Li Shuang, Lei Hong, Ahmed Zulfiqar, Duan Hongfeng, Li Jianbo, Li Haobang, Lei Chuzhao, Zhang Baizhong, Yi Kangle
Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
Anim Genet. 2025 Jun;56(3):e70016. doi: 10.1111/age.70016.
The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.
溆浦黑山羊原产于中国南方湖南省衡阳市，历史悠久。这些山羊具有优异的特性，包括耐热、抗虫、繁殖能力强和产肉性能优良。尽管有这些优点，但目前数量有限，需要立即进行保护。在本研究中，我们对21只溆浦黑山羊进行了全基因组重测序。此外，我们利用已发表的来自119只山羊的全基因组数据进行了联合分析，这些山羊包括成都麻羊、马头山羊、武穴山羊、湘东黑山羊、柴达木绒山羊、乌珠穆沁绒山羊和陕北绒山羊。结果表明，溆浦黑山羊在基因上比其他中国南方山羊品种更纯。此外，在这八个品种中，溆浦黑山羊基因组的遗传多样性（核苷酸多样性、连锁不平衡、纯合子片段和近亲繁殖系数）处于较低水平，这表明需要进一步保护。我们采用复合似然比、核苷酸多样性、综合单倍型得分、固定指数和跨群体扩展单倍型纯合性等分析方法，系统地扫描了溆浦黑山羊基因组中的选择信号。结果强调了与免疫反应、耐热性、繁殖性能和肉质相关基因的强烈选择信号。这些发现为我们理解溆浦黑山羊适应性状的遗传框架做出了重要贡献。此外，本研究探索了溆浦黑山羊的遗传多样性，这可能有助于建立其遗传资源保护的理论框架，而鉴定出的与性状相关的变异可为未来优化选择育种计划的策略提供参考。
