Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens
ABSTRACT: Understanding the genetic mechanisms underlying egg production is crucial for improving laying performance in chickens. However, traditional genome-wide association studies (GWAS) have not effectively utilized the information regarding the longitudinal trajectories and dynamics of egg-layi...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-08-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S003257912500522X |
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| _version_ | 1849421607360004096 |
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| author | Lizhi Tan Ning Xu Zexuan Liu Xinyu Cai Yuan Kong Zilong Wen Yuzhan Wang Yiqiang Zhao |
| author_facet | Lizhi Tan Ning Xu Zexuan Liu Xinyu Cai Yuan Kong Zilong Wen Yuzhan Wang Yiqiang Zhao |
| author_sort | Lizhi Tan |
| collection | DOAJ |
| description | ABSTRACT: Understanding the genetic mechanisms underlying egg production is crucial for improving laying performance in chickens. However, traditional genome-wide association studies (GWAS) have not effectively utilized the information regarding the longitudinal trajectories and dynamics of egg-laying phenotype. In this study, based on individual egg production records over time, we first utilized the Yang-Ning model to characterize four egg production parameters. Our SNP-based GWAS on these parameters, along with three multidimensional GWAS models, captured different aspects of egg-laying dynamics. The novel significant associations and candidate genes identified, including C3, CADPS2, and TLN2, contribute significantly to egg-laying traits. By quantifying both direct and indirect effects of egg production parameters on egg number (EN) through the integration of Bayesian networks and structural equation modeling, we demonstrated that an earlier age at first egg directly promotes EN. The findings from this study enhance our understanding of the genetic mechanisms involved in egg production and provide valuable insights for optimizing chicken breeding strategies. |
| format | Article |
| id | doaj-art-b19dddf73e224f528e0537bbf1672af2 |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-b19dddf73e224f528e0537bbf1672af22025-08-20T03:31:25ZengElsevierPoultry Science0032-57912025-08-01104810528010.1016/j.psj.2025.105280Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickensLizhi Tan0Ning Xu1Zexuan Liu2Xinyu Cai3Yuan Kong4Zilong Wen5Yuzhan Wang6Yiqiang Zhao7State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 ChinaCollege of Biological Sciences, China Agricultural University, Beijing 100193 ChinaState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 ChinaState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 ChinaState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 ChinaState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 ChinaCollege of Animal Science and Technology, China Agricultural University, Beijing 100193 China; National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193 China; National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China; Corresponding author: Yiqiang ZhaoABSTRACT: Understanding the genetic mechanisms underlying egg production is crucial for improving laying performance in chickens. However, traditional genome-wide association studies (GWAS) have not effectively utilized the information regarding the longitudinal trajectories and dynamics of egg-laying phenotype. In this study, based on individual egg production records over time, we first utilized the Yang-Ning model to characterize four egg production parameters. Our SNP-based GWAS on these parameters, along with three multidimensional GWAS models, captured different aspects of egg-laying dynamics. The novel significant associations and candidate genes identified, including C3, CADPS2, and TLN2, contribute significantly to egg-laying traits. By quantifying both direct and indirect effects of egg production parameters on egg number (EN) through the integration of Bayesian networks and structural equation modeling, we demonstrated that an earlier age at first egg directly promotes EN. The findings from this study enhance our understanding of the genetic mechanisms involved in egg production and provide valuable insights for optimizing chicken breeding strategies.http://www.sciencedirect.com/science/article/pii/S003257912500522Xgenome-wide association studyegg productionlongitudinal phenotypeBayesian network |
| spellingShingle | Lizhi Tan Ning Xu Zexuan Liu Xinyu Cai Yuan Kong Zilong Wen Yuzhan Wang Yiqiang Zhao Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens Poultry Science genome-wide association study egg production longitudinal phenotype Bayesian network |
| title | Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| title_full | Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| title_fullStr | Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| title_full_unstemmed | Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| title_short | Genome-wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| title_sort | genome wide association studies on longitudinal phenotypes reveal genetic mechanisms of egg production in chickens |
| topic | genome-wide association study egg production longitudinal phenotype Bayesian network |
| url | http://www.sciencedirect.com/science/article/pii/S003257912500522X |
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