4.6 Article

Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

期刊

FRONTIERS IN GENETICS
卷 13, 期 -, 页码 -

出版社

FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2022.816379

关键词

Xiangxi cattle; genetic diversity; selection signatures; DNAJC8; whole genome analysis

资金

  1. key research and development project of Hunan Province, China [2020NK 2066]
  2. Innovation platform and talent plan of Hunan Province, China [2019TP 2010]
  3. China Agriculture Research System of MOF and MARA [CARS-37]

向作者/读者索取更多资源

This study compared the genomic variations of Xiangxi cattle with other breeds and found higher genetic diversity and weaker artificial selection in Xiangxi cattle. The study also identified important genes related to reproduction, growth, meat quality, heat tolerance, and immune response in Xiangxi cattle.
Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (theta pi, CLR, F-ST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.

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