Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing
Abstract Background As an important genetic resource of chickens, gamecock has unique morphological and behavioral characteristics such as large size, muscular development and strong aggression, making it a good model for studying muscle development and behavior patterns, as well as an excellent bre...
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| Format: | Article |
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BMC
2025-02-01
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| Series: | Journal of Animal Science and Biotechnology |
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| Online Access: | https://doi.org/10.1186/s40104-025-01154-4 |
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| author | Naiyi Xu Linyun Zhang Feifan Chen Zhengfu Feng Jiangtao Zheng DongHua Li Yongju Zhao Xiangtao Kang |
| author_facet | Naiyi Xu Linyun Zhang Feifan Chen Zhengfu Feng Jiangtao Zheng DongHua Li Yongju Zhao Xiangtao Kang |
| author_sort | Naiyi Xu |
| collection | DOAJ |
| description | Abstract Background As an important genetic resource of chickens, gamecock has unique morphological and behavioral characteristics such as large size, muscular development and strong aggression, making it a good model for studying muscle development and behavior patterns, as well as an excellent breeding material. Gamecocks are distributed worldwide, forming different breeds and strains. However, the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens. Therefore, in this study, based on whole genome data of gamecocks, Chinese indigenous chickens, commercial chickens and wild jungle fowls, we performed population structure analysis, selection signal analysis, and genomic introgression analysis of gamecocks. Results The population structure analysis revealed that gamecocks have multiple origins. In addition, we used Fst, π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks. A total number of fifteen shared candidate genes were identified using the three different detection strategies. Among these candidate genes, ETV1, DGKB, AGMO, MEOX2, ISPD and PLCB4 are related to the growth and muscle development, fighting performance and neurodevelopment of gamecocks. Furthermore, we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations, respectively, indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks. Conclusions In summary, we conducted a genome-wide exploration of gamecocks from multiple regions worldwide. Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks. More importantly, this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks, which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks. Our findings offer new perspectives on the impact of introgression on gamecocks, and provide a basis for further resource conservation and utilization of gamecock, as well as provide excellent material for the genetic improvement of domestic chickens. |
| format | Article |
| id | doaj-art-2cdb9f5dd36f4da3a50ff638d0957097 |
| institution | Kabale University |
| issn | 2049-1891 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Animal Science and Biotechnology |
| spelling | doaj-art-2cdb9f5dd36f4da3a50ff638d09570972025-02-09T12:49:09ZengBMCJournal of Animal Science and Biotechnology2049-18912025-02-0116111310.1186/s40104-025-01154-4Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencingNaiyi Xu0Linyun Zhang1Feifan Chen2Zhengfu Feng3Jiangtao Zheng4DongHua Li5Yongju Zhao6Xiangtao Kang7College of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Henan Agricultural UniversityCollege of Animal Science and Technology, Southwest UniversityCollege of Animal Science and Technology, Henan Agricultural UniversityAbstract Background As an important genetic resource of chickens, gamecock has unique morphological and behavioral characteristics such as large size, muscular development and strong aggression, making it a good model for studying muscle development and behavior patterns, as well as an excellent breeding material. Gamecocks are distributed worldwide, forming different breeds and strains. However, the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens. Therefore, in this study, based on whole genome data of gamecocks, Chinese indigenous chickens, commercial chickens and wild jungle fowls, we performed population structure analysis, selection signal analysis, and genomic introgression analysis of gamecocks. Results The population structure analysis revealed that gamecocks have multiple origins. In addition, we used Fst, π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks. A total number of fifteen shared candidate genes were identified using the three different detection strategies. Among these candidate genes, ETV1, DGKB, AGMO, MEOX2, ISPD and PLCB4 are related to the growth and muscle development, fighting performance and neurodevelopment of gamecocks. Furthermore, we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations, respectively, indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks. Conclusions In summary, we conducted a genome-wide exploration of gamecocks from multiple regions worldwide. Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks. More importantly, this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks, which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks. Our findings offer new perspectives on the impact of introgression on gamecocks, and provide a basis for further resource conservation and utilization of gamecock, as well as provide excellent material for the genetic improvement of domestic chickens.https://doi.org/10.1186/s40104-025-01154-4GamecockGenomic introgressionPopulation structureSelection signalWhole genome re-sequence |
| spellingShingle | Naiyi Xu Linyun Zhang Feifan Chen Zhengfu Feng Jiangtao Zheng DongHua Li Yongju Zhao Xiangtao Kang Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing Journal of Animal Science and Biotechnology Gamecock Genomic introgression Population structure Selection signal Whole genome re-sequence |
| title | Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing |
| title_full | Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing |
| title_fullStr | Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing |
| title_full_unstemmed | Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing |
| title_short | Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing |
| title_sort | population structure selection signal and introgression of gamecocks revealed by whole genome sequencing |
| topic | Gamecock Genomic introgression Population structure Selection signal Whole genome re-sequence |
| url | https://doi.org/10.1186/s40104-025-01154-4 |
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