Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes

• Published in: Journal of dairy science 2022-02, Vol.105 (2), p.1327-1337
• Main Authors: Deng, T.X., Ma, X.Y., Lu, X.R., Duan, A.Q., Shokrollahi, Borhan, Shang, J.H.
• Format: Article
• Language: English
• Subjects: Animals; Buffaloes - genetics; Cattle - genetics; China; crossbred buffalo; Homozygote; milk performance; Phenotype; Polymorphism, Single Nucleotide - genetics; Quantitative Trait Loci - genetics; signature of selection
• ISSN: 0022-0302; 1525-3198
• DOI: 10.3168/jds.2021-21102

Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.