Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditions

Yurim Kim; Myoung-Goo Choi; Myoung Hui Lee; Chuloh Cho; Jun Yong Choi; Suk-Jin Kim; Chon-Sik Kang; Chul Soo Park; Ki-Chang Jang; Youngjun Mo; Changhyun Choi

doi:10.1371/journal.pone.0322306

Peer Review History

Original SubmissionAugust 28, 2024
28 Aug 2024 Author Response https://doi.org/10.1371/journal.pone.0322306.r001
18 Nov 2024 Decision Letter - Harsh Raman, Editor PONE-D-24-37356Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditionsPLOS ONE Dear Dr. Choi, 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. There are several comments related to methodology and results that need to be addressed. Please go through the comments for further details Please submit your revised manuscript by Jan 02 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 . 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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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The paper is well written. The introduction sets out the reasons for the study, but the methods and data do not adequately answer the questions being posed. A high percentage of alleles at known genetic loci for heading date in wheat are described as unknown. These should be further investigated, as they could represent novel alleles or genes, and would add quality to the manuscript. I suggest to do this and resubmit. ****** 6. 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 #1: Yes: Livinus Emebiri ******** [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. Attachments Attachment Submitted filename: PlosOne-Review.docx Attachment Submitted filename: flowwering time_Manuscript (1).docx https://doi.org/10.1371/journal.pone.0322306.r002
Revision 1
3 Jan 2025 Author Response Response to Reviewer’s comments We sincerely appreciate the reviewer’s valuable comments, which have greatly contributed to improving the quality of our manuscript. Below, we provide our response to the reviewer’s comments. Major revisions 1. In general, the manuscript would be of limited interest, as the findings are supportive of well known information. The study identified a percentage of alleles at Vrn and Ppd loci that were listed as ‘unknown’ and with no record of the associated DTH. These could represent rare alleles and should be investigated further to deliver quality science, otherwise the content of paper is only of regional interest. - As the reviewer pointed out, our study deals with well-known loci, which may limit its novelty. However, our study employed a differentiated strategy to identify new genetic markers influencing heading date beyond the well-known loci using GWAS. Specifically, we selected resources from a wheat core set that had the same VRN1 and PPD1 genotypes as those of Korean wheat varieties, which are known globally for their early heading characteristics. Using this approach, we were able to discover new SNP markers associated with heading date variation. Additionally, we revised the Abstract and Discussion sections of the manuscript to better highlight this differentiated methodology. - I believe that this paper not only proposes an innovative experimental approach in GWAS analysis but also provides valuable information for the development of more effective heading date markers applicable to countries such as Japan and China. - Despite repeated PCR experiments performed multiple times to confirm the Vrn and Ppd genotypes, resources with unresolved genotypes are still classified as 'unknown.' I believe this issue cannot be resolved using the same approach. To address this problem, it will be necessary to sequence the full nucleotide sequences of the Vrn and Ppd loci and design various primer combinations based on this information. This could present a new and independent challenge. 2. The paper is well written. The introduction sets out the reasons for the study, but the methods and data do not adequately answer the questions being posed. A high percentage of alleles at known genetic loci for heading date in wheat are described as unknown. These should be further investigated, as they could represent novel alleles or genes, and would add quality to the manuscript. I suggest to do this and resubmit. - I agree with the reviewer's opinion. Therefore, we conducted a statistical analysis of the number of days to heading by allele for the newly discovered genetic marker loci, as well as for each of the already known heading genes (Vrn and Ppd), as presented in Table 1 and Table 2, respectively, in line with the reviewer’s suggestion. Additionally, we incorporated explanations into the Results and Discussion sections, highlighted in blue text. Minor revisions 2 page 32 line : Pl present data Response: Corrected 2 page 36 line : Which loci-describe here Response: Specifically provided information about the loci in the abstract. 3 page 56 line : Describe this Response: Corrected 5 page 99 line : 40 are part of 530? Response: Indicated that the 530 wheat core collection resources and the 40 Korean varieties are separate. 5 page 101 line : This does not equates to 362 Response: The numbers provided in the manuscript represent the major contributors to the 362 accessions collected from 47 countries. Smaller contributions from other countries were not explicitly listed to maintain conciseness, but they are included in the total count of 362 accessions. 5 page 110 line : Not self explanatory Response: Corrected 6 page 113 line : What this means, regeneration stage? Response: Added explanations for the terms. 7 page 138 line : Have authors used VRN-A1, VRN-B1, and VRN-D1 data for GWAS? Response: The VRN-1 data was indirectly utilized in GWAS, as the second GWAS (Group B) was performed using accessions that possess the vrn-A1 allele, reflecting the allelic composition of Korean wheat varieties. 7 page 145 line : What were the values for heterozygosity? + and - 3 SD? Response: Provided the values. 11 page table : Average?, Author should have conducted MET analysis Response: Reanalyzed the data to present stability index by genotype and revised the relevant content in the manuscript accordingly. page 237 line : What this means, in relation to population structure? Response: The percentages of the principal components (PC1, PC2, and PC3) indicate the proportion of total genetic variation explained by each component. PC1, explaining 6.0% of the variance, captures the primary axis of genetic variation, while PC2 and PC3, explaining 3.8% and 2.7% respectively capture additional axes of variation. These values reflect the genetic structure within the population. 14 page 273 line : ? Response: Corrected 15 page table : Provide R2 values-phenotypic or genetic variance accounted Response: Added proportion of variance explained (PVE). 30 page 402 line : data not shown Response: Corrected In addition, some revisions were made to improve the clarity of the manuscript. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0322306.r003
19 Feb 2025 Decision Letter - Harsh Raman, Editor PONE-D-24-37356R1Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditionsPLOS ONE Dear Dr. Choi, 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. Lines 257: -… located on the short arm of chromosome 2A, in close proximity to PPD-A1 (TraesCS2A01G081900; 2A: 36,936,362–36,938,400). The search for 'TraesCS2A01G081900' returned no results. Please recheck and submit these manuscriptPlease ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. Please submit your revised manuscript by Apr 05 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, Harsh Raman, 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. Additional Editor Comments: I have gone thru the manuscript and the authors addressed queries raised by the reviewer. I am happy to accept this manuscript if author address the following comment Lines 257: -… located on the short arm of chromosome 2A, in close proximity to PPD-A1 (TraesCS2A01G081900; 2A: 36,936,362–36,938,400). The search for 'TraesCS2A01G081900' returned no results. Please, check and correct. [Note: HTML markup is below. Please do not edit.] [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. https://doi.org/10.1371/journal.pone.0322306.r004
Revision 2
13 Mar 2025 Author Response Response to Reviewer’s comments We sincerely appreciate the reviewer’s additional comments, which have helped us further improve our manuscript. Below, we provide our response to the reviewer’s comments. Minor revisions 1. Lines 257: -… located on the short arm of chromosome 2A, in close proximity to PPD-A1 (TraesCS2A01G081900; 2A: 36,936,362–36,938,400). The search for 'TraesCS2A01G081900' returned no results. Please recheck and submit these manuscript. Response: The reason why the gene TraesCS2A01G081900 (2A: 36,936,362–36,938,400) could not be found is that it was annotated in the IWGSC 1.0 assembly version. This information can be verified in Reference 9 of our manuscript. In the IWGSC 2.1 assembly version, the gene has been renamed to TraesCS2A02G081900. Therefore, we have updated our manuscript accordingly, replacing TraesCS2A01G081900 with TraesCS2A02G081900 and specifying the corresponding genomic location Attachments Attachment Submitted filename: Response_to_Reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0322306.r005
19 Mar 2025 Decision Letter - Harsh Raman, Editor Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditions PONE-D-24-37356R2 Dear Dr. Choi, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Harsh Raman, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0322306.r006
Formally Accepted
Acceptance Letter - Harsh Raman, Editor PONE-D-24-37356R2 PLOS ONE Dear Dr. Choi, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Harsh Raman Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0322306.r007

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