ORIGINAL RESEARCH article

Front. Vet. Sci.

Sec. Livestock Genomics

Volume 12 - 2025 | doi: 10.3389/fvets.2025.1559764

This article is part of the Research TopicInsights in Livestock GenomicsView all 8 articles

Whole-genome resequencing reveals genetic diversity and selection signatures of Tongjiang and five goat breeds

Provisionally accepted
Siyuan  ZhanSiyuan Zhan1Jing  LuoJing Luo1Ruiyang  LiRuiyang Li1Guangyao  LiGuangyao Li1Linxiang  LiLinxiang Li2Dandan  LiDandan Li1Tao  ZhongTao Zhong1Linjie  WangLinjie Wang1Jiazhong  GuoJiazhong Guo1Jiaxue  CaoJiaxue Cao1Hongping  ZhangHongping Zhang1Li  LiLi Li1*
  • 1College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
  • 2Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, China

The final, formatted version of the article will be published soon.

One of the first livestock that humans domesticated was the goat. They give people access to vital supplies. However, the exploration and conservation of the genetic resources of goats are not comprehensive enough. Here, we generated whole-genome sequencing data for 35 samples from three populations (Tongjiang, Banjiao, and Chuandong white) and downloaded the genome sequence data of 30 individuals from three breeds (Jintang black, Chengdu grey, and Tibetan cashmere) to characterize the genomic variations of Tongjiang and other goat breeds. Among the six goat populations studied, the Tongjiang goat exhibits the highest levels of observed heterozygosity and runs of homozygosity, alongside the lowest inbreeding coefficient.The nucleotide diversity and linkage disequilibrium in this population were observed to be at intermediate levels. The population genetic structure analysis showed that significant differentiation of Tongjiang goats from other goat breeds, as evidenced by their distinct clustering and considerable genetic distance from other groups. Furthermore, based on selective sweeps, we identified positive selection genes in Tongjiang goats, which were probably related to important traits such as development (BMP4), reproduction (HTR1E), meat quality (HDAC9, PITX2, PDGFD), and immune response (IKBKB, DLG1). Our findings indicate that Tongjiang goats possess elevated genomic diversity and exhibit minimal inbreeding. The unique genetic structure of Tongjiang goats can be partly attributed to the specific geographic conditions of the region. We have identified several selection signatures within the genomic regions of Tongjiang goats, which may play a role in their meat quality and environmental adaptation. All of our findings have the potential to provide an invaluable genomic resource for future genetic research and conservation efforts.

Keywords: Whole-genome resequencing, Tongjiang goat, genetic diversity, population structure, selection signatures

Received: 13 Jan 2025; Accepted: 30 Apr 2025.

Copyright: © 2025 Zhan, Luo, Li, Li, Li, Li, Zhong, Wang, Guo, Cao, Zhang and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Li Li, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China

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