Genomic screening of allelic and genotypic transmission ratio distortion in horse

Nora Laseca; Ángela Cánovas; Mercedes Valera; Samir Id-Lahoucine; Davinia I. Perdomo-González; Pablo A. S. Fonseca; Sebastián Demyda-Peyrás; Antonio Molina

doi:10.1371/journal.pone.0289066

Peer Review History

Original SubmissionApril 10, 2023
31 May 2023 Decision Letter - Qinghua Shi, Editor PONE-D-23-10812Genomic screening of allelic and genotypic transmission ratio distortion in horsePLOS ONE Dear Dr. Laseca, 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 Jul 15 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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Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. [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 ******** 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? 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Reviewer #1: 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: This study aimed to find regions with transmission ratio distortion (TRD) in the horse genome. The authors used data from 277 horses genotyped in offspring-stallion-mare trios at 670,804 markers distributed uniformly across the genome. By implementing allelic and genotypic TRD models of the software TRDscan, and filtering for stringent statistical criteria, the authors found 140 SNPs with allelic TRD and 42 SNPs with a genotypic TRD pattern. Functional enrichment analysis was performed for genes located in a 1Mb window around the identified TRD SNPs, and identified a significant enrichment of GO terms, such as spermatogenesis, gametogenesis, oocyte division, embryonic development and hormonal activity. The research leading to this manuscript was performed properly and rigorously. The authors followed the protocol of the TRDscan software developers, and used stringent criteria for selecting candidate SNPs for TRD: SNPs with TRD pattern showing decisive evidence (BF>100), with <0.1% margin error, with at least 20 informative offspring and with \|TRD\| > 0.2. When conducting functional enrichment analysis, a Benjamini-corrected P-value cutoff of 0.05 was used. Major revisions: I would suggest that the authors put more emphasis on investigating the genomic characteristics of the regions with TRD, and test for patterns typically associated with TRD regions. Also, I suggest putting less emphasis on the functional enrichment analysis around the candidate SNPs. In particular, the authors identified large TRD regions that contain multiple SNPs with similar TRD magnitudes. TRDs often involve multiple genes for their function, which they link together using inversions. It would be interesting to see if the identified regions contain inversions, have elevated polymorphism levels or lethal genes. One could obtain these parameters from the horse genome and its annotation. Also, is there a correlation of TRD strength and size of the region? A scatterplot would be informative of the relationship of these two, if there is correlation. Figure 1 could include a panel b, which would be the same Manhattan plot as Figure 1, but with \|TRD\| on the y axis, like in Figure 4 of Id-Lahoucine et al. (2019). The authors observed that SNPs with significant genotypic TRD show higher absolute TRD than those with allelic TRD. This comparison would be nice to see in a violinplot or a boxplot. Table 1 and Table 2 list the top candidate SNPs with TRD, and they would be better suited for the Supplementary material, in my opinion. The functional enrichment analysis is based on genes that are within 500 Kb of a TRD SNP. One concern is that 500 Kbs seem too inclusive, and one should maybe consider smaller windows. The other concern is that the authors end up with a total of 562 genes near SNPs with allelic TRD, of which one expects only a small proportion to be actually involved in TRD, the rest most likely just linked to the causal genes. Therefore, I think that the authors should less emphasis on the functional enrichment analysis and devote less space in the manuscript to reporting and discussing its results, as this part of the manuscript is too speculative. For example, the authors could include Table 3, which reports the candidate fertility and reproductive process genes, and choose one Venn diagram to show in the main text, and include the rest in the Supplementary material. ****** 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 ******** [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". 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Revision 1
19 Jun 2023 Author Response Dear editor, we have followed your advice and comments: we have checked and corrected the style of PlosOne. We have added additional information in the Methods section: no animal experiments have been performed. Finally, we have added the dataset to a public repository and provided the URL code. In addition to the data and results already presented in the manuscript and in the additional information. Dear reviewer, we have followed your advice and comments to improve the manuscript. Major revisions: I would suggest that the authors put more emphasis on investigating the genomic characteristics of the regions with TRD, and test for patterns typically associated with TRD regions. Also, I suggest putting less emphasis on the functional enrichment analysis around the candidate SNPs. Author Answer: The authors appreciate your opinion and considerations. In particular, the authors identified large TRD regions that contain multiple SNPs with similar TRD magnitudes. TRDs often involve multiple genes for their function, which they link together using inversions. It would be interesting to see if the identified regions contain inversions, have elevated polymorphism levels or lethal genes. One could obtain these parameters from the horse genome and its annotation. Also, is there a correlation of TRD strength and size of the region? A scatterplot would be informative of the relationship of these two, if there is correlation. Author Answer: Thank you for your comment. In order to identify inversions in TRD regions with SNPs with similar TRD magnitudes it would be necessary to sequence animals carrying these alleles in order to investigate the inversions. With array genotyping methodology it would only be possible to analyze copy number variation as we already did in another study [1]. On the other hand, regions annotated in the study with SNPs of similar TRD magnitude exhibit moderate levels of polymorphism (mean frequency is ~0.29). In particular these frequencies occur in SNPs with mare- or stallion- TRD where TRD occurs through only one single parent, while it is null through the other parent, resulting in maintenance of the level of polymorphism. Regarding the search for lethal genes in these regions, we have not found any lethal mutation annotated in these regions, probably due to the insufficient annotation of the horse genome (so far) compared to the human or cow genome (Line 325-330). Finally, it is important to note that we have not observed a generalized relationship between TRD strength and region size. Our findings indicate that there is no correlation in this regard. Instead, the magnitude of the TRD is influenced by the linkage disequilibrium of the SNPs present in the specific TRD region with the causal mutation. In other words, the strength of the TRD depends on how closely related the marker is to the causal mutation. When the marker is more closely related, it has the potential to capture a stronger TRD with a greater magnitude (Line 318-324). Figure 1 could include a panel b, which would be the same Manhattan plot as Figure 1, but with \|TRD\| on the y axis, like in Figure 4 of Id-Lahoucine et al. (2019). Author Answer: Thank you for your comment. The new Manhattan plot with \|TRD\| on the y axis have been included as panel b. (Line 158-159) The authors observed that SNPs with significant genotypic TRD show higher absolute TRD than those with allelic TRD. This comparison would be nice to see in a violinplot or a boxplot. Author Answer: Thank you for your comment. This is just a consequence of the implemented models which are based on different parameterizations. The parametric space of allelic parameterization ranges from -0.5 to 0.5, so the absolute maximum value is 0.5. In contract, the absolute maximum value for genotypic parameters is 1, as the parametric space of genotypic model is -1 to 1. This difference is because, form an allelic perspective, a parent could transmit one allele (e.g., A) with 0.5 (50%) and the opposite allele (e.g. B) with 0.5 (50%) under null TRD (TRD=0). If there is TRD, the probability of transmission of one particular allele could decrease up to 0 (0.5 - 0.5 = 0) or increase up to 1 (0.5 + 0.5 =1). Thus, the parameter space ranges from -0.5 to 0.5. In contrast, with the genotypic model, we do not focus on alleles but on the combination of alleles in the genotype and including additive and dominance TRD parameters, and the maximum probability of observing a particular genotype in the offspring generation is 1; thus, the parametric space ranges from -1 to 1 as described in Materials and Methods section. Table 1 and Table 2 list the top candidate SNPs with TRD, and they would be better suited for the Supplementary material, in my opinion. Author Answer: Thank you for your comment. Following your suggestions, Table 1 and Table 2 have been suited for the Supplementary material. A new column has been added to S1 Table to mark the top candidate SNPs. The functional enrichment analysis is based on genes that are within 500 Kb of a TRD SNP. One concern is that 500 Kbs seem too inclusive, and one should maybe consider smaller windows. The other concern is that the authors end up with a total of 562 genes near SNPs with allelic TRD, of which one expects only a small proportion to be actually involved in TRD, the rest most likely just linked to the causal genes. Therefore, I think that the authors should less emphasis on the functional enrichment analysis and devote less space in the manuscript to reporting and discussing its results, as this part of the manuscript is too speculative. For example, the authors could include Table 3, which reports the candidate fertility and reproductive process genes, and choose one Venn diagram to show in the main text, and include the rest in the Supplementary material. Author Answer: Thank you for your comment. Following your suggestions, we have performed the functional enrichment analysis by reducing the search interval of genes around the SNPs showing TRD in ±250Kb upstream-downstream. In this way, thanks to their advice, we have focused on the genes with the strongest association to TRD, thus avoiding speculation. We have also reduced some of the information from the functional enrichment analysis by including the information in the Supplementary material. 1. Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S. Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals. 2022;12(11). doi: 10.3390/ani12111435. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0289066.r002
11 Jul 2023 Decision Letter - Qinghua Shi, Editor Genomic screening of allelic and genotypic transmission ratio distortion in horse PONE-D-23-10812R1 Dear Dr. Nora Laseca, 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, Qinghua Shi Academic Editor PLOS ONE Additional Editor Comments (optional): Dear Dr. Nora Laseca, Based on the suggestion of the reviewer and my thinking, I am pleased to tell you that your manuscript has been accepted for publish in this journal. 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 addressed the issues and questions that I raised with regards to their manuscript. They have conducted the suggested analyses to further assess the genomic characteristics of the candidate regions causing TRD. They have also modified their figures, tables and the main text, as recommended. They have chosen more stringent criteria for their GO analysis, which makes their analyses and results more meaningful. ****** 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.0289066.r003
Formally Accepted
1 Aug 2023 Acceptance Letter - Qinghua Shi, Editor PONE-D-23-10812R1 Genomic screening of allelic and genotypic transmission ratio distortion in horse Dear Dr. Laseca: 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 Professor Qinghua Shi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0289066.r004

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