Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data

IF 1.8 3区 生物学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Animal genetics Pub Date : 2025-05-14 DOI:10.1111/age.70016
Shuang Li, Hong Lei, Zulfiqar Ahmed, Hongfeng Duan, Jianbo Li, Haobang Li, Chuzhao Lei, Baizhong Zhang, Kangle Yi
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Abstract

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.

利用全基因组测序数据分析扎市棕色山羊的遗传多样性和选择特征
扎市棕羊原产于中国南方湖南省衡阳市,有着悠久的历史。山羊表现出特殊的性状,包括耐热性和抗虫性,强大的繁殖能力和优越的肉类产量。尽管有这些优点,但目前数量有限,需要立即采取保护措施。在这项研究中,我们对21只扎市棕色山羊进行了全基因组重测序。此外,我们还对已发表的119只山羊的全基因组数据进行了联合分析,包括成都褐山羊、马头山羊、武雪山羊、湘东黑山羊、柴达木绒山羊、乌朱姆沁绒山羊和陕北绒山羊。结果表明,与其他南方山羊品种相比,扎市棕色山羊的遗传纯度更高。此外,扎市褐山羊基因组的遗传多样性(核苷酸多样性、连锁不平衡、纯合子数和近交系数)在8个品种中处于较低水平,需要进一步保护。采用复合似然比、核苷酸多样性、综合单倍型评分、固定指数和跨群体扩展单倍型纯合性等分析方法,系统扫描了扎市褐山羊基因组景观中的选择信号。这些结果强调了与免疫反应、耐热性、繁殖性能和肉质相关的基因的强选择信号。这些发现对我们理解与扎西褐山羊适应性状相关的遗传学框架有重要贡献。此外,本研究还探讨了扎西褐山羊的遗传多样性,这可能有助于保护其遗传资源的理论框架,而所确定的性状相关变异可以为未来优化选择育种计划提供信息。
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来源期刊
Animal genetics
Animal genetics 生物-奶制品与动物科学
CiteScore
4.60
自引率
4.20%
发文量
115
审稿时长
5 months
期刊介绍: Animal Genetics reports frontline research on immunogenetics, molecular genetics and functional genomics of economically important and domesticated animals. Publications include the study of variability at gene and protein levels, mapping of genes, traits and QTLs, associations between genes and traits, genetic diversity, and characterization of gene or protein expression and control related to phenotypic or genetic variation. The journal publishes full-length articles, short communications and brief notes, as well as commissioned and submitted mini-reviews on issues of interest to Animal Genetics readers.
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