Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat

IF 1.8 3区 生物学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Animal genetics Pub Date : 2024-05-28 DOI:10.1111/age.13437
Chuanqing Li, Xianglin Wang, Haobang Li, Zulfiqar Ahmed, Yang Luo, Mao Qin, Qiong Yang, Zhangcheng Long, Chuzhao Lei, Kangle Yi
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Abstract

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

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全基因组重测序揭示了武穴山羊的多样性和选择性信号。
动物遗传资源对确保全球粮食安全至关重要。然而,近年来,全球牲畜遗传多样性明显下降。这种下降在发展中国家尤为明显,因为这些国家对这些资源的管理不足。在本研究中,我们对 20 只武穴山羊(WX)和 5 只贵州白山羊(GW)进行了全基因组测序。此外,我们还利用了代表中国不同地区五个不同山羊品种的 131 个样本的已发表基因组。我们研究并比较了 WX 山羊的遗传多样性和选择特征。对 WX 和 GW 群体的全基因组测序分析得出了 120 425 063 个 SNPs,这些 SNPs 主要位于基因间区和内含子区。种群遗传结构显示,WX 在遗传上与 GW、成都褐山羊和金堂黑山羊相似,而与其他山羊品种存在显著差异。此外,三种方法(核苷酸多样性、连锁不平衡衰减和同源性)显示 WX 山羊具有适度的遗传多样性。我们使用核苷酸多样性和复合似然比方法确定了 WX 山羊的种内正选择特征。这两种检测方法共鉴定出 369 个基因,包括与繁殖(GRID2、ZNF276、TCF25 和 SPIRE2)、生长(HMGA2 和 GJA3)和免疫(IRF3 和 SRSF3)相关的基因。总之,这项研究探索了 WX 山羊的适应性,揭示了它们丰富的基因以及在气候变化和疾病挑战中茁壮成长的潜力。我们有必要开展进一步的研究,利用这些洞察力来提高山羊育种的效率和可持续性。
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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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