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枣北肉牛遗传多样性与选择信号的全基因组分析

Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle.

作者信息

Shi Liangyu, Zhang Pu, Liu Qing, Liu Chenhui, Cheng Lei, Yu Bo, Chen Hongbo

机构信息

Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China.

Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan 430208, China.

出版信息

Animals (Basel). 2024 Aug 22;14(16):2447. doi: 10.3390/ani14162447.

DOI:10.3390/ani14162447
PMID:39199980
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11350888/
Abstract

This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (, , , , , , , and ), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle.

摘要

本研究对枣北肉牛的基因组多样性和选择印记进行了全面分析。枣北肉牛是一种本土品种，以适应炎热潮湿气候和肉质优良而闻名。对23头枣北牛进行了全基因组重测序，并与46头西门塔尔牛进行比较，以突出遗传差异。群体结构分析证实了枣北牛的遗传独特性。使用DASDC v1.01、XPEHH和θπ比率等方法，我们通过DASDC分别鉴定出230、232和221个基因，包括硬选择清除基因、软选择清除基因和连锁选择清除基因。巧合的是，使用XPEHH和θπ比率方法时鉴定出109个基因。综合这些分析，揭示了8个正选择基因（、、、、、、和），它们与热应激适应、繁殖力和肉质等关键性状相关。此外，功能富集分析显示了与自噬、免疫反应、能量代谢和肌肉发育相关的通路。本研究获得的全面基因组见解为旨在增强枣北牛有益性状育种计划提供了有价值的知识。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/4d8e0f165914/animals-14-02447-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/0de4e6d9a899/animals-14-02447-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/b213ab3dd16f/animals-14-02447-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/8fad59cbdd24/animals-14-02447-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/2b2872d2d010/animals-14-02447-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/e36b4b5bdfb7/animals-14-02447-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/c73b8ec9ed21/animals-14-02447-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/4d8e0f165914/animals-14-02447-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/0de4e6d9a899/animals-14-02447-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/b213ab3dd16f/animals-14-02447-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/8fad59cbdd24/animals-14-02447-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/2b2872d2d010/animals-14-02447-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/e36b4b5bdfb7/animals-14-02447-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/c73b8ec9ed21/animals-14-02447-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1891/11350888/4d8e0f165914/animals-14-02447-g007.jpg

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