数字农科院2.0

A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array

文献类型： 外文期刊

作者： Tao Zhong;Xinlu Wang;Chunhua Huang;Liu Yang;Qianjun Zhao;Xiaoyong Chen;Aline Freitas-de-Melo;Siyuan Zhan;Linjie Wang;Dinghui Dai;Jiaxue Cao;Jiazhong Guo;Li Li;Hongping Zhang;Lili Niu

作者机构：

关键词： Chinese goats;Genetic signature;Polymorphism;Population structure;Runs of homozygosity (ROH)

期刊名称： Animal

ISSN： 1751-7311

年卷期： 2023 年 17 卷 3 期

页码：

收录情况： SCIE（2023版）

摘要： Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5–10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.

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