Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters

Jiraporn Juiputta; Wipas Loengbudnark; Thirawat Koedkanmark; Vibuntita Chankitisakul; Wuttigrai Boonkum

doi:10.1371/journal.pone.0319537

Peer Review History

Original SubmissionJuly 23, 2024
23 Jul 2024 Author Response https://doi.org/10.1371/journal.pone.0319537.r001
25 Oct 2024 Decision Letter - Lamiaa Radwan, Editor PONE-D-24-30630Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roostersPLOS ONE Dear Dr. Boonkum, 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 Dec 09 2024 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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Kind regards, Prof. Lamiaa Mostafa Radwan, Ph.D. Academic Editor PLOS ONE Reviewer 1 The paper evaluates genetic parameters for semen quality traits in local chickens. The methodology for variance components estimation is adequate but the design is poorly described (particularly populations structure and division into groups), the rationale for choosing traits and their economic weights in index is not correct. Recommendation of 10% selected is ad hoc without considering long term response to selection. The paper needs significant improvements in both analysis and writing. Detailed comments Data access – there was no link or access to the data files provided L 40 Why does genetic correlation between the semen traits instead of genetic correlation to fertility determine which traits are important? L41-46 Not clear what the authors are trying to say L 71. Do you mean high breeding value for egg production? Roosters don’t have egg production L73-76 Please clarify the thought process because these seem to be unrelated statements. Is the small number of offspring produced in order to constrain inbreeding rate or because of low fertility? Can pooled semen be used to increase fertility? L79 Which quality trait or combination of traits has the strongest association with fertility? L87 “of age” not needed? L90 check language L127 The description of the design is not clear. What were the age groups if semen was collected at 32weeks? If “the data were recorded for genetic analysis only when they were 32 weeks.” where does repeatability come from? Was it the same group of roosters recorded at different ages or is there a confounding between group and age? How many roosters were in each group? What was the genetic relationship between them? How deep was the pedigree? L197 unfinished sentence L199-211 Not needed – these are textbook definitions of genetic parameters The rationale for the index weights is incorrect. Economic weight should be based on how much more profit is generated by increasing that trait by one unit not by heritability and correlations between the indicator traits. If the goal trait is fertility subindex should be determined by optimizing weights to maximize fertility. L 417-420 If young roosters have good fertility maybe selection focus should focus on improving persistency of fertility so older age records would be more relevant. L433 indicator traits not only have to have high heritability but also strong genetic correlation to the target trait L454 or make it more difficult if the direction is undesirable L484 high selection intensity results in higher inbreeding rate which can reduce long term response to selection, also other traits will be included in the selection index such as growth, meat quality, feed efficiency. Expected results of alternative programs can be compared using deterministic or stochastic simulations Reviewer 2 If the goal is to publish in a prestigious journal, it would be advisable to reconsider the analysis of the results, expand the scope of the research, perhaps by adding additional data or conducting broader comparisons with other types or breeds of poultry, and deepen the theoretical discussion. [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: Partly Reviewer #2: Partly ******** 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: No 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: No 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 paper evaluates genetic parameters for semen quality traits in local chickens. The methodology for variance components estimation is adequate but the design is poorly described (particularly populations structure and division into groups), the rationale for choosing traits and their economic weights in index is not correct. Recommendation of 10% selected is ad hoc without considering long term response to selection. The paper needs significant improvements in both analysis and writing. Detailed comments Data access – there was no link or access to the data files provided L 40 Why does genetic correlation between the semen traits instead of genetic correlation to fertility determine which traits are important? L41-46 Not clear what the authors are trying to say L 71. Do you mean high breeding value for egg production? Roosters don’t have egg production L73-76 Please clarify the thought process because these seem to be unrelated statements. Is the small number of offspring produced in order to constrain inbreeding rate or because of low fertility? Can pooled semen be used to increase fertility? L79 Which quality trait or combination of traits has the strongest association with fertility? L87 “of age” not needed? L90 check language L127 The description of the design is not clear. What were the age groups if semen was collected at 32weeks? If “the data were recorded for genetic analysis only when they were 32 weeks.” where does repeatability come from? Was it the same group of roosters recorded at different ages or is there a confounding between group and age? How many roosters were in each group? What was the genetic relationship between them? How deep was the pedigree? L197 unfinished sentence L199-211 Not needed – these are textbook definitions of genetic parameters The rationale for the index weights is incorrect. Economic weight should be based on how much more profit is generated by increasing that trait by one unit not by heritability and correlations between the indicator traits. If the goal trait is fertility subindex should be determined by optimizing weights to maximize fertility. L 417-420 If young roosters have good fertility maybe selection focus should focus on improving persistency of fertility so older age records would be more relevant. L433 indicator traits not only have to have high heritability but also strong genetic correlation to the target trait L454 or make it more difficult if the direction is undesirable L484 high selection intensity results in higher inbreeding rate which can reduce long term response to selection, also other traits will be included in the selection index such as growth, meat quality, feed efficiency. Expected results of alternative programs can be compared using deterministic or stochastic simulations Reviewer #2: If the goal is to publish in a prestigious journal, it would be advisable to reconsider the analysis of the results, expand the scope of the research, perhaps by adding additional data or conducting broader comparisons with other types or breeds of poultry, and deepen the theoretical discussion. ****** 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
11 Dec 2024 Author Response We are very grateful for the critical reading and your efforts to improve the quality of the manuscript. We hope that the manuscript in its revised form will please you. The responses to each comment are listed below. Reviewers’ comments: Reviewer #1: The paper evaluates genetic parameters for semen quality traits in local chickens. The methodology for variance components estimation is adequate but the design is poorly described (particularly populations structure and division into groups), the rationale for choosing traits and their economic weights in index is not correct. Recommendation of 10% selected is ad hoc without considering long term response to selection. The paper needs significant improvements in both analysis and writing. Response: Thank you for your insightful comments. We have addressed your concerns regarding the population structure, economic weights, and selection intensity as follows: Population structures and group division: We have added a subheading, "Animal Population Samples and Management" (lines 133-142), to provide a detailed description of the animal grouping and sampling strategy. Economic Weights: Direct economic valuation of semen traits proved impractical given data limitations. Therefore, a simplified relative weighting approach was employed, assigning weights to traits based on heritability, genetic correlations, and estimated economic importance. This method offers a practical alternative to complex bioeconomic modeling, enabling efficient genetic selection while optimizing for both direct and correlated genetic gains Selection Intensity (10%): Our choice of a 10% selection intensity represents a balance between achieving rapid genetic improvement and mitigating the risks of inbreeding and genetic drift. This selection rate is commonly used in similar livestock improvement programs. To minimize inbreeding, we implemented a breeding strategy incorporating careful selection of breeding pairs, rigorous monitoring of inbreeding coefficients, and a plan to introduce new, unrelated genetic material into the population after 2-3 generations. This strategy is rewritten in detail in the Discussion section, where we outline our approach to maintaining genetic diversity over the long term; See lines 489-499 in the revised MS. Query 1: Data access – there was no link or access to the data files provided Response 1: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Query 2: L 40 Why does genetic correlation between the semen traits instead of genetic correlation to fertility determine which traits are important? Response 2: Direct selection for fertility is hampered by its low heritability and complex polygenic architecture. Focusing on the genetic correlations between semen traits provides a more efficient and practical alternative. This approach identifies groups of traits that influence the key physiological processes underlying fertility (e.g., spermatogenesis, sperm transport). Improving these readily measurable traits (motility, concentration, morphology) with stronger heritabilities is expected to positively impact overall fertility. Query 3: L41-46 Not clear what the authors are trying to say Response 3: I have revised the sections you mentioned to enhance understanding by clarifying key concepts. See lines 42-47. Query 4: L 71. Do you mean high breeding value for egg production? Roosters don’t have egg production Response 4: You raise a valid point. While roosters themselves do not lay eggs, they are crucial in determining the egg-laying potential of their female progeny. Line 71 refers to the indirect selection of superior egg-laying traits in female offspring through careful selection of roosters. This indirect selection is based on the rooster's breeding value for traits known to have a strong genetic correlation with egg production. We have rewritten the relevant section to clearly explain how the selection of roosters based on their breeding values for traits genetically correlated with egg production. The revised text also includes additional references to support this approach. See lines 70-79 in the revised MS. Query 5: L73-76 Please clarify the thought process because these seem to be unrelated statements. Is the small number of offspring produced in order to constrain inbreeding rate or because of low fertility? Can pooled semen be used to increase fertility? Response 5: Thank you for pointing out the unclear connection between offspring numbers, inbreeding, and cost. The low number of offspring per hen is primarily due to the naturally low egg production rate of the native breed, not a deliberate inbreeding control strategy or AI-related fertility issues. This lower fecundity, as explained in lines 81-83, directly contributes to higher production costs. Query 6: L79 Which quality trait or combination of traits has the strongest association with fertility? Response 6: We have expanded the dataset to include quality traits that have the strongest association with fertility. This is detailed in the revised manuscript, see lines 83-88. Query 7: L87 “of age” not needed? Response 7: We have removed the word from "of age". Query 8: L90 check language Response 8: We have revised the statement for clarity. See line 98-100. Query 9: L127 The description of the design is not clear. What were the age groups if semen was collected at 32 weeks? If “the data were recorded for genetic analysis only when they were 32 weeks.” where does repeatability come from? Was it the same group of roosters recorded at different ages or is there a confounding between group and age? How many roosters were in each group? What was the genetic relationship between them? How deep was the pedigree? Response 9: For more clearly, we have added a subheading, "Animal Population Samples and Management" (lines 133-142), to provide a detailed description of the animal grouping and sampling strategy. Query 10: L197 unfinished sentence Response 10: We have checked and correct the sentence. See line 207. Query 11: L199-211 Not needed – these are textbook definitions of genetic parameters Response 11: As suggested, the textbook definitions of genetic parameters (lines 199-211) have been removed. The revised text (lines 208-209) now simply states that these parameters—heritability, repeatability, and genetic and phenotypic correlations—were estimated using a multi-trait animal model. Query 12: The rationale for the index weights is incorrect. Economic weight should be based on how much more profit is generated by increasing that trait by one unit not by heritability and correlations between the indicator traits. If the goal trait is fertility subindex should be determined by optimizing w eights to maximize fertility. Response 12: We understand that determining economic values in livestock involves assigning monetary values to genetic traits based on their contribution to overall economic efficiency or profitability. However, with the current level of knowledge, accurately calculating the true monetary value of each semen trait may not be feasible. As a result, we opted for an alternative method that provides sufficient explanation of the results and can be effectively used for genetic selection of these traits. For this purpose, we selected the method of simple relative weight economic value. Simple relative weight economic value is a simplified method for assigning economic values to traits in a breeding program. Rather than calculating precise monetary values, traits are assigned weights relative to one another based on their heritability, genetic correlations, and economic significance. These weights reflect the traits' contributions to overall profitability and efficiency in breeding programs. This approach is particularly useful when precise financial data or bioeconomic modeling is unavailable. Additionally, this method does not require extensive data or complex modeling, making it practical for small-scale or resource-limited breeding programs. It enables breeders to make quick and effective selection decisions without complicated calculations. In conclusion, heritability and genetic correlations play a vital role in calculating economic values and developing a reliable selection index. By considering both direct genetic improvements and correlated responses, this approach helps optimize genetic progress and achieve breeding goals efficiently. Query 13: L 417-420 If young roosters have good fertility maybe selection focus should focus on improving persistency of fertility so older age records would be more relevant. Response 13: Thank you for raising this point. Our study indeed highlighted the importance of persistency in genetic traits; however, our findings demonstrated that the semen characteristics of semen volume, mass movement, and sperm concentration consistently showed the highest heritability across all rooster age groups. This consistency implies that these traits are genetically stable and do not decline significantly with age relative to others. Moreover, our results suggest that selecting roosters at a younger age (Group 1: 32–52 weeks) is most advantageous. This is due to the higher genetic and phenotypic performance observed in this age group, coupled with the opportunity for rapid genetic improvement without the need to wait for older age records. These findings advocate for prioritizing young rooster traits, as they provide both accuracy and efficiency in genetic evaluation. While this study focuses on the genetic improvement of semen traits in younger roosters, future research could investigate fertility persistency across a rooster's lifespan, incorporating GWAS and hormonal analyses to identify loci and physiological mechanisms affecting reproductive longevity. This would ultimately improve both early and long-term productivity. We have added more details in the revised manuscript's conclusion; see lines 505-512. Query 14: L433 indicator traits not only have to have high heritability but also strong genetic correlation to the target trait Response 14: To address the low heritability of the target trait, the revised text (lines 440-441) emphasizes the importance of identifying indicator traits exhibiting both high heritability and a strong genetic correlation with the target trait for effective genetic improvement. Query 15: L454 or make it more difficult if the direction is undesirable Response 15: As suggested, the revised text (lines 460-464) now explains that strong positive correlations between traits facilitate efficient selection, whereas strong negative correlations present challenges for simultaneous improvement. Query 16: L484 high selection intensity results in higher inbreeding rate which can reduce long term response to selection, also other traits will be included in the selection index such as growth, meat quality, and feed efficiency. Expected results of alternative programs can be compared using deterministic or stochastic simulations Response 16: To minimize inbreeding, we implemented a breeding strategy incorporating careful selection of breeding pairs, rigorous monitoring of inbreeding coefficients, and a plan to introduce new, unrelated genetic material into the population after 2-3 generations. This strategy is rewritten in detail in the Discussion section, where we outline our approach to maintaining genetic diversity over the long term; See lines 489-499 in the revised MS. Reviewer #2: If the goal is to be published in a prestigious journal, it would be advisable to reconsider the analysis of the results, expand the scope of the research, perhaps by adding additional data or conducting broader comparisons with other types or breeds of poultry, and deepen the theoretical discussion. Response: We have significantly expanded the discussion section to provide more comprehensive insights. In addition, the study identifies semen volume, mass movement, and sperm concentration as the top three traits with the highest heritability, offering breeders a clear genetic focus. This targeted approach enhances the efficiency of breeding programs by prioritizing traits that are most likely to improve reproductive performance. Additionally, the development of a selection index based on economic weights and genetic parameters represents a sophisticated yet practical strategy for multi-trait improvement. This method ensures a balanced genetic gain across multiple semen quality traits, ultimately enhancing economic outcomes. The findings highlight the value of genetic selection for roosters with superior reproductive performance, leading to increased fertility rates and chick production. This improvement reduces costs and enhances the profitability of poultry operations. Furthermore, by focusing on a native breed, the study supports both genetic conservation and commercial viability. This dual approach preserves valuable genetic resources while meeting the demands of the market. Attachments Attachment Submitted filename: Reponse to Reviewers.docx https://doi.org/10.1371/journal.pone.0319537.r003
12 Jan 2025 Decision Letter - Lamiaa Radwan, Editor PONE-D-24-30630R1Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roostersPLOS ONE Dear Dr. Boonkum, 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. ============================== Dear Dr., Wuttigrai Boonkum Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision. Comment editor Additional Editor Comments: It is necessary to show the scientific and economic importance of the manuscript in abstract and discussion of results Kind regards, Prof. Lamiaa Mostafa Radwan, Ph.D. Academic Editor PLOS ONE Reviewer 2 Accept Reviewer 3 2- The present article delineates a scientific study that yielded predictable and consistent results with existing literature. 3- I am does not possess sufficient information regarding the appropriateness of statistical analysis. 4-The authors have made fully available all the data underlying the findings in their article. 5-The manuscript is presented in a lucid manner and is written in standard English. The objective of this study was to develop a suitable selection index for semen characteristics by age in native Thai grandparent roosters. The findings from this research, although predictable, may provide a framework for the genetic improvement of domestic chickens. Reviewer 4 After carefully revised the Manuscript Number PONE-D-24-30630R1 under the title of "Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters" I think the manuscript lakes the originality and creativity. The authors must introduce new and original ideas to the scientific community, producers, and breeders. However, the manuscript just introduces and offers traditional information and results, which are known to all scientists and breeders. ============================== Please submit your revised manuscript by Feb 26 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. 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Comment editor Additional Editor Comments: It is necessary to show the scientific and economic importance of the manuscript in abstract and discussion of results Kind regards, Prof. Lamiaa Mostafa Radwan, Ph.D. Academic Editor PLOS ONE Reviewer 2 Accept Reviewer 3 2- The present article delineates a scientific study that yielded predictable and consistent results with existing literature. 3- I am does not possess sufficient information regarding the appropriateness of statistical analysis. 4-The authors have made fully available all the data underlying the findings in their article. 5-The manuscript is presented in a lucid manner and is written in standard English. The objective of this study was to develop a suitable selection index for semen characteristics by age in native Thai grandparent roosters. The findings from this research, although predictable, may provide a framework for the genetic improvement of domestic chickens. Reviewer 4 After carefully revised the Manuscript Number PONE-D-24-30630R1 under the title of "Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters" I think the manuscript lakes the originality and creativity. The authors must introduce new and original ideas to the scientific community, producers, and breeders. However, the manuscript just introduces and offers traditional information and results, which are known to all scientists and breeders. [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 #2: (No Response) Reviewer #3: (No Response) Reviewer #4: 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 #2: (No Response) Reviewer #3: Partly Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: (No Response) Reviewer #3: I Don't Know 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 #2: (No Response) 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 #2: (No Response) 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 #2: (No Response) Reviewer #3: 2- The present article delineates a scientific study that yielded predictable and consistent results with existing literature. 3- I am does not possess sufficient information regarding the appropriateness of statistical analysis. 4-The authors have made fully available all the data underlying the findings in their article. 5-The manuscript is presented in a lucid manner and is written in standard English. The objective of this study was to develop a suitable selection index for semen characteristics by age in native Thai grandparent roosters. The findings from this research, although predictable, may provide a framework for the genetic improvement of domestic chickens. Reviewer #4: After carefully revised the Manuscript Number PONE-D-24-30630R1 under the title of "Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters" I think the manuscript lakes the originality and creativity. The authors must introduce new and original ideas to the scientific community, producers, and breeders. However, the manuscript just introduces and offers traditional information and results, which are known to all scientists and breeders. ****** 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 #2: Yes: Ahmed Khalid 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. https://doi.org/10.1371/journal.pone.0319537.r004
Revision 2
23 Jan 2025 Author Response Additional Editor Comments: Dear Dr., Wuttigrai Boonkum Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript needs Minor Revision. Comment editor It is necessary to show the scientific and economic importance of the manuscript in abstract and discussion of results Kind regards, Prof. Lamiaa Mostafa Radwan, Ph.D. Academic Editor PLOS ONE Response: We are very grateful for the critical reading and your efforts to improve the quality of the manuscript. We have revised the abstract to highlight its scientific and economic significance, as shown below and in lines 20-54. This revised abstract provides crucial insights into the genetic evaluation of semen traits in Thai native grandparent roosters, offering a foundation for targeted genetic improvement. By enhancing reproductive efficiency through selective breeding, the study not only accelerates genetic progress but also boosts the economic sustainability of native chicken production, benefiting smallholder farmers and supporting the poultry industry's long-term viability in tropical regions. “Semen characteristics are crucial indicators of reproductive success and directly influence the production efficiency of native chickens, which play a vital role in sustainable poultry production systems in Thailand. Key semen traits, including mass movement, semen pH, semen volume, sperm viability, sperm abnormalities, and sperm concentration, are routinely evaluated to assess the reproductive performance of Thai native grandparent roosters. Improved reproductive efficiency in these chickens can lead to increased fertility rates, better hatchability, and enhanced productivity, significantly benefiting smallholder farmers and the poultry industry. To enhance the accuracy and efficiency of evaluating the genetic potential of grandparent roosters, this study aimed to compare rooster age groups, estimate genetic parameters and breeding values, and develop an optimal selection index for semen traits. A total of 3,475 test-day records of six semen traits from Thai native grandparent roosters (Pradu Hang Dum), obtained from the Khon Kaen University native chicken experimental farm, were analyzed using a multi-trait animal model with average information restricted maximum likelihood (AI-REML). The heritability estimates for semen volume, mass movement, sperm concentration, sperm abnormalities, sperm viability, and semen pH across age groups were low, ranging from 0.128 to 0.161, 0.102 to 0.115, 0.101 to 0.111, 0.090 to 0.091, 0.067 to 0.083, and 0.043 to 0.057, respectively. Repeatability estimates ranged from low to moderate, between 0.119 and 0.384 for all traits and age groups. Genetic correlations among semen traits ranged from -0.332 to 0.580, -0.554 to 0.640, and -0.631 to 0.773 for rooster age Groups 1, 2, and 3, respectively. Based on heritability and genetic correlations, the three most important semen traits identified were semen volume, mass movement, and sperm concentration. The study revealed a strong relationship between rooster age and semen quality, with the highest selection index values observed in the youngest age group (32–52 weeks). This finding highlights the potential for genetic improvement by implementing a selective breeding program targeting the top 10% of young roosters based on the developed selection index. Such a strategy would significantly accelerate genetic progress in semen traits, improving reproductive efficiency and boosting the economic viability of native chicken production. Furthermore, these findings contribute to a deeper understanding of genetic evaluation in native chicken populations and can serve as a model for developing sustainable breeding programs for other poultry breeds under tropical conditions.” In addition, we have also revised the discussion section to include original ideas relevant to the scientific community, producers, and breeders, while highlighting the economic significance of this study. See the detail below and lines 506-544 in the revised manuscript. “This study emphasizes the importance of considering age as a critical factor in genetic evaluation models for reproductive traits. The significant decline in semen quality with increasing age underscores the need for further research into the physiological mechanisms behind age-related changes in male fertility. Additionally, these findings open opportunities for exploring strategies to extend the productive lifespan of roosters through dietary, hormonal, or environmental interventions. The study also demonstrates the utility of genetic parameters and selection indices tailored to specific age groups. By focusing on younger roosters with optimal semen quality, future research could refine breeding objectives to maximize genetic gains in reproductive traits, ensuring the long-term sustainability of native chicken populations. From a practical perspective, the results offer valuable insights for poultry breeders and producers. Younger roosters demonstrate superior reproductive efficiency and provide a cost-effective way to enhance flock fertility and productivity. Adopting age-specific breeding strategies, such as prioritizing roosters aged 32–52 weeks for semen collection and artificial insemination, can significantly improve fertility rates and hatchability in commercial operations. Furthermore, the study highlights the economic advantages of optimizing reproductive performance in Thai native chickens. By selectively breeding roosters with superior semen traits, producers can achieve greater genetic progress, resulting in improved flock productivity and profitability. This approach aligns with sustainable poultry production systems, particularly in smallholder farming contexts where native chickens play an essential role in household income and food security. The economic importance of this study goes beyond the immediate advantages for smallholder farmers. Improving reproductive efficiency helps reduce input costs by minimizing the need to maintain older, less productive roosters, thereby enhancing overall production efficiency. Moreover, since Thai native chickens play a vital role in sustainable poultry production systems in tropical regions, enhancing their genetic potential supports the preservation of local breeds and biodiversity. These findings also provide a model for improving other tropical poultry breeds, demonstrating how scientific advancements can be applied to develop practical solutions that address both economic and environmental challenges (64–66). In summary, this study establishes a framework for age-specific genetic improvement programs that benefit not only the poultry industry but also the scientific community. By combining genetic insights with practical breeding strategies, it offers a pathway to achieving sustainable and economically viable native chicken production systems in tropical environments.” Reviewers’ comments: Reviewer 2 Accept Response: Thank you very much for your support. Reviewer 3 2- The present article delineates a scientific study that yielded predictable and consistent results with existing literature. Response: We are pleased that the consistency and predictability of our results were recognized. This further supports the reliability and relevance of our research methodology. 3- I am does not possess sufficient information regarding the appropriateness of statistical analysis. Response: We would like to emphasize that this study highlights the importance of carefully selecting suitable tools for genetic estimation to ensure accurate, reliable, and meaningful results for future research. 4-The authors have made fully available all the data underlying the findings in their article. Response: Thank you for acknowledging that all data underlying the findings in our article have been made fully available. Ensuring data transparency and accessibility is an important aspect of our work, and we are pleased this has been recognized. 5-The manuscript is presented in a lucid manner and is written in standard English. Response: Thank you for your positive feedback on the clarity and language of our manuscript. We are glad to hear that the manuscript is presented lucidly and meets the standard for English writing. We appreciate your acknowledgment, as we have strived to ensure the content is accessible and well-written for the readership. The objective of this study was to develop a suitable selection index for semen characteristics by age in native Thai grandparent roosters. The findings from this research, although predictable, may provide a framework for the genetic improvement of domestic chickens. Response: Thank you very much for your support. Reviewer 4 After carefully revised the Manuscript Number PONE-D-24-30630R1 under the title of "Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters" I think the manuscript lacks originality and creativity. The authors must introduce new and original ideas to the scientific community, producers, and breeders. However, the manuscript just introduces and offers traditional information and results, which are known to all scientists and breeders. Response: Thank you for your insightful comments. We have also revised the discussion section to include original ideas relevant to the scientific community, producers, and breeders, while highlighting the economic significance of this study. See the detail below and lines 506-544 in the revised manuscript. “This study emphasizes the importance of considering age as a critical factor in genetic evaluation models for reproductive traits. The significant decline in semen quality with increasing age underscores the need for further research into the physiological mechanisms behind age-related changes in male fertility. Additionally, these findings open opportunities for exploring strategies to extend the productive lifespan of roosters through dietary, hormonal, or environmental interventions. The study also demonstrates the utility of genetic parameters and selection indices tailored to specific age groups. By focusing on younger roosters with optimal semen quality, future research could refine breeding objectives to maximize genetic gains in reproductive traits, ensuring the long-term sustainability of native chicken populations. From a practical perspective, the results offer valuable insights for poultry breeders and producers. Younger roosters demonstrate superior reproductive efficiency and provide a cost-effective way to enhance flock fertility and productivity. Adopting age-specific breeding strategies, such as prioritizing roosters aged 32–52 weeks for semen collection and artificial insemination, can significantly improve fertility rates and hatchability in commercial operations. Furthermore, the study highlights the economic advantages of optimizing reproductive performance in Thai native chickens. By selectively breeding roosters with superior semen traits, producers can achieve greater genetic progress, resulting in improved flock productivity and profitability. This approach aligns with sustainable poultry production systems, particularly in smallholder farming contexts where native chickens play an essential role in household income and food security. The economic importance of this study goes beyond the immediate advantages for smallholder farmers. Improving reproductive efficiency helps reduce input costs by minimizing the need to maintain older, less productive roosters, thereby enhancing overall production efficiency. Moreover, since Thai native chickens play a vital role in sustainable poultry production systems in tropical regions, enhancing their genetic potential supports the preservation of local breeds and biodiversity. These findings also provide a model for improving other tropical poultry breeds, demonstrating how scientific advancements can be applied to develop practical solutions that address both economic and environmental challenges (64–66). In summary, this study establishes a framework for age-specific genetic improvement programs that benefit not only the poultry industry but also the scientific community. By combining genetic insights with practical breeding strategies, it offers a pathway to achieving sustainable and economically viable native chicken production systems in tropical environments.” Best Regards, Wuttigrai Boonkum Corresponding author Attachments Attachment Submitted filename: Reponse_to_Reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0319537.r005
5 Feb 2025 Decision Letter - Lamiaa Radwan, Editor Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters PONE-D-24-30630R2 Dear Dr. Boonkum, 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, Lamiaa Mostafa Radwan, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Accept 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: All comments have been addressed Reviewer #4: 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 #3: Partly Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: I Don't Know 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: The study's findings underscore the significance of genetic composition in roosters exhibiting superior reproductive performance. Following a thorough review, the authors appear to have re-evaluated their data, expanded the scope of programming, and enhanced the theoretical discourse. Reviewer #4: After carefully revised the Manuscript Number PONE-D-24-30630R1 under the title of "Determining the priority semen characteristics and appropriate age for genetic improvement in Thai native roosters" The authors made a hard effort to address all comments, and I think the manuscript could be accepted. ****** 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: Yes: KÜRŞAT TETİK Reviewer #4: No ******** https://doi.org/10.1371/journal.pone.0319537.r006
Formally Accepted
Acceptance Letter - Lamiaa Radwan, Editor PONE-D-24-30630R2 PLOS ONE Dear Dr. Boonkum, 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 Prof. Dr. Lamiaa Mostafa Radwan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0319537.r007

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