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

Identification of selection signature is important for a better understanding of genetic mechanisms affecting phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffalo. In this study, an SNP dataset of 133 buffaloes (Chinese crossbred buffalo, n=45; Chinese local swamp buffalo, n=88) was collected from the public database. Population genetics analysis showed that these buffaloes were divided into two groups: crossbred buffalo (CRO) and swamp buffalo (SWAMP). The CRO had higher genetic diversity than the SWAMP. Using the three complementary statistical methods (iHS, XP-EHH, and CLR), 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 overlapped with bovine QTLs that 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 influencing production performance.