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

第一作者： Zhong, Tao

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

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

期刊名称：ANIMAL （ 影响因子：3.6； 五年影响因子：3.7 ）

ISSN： 1751-7311

年卷期： 2023 年 17 卷 3 期

页码：

收录情况： SCI

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 selec-tion 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 sig-natures. 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 selec-tion signatures of Chinese indigenous goats.(c) 2023 The Author(s). Published by Elsevier B.V. on behalf of The Animal Consortium. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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