. Kisten,

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.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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,

Aimin Zhang, 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: (No Response)

**********

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: (No Response)

**********

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

Reviewer #3: (No Response)

**********

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: (No Response)

**********

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: (No Response)

**********

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: (No Response)

**********

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