Shi Liangyu, Zhang Pu, Yu Bo, Cheng Lei, Liu Sha, Liu Qing, Zhou Yuan, Xiang Min, Zhao Pengju, Chen Hongbo
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.
Animals (Basel). 2025 Jun 13;15(12):1755. doi: 10.3390/ani15121755.
The genetic diversity of cattle plays a crucial role in adapting to environmental challenges and enhancing production traits. While research has predominantly focused on single nucleotide polymorphisms (SNPs), small indel and structural variants (SVs) also significantly contribute to genetic variation. This study investigates the distribution and functional impact of insertions and deletions in five Hubei indigenous cattle breeds. A total of 3,208,816 deletions and 2,082,604 insertions were identified, with the majority found in intergenic and intronic regions. Hotspot regions enriched in immune-related genes were identified, underscoring the role of these variants in disease resistance and environmental adaptation. Our analysis revealed a strong influence of transposable elements (TEs), particularly LINEs and SINEs, on genomic rearrangements. The variants were also found to overlap with economically important traits, such as meat quality, reproduction, and immune response. Population structure analysis revealed genetic differentiation among the breeds, with Wuling cattle showing the highest differentiation. Notably, the gene was identified as a candidate for regional adaptation due to its significant differentiation across populations. These findings provide valuable genomic resources for enhancing breeding programs, aiming at improving the productivity and resilience of indigenous cattle breeds in China.
牛的遗传多样性在适应环境挑战和提高生产性状方面起着至关重要的作用。虽然研究主要集中在单核苷酸多态性（SNP）上，但小插入缺失和结构变异（SV）也对遗传变异有显著贡献。本研究调查了五个湖北本土牛品种中插入和缺失的分布及其功能影响。共鉴定出3,208,816个缺失和2,082,604个插入，其中大部分位于基因间区和内含子区。鉴定出富含免疫相关基因的热点区域，强调了这些变异在抗病性和环境适应性中的作用。我们的分析揭示了转座元件（TE），特别是长散在核元件（LINE）和短散在核元件（SINE）对基因组重排有强烈影响。这些变异还被发现与肉质、繁殖和免疫反应等经济重要性状重叠。群体结构分析揭示了品种间的遗传分化，武陵牛表现出最高的分化。值得注意的是， 基因因其在群体间的显著分化而被确定为区域适应性的候选基因。这些发现为加强育种计划提供了宝贵的基因组资源，旨在提高中国本土牛品种的生产力和适应能力。
