QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.)

Hongxian Mei; Chengqi Cui; Yanyang Liu; Zhenwei Du; Ke Wu; Xiaolin Jiang; Yongzhan Zheng; Haiyang Zhang

doi:10.1371/journal.pone.0293155

Peer Review History

Original SubmissionJuly 25, 2023
29 Aug 2023 Decision Letter - Maoteng Li, Editor PONE-D-23-23432QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.)PLOS ONE Dear Dr. Zheng, 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 Oct 13 2023 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The Manuscript provides information on QTLs linked to sesame seed size and shape, which is a rare report in the public. However, there were still some minor concerns in the study. Line 70,72 “SNP” should be “SNPs”. Line 133, “QTLs with more than 10% of PVE regarded as major QTLs”, What is the basis for this regarded? Line 260, “sequence analysis detected” is cloning in both parents? If so, the sequencing results are included as Supporting information in the manuscript The formatting of the references needs to be revised. Add units for traits in Table 1 How identification of the sesame seed size and shape QTLs could be useful in future molecular breeding program? Based on the gene mapping and QTL analysis, authors found three candidate genes for seed size and shape. Do you have any plan for the complementation study to confirm the gene function？ Reviewer #2: In this manuscript, F2 and BC1 populations were developed by crossing the Yuzhi 4 and Bengal small-seed (BS) lines for detecting the quantitative trait loci (QTLs) of traits related to seed size and shape. A total of 52 QTLs, including 13 in F2 21 and 39 in BC1 populations were identified. Three important co-localized loci were subsequently identified, harboring the stable major QTLs, which may provide useful information for future breeding strategies aimed at improving the seed yield of sesame, some questions and suggestions are as follows: 1 in line 146，’the seed size of the BS line was smaller’, there should be added statistical analysis for the phenotype of the parents. 2 in line 169-171, ‘the phenotypic values of the three traits were significantly positively correlated between environments in the BC1 population.’ The wording here is unclear. 3 the description of linkage map should be added in the results. 4 in line 260-262, non-synonymous SNPs were identified, maybe we can use software to predict whether the SNPs affect the protein function, http://www.ppved.org.cn/index.html. The transcription level of the candidate genes also should be considered. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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Revision 1
24 Sep 2023 Author Response Thank you for the reviewers’ comments concerning our manuscript entitled “QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.)”. Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our research. We have studied comments carefully and have made correction which we hope meet with approval. Revised manuscript has been uploaded. The main corrections in the paper and the responds to the reviewer’s comments are as flowing: Reviewer #1: The Manuscript provides information on QTLs linked to sesame seed size and shape, which is a rare report in the public. However, there were still some minor concerns in the study. 1. Line 70,72 “SNP” should be “SNPs”. We are grateful for the suggestion. Yes，“SNP” has been amended to “SNPs” 2. Line 133, “QTLs with more than 10% of PVE regarded as major QTLs”, What is the basis for this regarded? Mei et al (2021) reported that QTLs that explained more than 10% of phenotypic variation in at least one environment were considered major QTLs in the materials and methods. In results, they performed QTL mapping for yield‑related traits in sesame, and identified 20 major QTLs that explained more than 10% of the corresponding phenotypic variation in at least one environment. We added this reference in line 133. Mei H, Liu Y, Cui C, Hu C, Xie F, Zheng L, et al. QTL mapping of yield‑related traits in sesame. Mol Breeding. 2021; 41(7):43. doi:10.1007/s11032-021-01236-x. 3. Line 260, “sequence analysis detected” is cloning in both parents? If so, the sequencing results are included as Supporting information in the manuscript. Yes, the genes were cloned and sequenced in both parents. The sequencing results were provided as Supporting information (S3-S5 Figs). 4. The formatting of the references needs to be revised. Add units for traits in Table 1. How identification of the sesame seed size and shape QTLs could be useful in future molecular breeding program? Thank you for the suggestion. We have revised the formatting of the references and added units for traits in Table 1 (line 162). In this study, we identified several sesame seed size and shape QTLs. We will develop molecular markers closely linked to the related traits based on the QTLs, and use these markers to select objective trait. Furthermore, candidate genes and causative sites for these important traits will be identified by QTL fine-mapping or GWAS in sesame. With more genes that underlie quantitative traits identified, navigation breeding will be applied in sesame, which has been successfully used in rice (Wei et al. 2021). Wei X, Qiu J, Yong K, Fan J, Zhang Q, Hua H, et al. A quantitative genomics map of rice provides genetic insights and guides breeding. Nat Genet. 2021; 53(2):243-253. doi:10.1038/s41588-020-00769-9. 5. Based on the gene mapping and QTL analysis, authors found three candidate genes for seed size and shape. Do you have any plan for the complementation study to confirm the gene function？ Yes, we will analyze the expression patterns of three candidate genes using qRT-PCR, analyze the location of the proteins by subcellular localization, and verify the function of the genes using genetic transformation technology. Reviewer #2: 1. in line 146，‘the seed size of the BS line was smaller’, there should be added statistical analysis for the phenotype of the parents. Thanks for your suggestion. Yes, statistical analysis for the phenotype of the parents is shown in Figure 1B. 2. in line 169-171, ‘the phenotypic values of the three traits were significantly positively correlated between environments in the BC1 population.’ The wording here is unclear. We are very sorry for our unclear description. This sentence has been rephrased as follows: for each of the traits, a significantly positive correlation of the phenotypic values between each of environments in the BC1 population. (Line 170-171) 3. the description of linkage map should be added in the results. Yes, we have added the description of linkage map in manuscript. (Line 185-187; line 220) 4 in line 260-262, non-synonymous SNPs were identified, maybe we can use software to predict whether the SNPs affect the protein function, http://www.ppved.org.cn/index.html. The transcription level of the candidate genes also should be considered. Yes, we have performed prediction of protein function by the software, and found that SNPs did not affect the protein function. Therefore, we will perform the qRT-PCR to consider the transcription level of the candidate genes, and carry out the subcellular localization and genetic transformation to analyze function of the candidate genes in next steps. We tried our best to improve the manuscript and made some changes in the manuscript. These changes will not influence the content and framework of the paper. We appreciate for Editors/Reviewers’ warm work earnestly, and hope that the correction will meet with approval. Once again, thank you very much for your comments and suggestions. Sincerely yours Yongzhan Zheng Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0293155.r002
6 Oct 2023 Decision Letter - Maoteng Li, Editor QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.) PONE-D-23-23432R1 Dear Dr. Zheng, 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, Maoteng Li Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0293155.r003
Formally Accepted
24 Oct 2023 Acceptance Letter - Maoteng Li, Editor PONE-D-23-23432R1 QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.) Dear Dr. Zheng: I'm 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 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 plosone@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. Maoteng Li Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0293155.r004

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