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利用包括中国广西西林水牛在内的5头水牛的全基因组测序数据进行遗传多样性和选择特征分析。

Analysis of genetic diversity and selection characteristics using the whole genome sequencing data of five buffaloes, including Xilin buffalo, in Guangxi, China.

作者信息

Chen Zhefu, Zhu Min, Wu Qiang, Lu Huilin, Lei Chuzhao, Ahmed Zulfiqar, Sun Junli

机构信息

Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China.

College of Animal Science and Technology, Northwest A&F University, Xianyang, China.

出版信息

Front Genet. 2023 Jan 9;13:1084824. doi: 10.3389/fgene.2022.1084824. eCollection 2022.

Abstract

Buffalo is an economically important livestock that renders useful services to manhood in terms of meat, milk, leather, and draught. The Xilin buffalo is among the native buffalo breeds of China. In the present study, the genetic architecture and selection signature signals of Xilin buffalo have been explored. Correlation analysis of the population structure of Xilin buffalo was conducted by constructing NJ tree, PCA, ADMIXTURE and other methods. A total of twenty-five ( = 25) Xilin buffalo whole genome data and data of forty-six ( = 46) buffaloes published data were used. The population structure analysis showed that the Xilin buffalo belong to the Middle-Lower Yangtze. The genome diversity of Xilin buffalo was relatively high. The CLR, π ratio, and XP-EHH were used to detect the candidate genes characteristics of positive selection in Xilin buffalo. Among the identified genes, most of the enriched signal pathways were related to the nervous system and metabolism. The mainly reported genes were related to the nervous system (), reproductive genes (), and lactation (). The results of this study are of great significance for understanding the molecular basis of phenotypic variation of related traits of Xilin buffalo. We provide a comprehensive overview of sequence variations in Xilin buffalo genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Xilin buffalo and help in future breeding and conservation programs of this important livestock genetic resource.

摘要

水牛是一种具有重要经济价值的家畜,在肉、奶、皮革和役用方面为人类提供了有用的服务。西林水牛是中国本土水牛品种之一。在本研究中,对西林水牛的遗传结构和选择特征信号进行了探索。通过构建NJ树、主成分分析(PCA)、群体遗传结构分析(ADMIXTURE)等方法对西林水牛的群体结构进行了相关性分析。总共使用了25个西林水牛全基因组数据和46个已发表的水牛数据。群体结构分析表明,西林水牛属于长江中下游群体。西林水牛的基因组多样性相对较高。使用复合似然比(CLR)、π比值、固定指数(Fst)和跨群体扩展单倍型纯合度(XP-EHH)来检测西林水牛中正向选择的候选基因特征。在鉴定出的基因中,大多数富集的信号通路与神经系统和新陈代谢有关。主要报道的基因与神经系统()、生殖基因()和泌乳()有关。本研究结果对于理解西林水牛相关性状表型变异的分子基础具有重要意义。我们提供了西林水牛基因组序列变异的全面概述。在可能与西林水牛经济重要性状相关的基因组区域检测到选择特征,这有助于该重要家畜遗传资源未来的育种和保护计划。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/898c/9869173/ff596e06a711/fgene-13-1084824-g001.jpg

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