Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 9; p. 1327
• Main Authors: Guan, Xiwen, Zhao, Shuanping, Xiang, Weixuan, Jin, Hai, Chen, Ningbo, Lei, Chuzhao, Jia, Yutang, Xu, Lei
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 08.09.2022; MDPI
• Subjects: Cattle; Conservation; diversity; Domestication; Feed efficiency; Genetic diversity; Genetic resources; genetic signatures; Genetic structure; Genomes; Genomics; Heat resistance; Immune response; Immunological tolerance; indigenous cattle breeds; Laboratory animals; Linkage disequilibrium; Mitochondrial DNA; Natural selection; population structure; Single-nucleotide polymorphism; Software; Temperature tolerance; whole-genome sequencing; China
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11091327

Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.