Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross

Ajay Kumar; Eder E. Mantovani; Senay Simsek; Shalu Jain; Elias M. Elias; Mohamed Mergoum

doi:10.1371/journal.pone.0221826

Peer Review History

Original SubmissionMay 23, 2019
26 Jun 2019 Decision Letter - Aimin Zhang, Editor PONE-D-19-14666 Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross PLOS ONE Dear Dr. Kumar, 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. We would appreciate receiving your revised manuscript by Aug 10 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Aimin Zhang, Ph.D. Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [Note: HTML markup is below. Please do not edit.] 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 ******** 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 ****** 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 ****** 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 following expresses my opinion about the merits of the study: 1) The paper provides useful information for breeders of hard red spring wheat and for the wider wheat community, particularly since the paper addresses the association of wheat quality and yield traits with grain shape and size traits, a poorly studied area. 2) The use of a high-density map for the mapping procedures should enable high efficiency application of MAS in future breeding programmes based upon this germplasm or upon these general results. 3) The identification of novel alleles provided by the non-adapted line, especially (i) alleles for improved GPC with no detrimental effects on yield or other traits, and (ii) alleles influencing grain hardness, together potentially provide new opportunities for achieving genetic progress in these traits. 4) Other valuable features of the paper are: (i) the detailed analysis of epistasis, which provides additional evidence of the importance of taking this into account during selection; (ii) the evidence presented that selection for grain area during breeding might also provide dividends; and (iii) the extensive comparison between the QTLs mapped here and those published previously, which details which of the QTLs identifies here are truly novel. A comment: the study would probably have been more valuable still if more than 160 RILs had been evaluated and, to boot, more site-year combinations had been included; nonetheless, I do not see these drawbacks as sufficient motive to hold up publication of the study as it stands. Am I right in thinking that there is disagreement in the labelling of the parental phenotypic mean values between Table 1 and Fig. 1? I recommend checking this. Grammatically the writing is generally clear, although it might be further improved by being looked over once more. Based upon the above opinion, I feel the paper is well worthy of publication. Reviewer #2: The manuscript has some new finding in the area (specified for hard red spring wheat) which can be useful in the breeding program. It has dissected the genetics of wheat quality and yield traits and also identified novel QTL and markers closely associated with quality and yield. It shows data about the epistasis in the genetic control of quality and yield as well. The manuscript is well written. My only concern is that only two replicates were used in this experiment. I think it should be more. I think it is suitable for publication. ****** 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: No Reviewer #2: 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0221826.r001
Revision 1
2 Jul 2019 Author Response Response to reviewer’s comments Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Author’s response: We have formatted the manuscript according to PLOS One style and hope that it meet the journal requirements. 2. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Author’s response: The phrase “data not shown” was removed from the manuscript. [Note: HTML markup is below. Please do not edit.] 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 ________________________________________ 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 ________________________________________ 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 ________________________________________ 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 following expresses my opinion about the merits of the study: 1) The paper provides useful information for breeders of hard red spring wheat and for the wider wheat community, particularly since the paper addresses the association of wheat quality and yield traits with grain shape and size traits, a poorly studied area. 2) The use of a high-density map for the mapping procedures should enable high efficiency application of MAS in future breeding programmes based upon this germplasm or upon these general results. 3) The identification of novel alleles provided by the non-adapted line, especially (i) alleles for improved GPC with no detrimental effects on yield or other traits, and (ii) alleles influencing grain hardness, together potentially provide new opportunities for achieving genetic progress in these traits. 4) Other valuable features of the paper are: (i) the detailed analysis of epistasis, which provides additional evidence of the importance of taking this into account during selection; (ii) the evidence presented that selection for grain area during breeding might also provide dividends; and (iii) the extensive comparison between the QTLs mapped here and those published previously, which details which of the QTLs identifies here are truly novel. Author’s response: Thank you so much for your comments, wonderful observations about our manuscript and your recommendation for publication. A comment: the study would probably have been more valuable still if more than 160 RILs had been evaluated and, to boot, more site-year combinations had been included; nonetheless, I do not see these drawbacks as sufficient motive to hold up publication of the study as it stands. Author’s response: Thank you so much for your comment. We understand that larger sample size and more site-year combinations, may provide additional information. Larger population may help identify some additional minor QTL (if any). That being said, we strongly feel that (and as the results indicate), this study has identified important QTL with significant effects. In QTL mapping studies, it is a common and acceptable practice to have a population of >100 and minimum of three site-year combinations (our study used data for 160 RILs from four site-year combinations). One of the main reason for this is the large amount of resources required to carry out field evaluation at multiple locations. Moreover, the phenotypic assays for evaluation of quality traits are labor intensive and require huge amount of resources, thus limiting site-year combinations to a manageable and acceptable number. Am I right in thinking that there is disagreement in the labelling of the parental phenotypic mean values between Table 1 and Fig. 1? I recommend checking this. Author’s response: Thank you so much for noticing this mistake. We have now made necessary corrections to the legend of Figure 1. Grammatically the writing is generally clear, although it might be further improved by being looked over once more. Author’s response: Thank you for your comment. As can be seen in the manuscript, we have gone through the manuscript one more time to improve the manuscript. Based upon the above opinion, I feel the paper is well worthy of publication. Reviewer #2: The manuscript has some new finding in the area (specified for hard red spring wheat) which can be useful in the breeding program. It has dissected the genetics of wheat quality and yield traits and also identified novel QTL and markers closely associated with quality and yield. It shows data about the epistasis in the genetic control of quality and yield as well. The manuscript is well written. My only concern is that only two replicates were used in this experiment. I think it should be more. I think it is suitable for publication. Author’s response: Thank you so much for your review of our manuscript and your recommendation. We understand that more replications are always better, but due to resource and labor intensive phenotyping in multi-environment mapping studies, it is a standard and acceptable practice to have two replicates per environment. Moreover, the phenotypic assays for evaluation of quality traits are highly labor intensive and require huge amount of resources, thus limiting number of replicates and site-year combinations to a manageable and acceptable number. Attachments Attachment Submitted filename: Response to reviewers comments.docx https://doi.org/10.1371/journal.pone.0221826.r002
22 Jul 2019 Decision Letter - Aimin Zhang, Editor PONE-D-19-14666R1 Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross PLOS ONE Dear Dr. Kumar, 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. We would appreciate receiving your revised manuscript by Sep 05 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Aimin Zhang, Ph.D. Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 #1: (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 #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 #1: 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 #1: 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 #1: As requested, the authors have (i) adequately defended the questions posed on sample size and the number of site-year combinations included; (ii) corrected the discrepancy between Table 1 and Fig. 1; and (iii) improved the grammar. I therefore maintain my original opinion that the paper is well worthy of publication. Nonetheless, below I include additional modifications to the grammar, those that I have managed to identify in the time available: Personally, I would generally replace “QTL” with “QTLs” where it is used in the plural, but do not insist since papers vary in this respect. The following are more specific modifications suggested to particular lines in the manuscript: l. 56: insert “the” after “while”. l. 59: insert “it” after “although”. l. 60: replace “they do” with “does”. l. 61: insert “with them” after “loci”, insert “A” before “major”, insert “the” before “Rht8” and insert “the” before “reduced”. l. 62: replace “increase” with “increases”. l. 97: replace “more” with “a greater”. l. 259: insert “The” before “same”. l. 277: replace “negatively” with “negative”. l. 298: replace “has” with “had”. l. 299: replace “effect” with “effects”. l. 314: replace the phrase with “The majority (52 out of 60) of these QTL”. l. 362: insert “the” before “PI”. l. 363: insert “the” before “PI”. l. 364: insert “the” before “ND”. l. 415: replace “,” with “and” and insert “,” after “SPMS”. l. 420: replace “had association” with “were associated”. l. 432: replace “those” with “these”. l. 434: insert “the” before “PI” and replace “were” with “was”. l. 440: replace “interaction” with “interactions”. l. 444: replace “More” with “A greater”. l. 455: delete “each” and insert “for each trait” after “detected”. l. 456: replace “locus” with “loci”. l. 457: replace “interaction” with “interactions”. l. 458: delete “or”. l. 473: replace “helps” with “help” and replace “marker” with “market”. l. 484: insert “a” after “of”. l. 491: insert “,” after “effect”. l. 494: insert “the” after “that”, replace “increase” with “increased” and delete “Like this study”. l. 495: delete “as well”. l. 500: insert “the” after “by” and insert “,” after “genotype”. l. 502: insert “the” before “contribution” and “the” before “majority”. l. 505: insert “,” after “yield”. l. 506: insert “,” after “traits”. l. 508: delete “,”. l. 510: delete “,” after “Although”. l. 513: delete “,” before “were”. l. 515: replace “have” with “has”. l. 516: insert “,” after “however”. l. 519: replace “difference” with “differences”. l. 520: insert “,” before “does”. l. 521: insert “the” after “as”. l. 522: insert “the” after “allele of”. l. 523: insert “a” before “functional”. l. 525: insert “the” before “high” and insert “the” before “Gpc-B1”. l. 529: insert “,” before “where”. l. 531/2: delete “which is”. l. 534: insert “,” after “proteins”. l. 537: insert “the” after “of”. l. 538: delete “as well”. l. 539: delete “,” after “genotypes”. l. 541: replace “major” with “greater”. l. 553: delete “,” after “(SPMS)”. l. 554: insert “the” after “three”. l. 556: replace “trait” with “traits”, insert “,” after “traits” and delete “which is”. l. 560: insert “,” before “is”. l. 564: replace “effect” with “effects”. l. 566: replace “effect” with “effects”. l. 568: insert “,” after “alleles”, replace “increase” with “they increased” and delete “they”. l. 569: replace “decrease” with “decreases” and insert “,” after “components”. l. 570: replace “environment” with “environments”. l. 575: replace “an” with “on”. l. 583: replace “Till” with “To”. l. 585: insert “the” after “to”. l. 586: insert “the” after “in”. l. 587: insert “,” after “2D”. l. 588: replace “papulation” with “population”. l. 589: insert “the” before “alleles”. l. 599: insert “the” after “since”. l. 601: insert “the” before “Japonese”. l. 604: delete “,” after “although” and replace “differ” with “differed”. l. 607: insert “the” before “Rht8” and insert “a” before “larger”. l. 608: replace “suggest” with “suggests”. l. 609: insert “the” after “at”. l. 617: insert “the” after “at”. l. 618: insert “the” after “at”. l. 619: delete “,”, insert “a” after “showed” and insert “the” after “in”. l. 620: insert “the” after “of”. l. 623: insert “,” after “estimates”. l. 626: insert “the” after “while”. l. 627: insert “the” after “by” and insert “the” after “using”. l. 628: delete “,” after “[86]”. l. 629: delete “,” after “Since”. l. 630: insert “the” after “harbors” and replace “alleles” with “allele”. l. 632: insert “the” after “either” and replace “loci” with “locus”. l. 634: delete “,”. l. 635: insert “the” after “of” and replace “gene” with “genes”. l. 641: insert “,” after “is”, insert “,” after “important” and delete “but”. l. 643: delete “although” and insert “although” after “,”. l. 647: delete “,” after “Although”. l. 655: replace “more” with “a greater”. l. 657: delete “,”. l. 659: delete “,” after “thus”. l. 660: replace “component” with “components” and delete “,” after “Since”. l. 661: delete “,”. l. 667: insert “,” after “crucial”. l. 668: delete “,” and replace “effects” with “affects”. l. 672: insert “,” after “own”. l. 674: replace “has” with “have”. l. 675: insert “The” before “Role” (role). l. 677: insert “a” after “contributed”. l. 681: delete “,”. l. 692: replace “trait” with “traits”. l. 698: delete “,”. l. 700: insert “,” after “GA”. l. 704: insert “,” after “trait” and delete “an”. l. 707: insert “,” before “which” and insert “the” before “allele”. l. 710: delete “a”. l. 713: insert “be” after “to” and delete “the”. l. 714: replace “program” with “programs”. l. 715: delete “~”. l. 721: delete “an”. ****** 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 #1: 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0221826.r003
Revision 2
23 Jul 2019 Author Response Authors’ response: We HIGHLY appreciate the reviewer for thoroughly going through our manuscript and for suggesting all the corrections. We have gone through the whole manuscript again and made all the necessary corrections in the grammar (using track changes). Attachments Attachment Submitted filename: Response to reviewers comments.docx https://doi.org/10.1371/journal.pone.0221826.r004
16 Aug 2019 Decision Letter - Aimin Zhang, Editor Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross PONE-D-19-14666R2 Dear Dr. Kumar, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With 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 #1: 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 #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 #1: 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 #1: 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 #1: The authors have gone to great lengths to amend the manuscript based upon the suggestions made, which is much appreciated. I therefore have no further suggestions and wish the authors all the best of luck in their future studies, which I am sure will be very fruitful. ****** 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 #1: No https://doi.org/10.1371/journal.pone.0221826.r005
Formally Accepted
21 Aug 2019 Acceptance Letter - Aimin Zhang, Editor PONE-D-19-14666R2 Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross Dear Dr. Kumar: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Prof. Aimin Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0221826.r006

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .