Assessing the Role of Ancestral Fragments and Selection Signatures by Whole-Genome Scanning in Dehong Humped Cattle at the China–Myanmar Border

SIMPLE SUMMARY: We provide a comprehensive overview of sequence variations in Dehong humped cattle genomes with important implications for the future; moreover, we unravel the characteristics of other native cattle in China. In the current study, we investigated a high level of genomic diversities using whole-genome resequencing data in 18 Dehong humped cattle. It is speculated that Dehong humped cattle were influenced by two ancestral segments (Chinese indicine and Indian indicine cattle). Additionally, the selection signatures were detected in genomic regions that are possibly related to economically important traits in Dehong humped cattle. These results will establish a foundation for conservation and breeding programs in the future. ABSTRACT: Dehong humped cattle are precious livestock resources of Yunnan Province, China; they have typical zebu traits. Here, we investigated their genetic characteristics using whole-genome resequencing data of Dehong humped animals (n = 18). When comparing our data with the publicly-available data, we found that Dehong humped cattle have high nucleotide diversity. Based on clustering models in a population structure analysis, Dehong humped cattle had a mutual genome ancestor with Chinese and Indian indicine cattle. While using the RFMix method, it is speculated that the body sizes of Dehong humped cattle were influenced by the Chinese indicine segments and that the immune systems of Dehong humped cattle were affected by additional ancestral segments (Indian indicine). Furthermore, we explored the position selection regions harboring genes in the Dehong humped cattle, which were related to heat tolerance (FILIP1L, ABHD6) and immune responses (GZMM, PRKCZ, STOML2, LRBA, PIK3CD). Notably, missense mutations were detected in the candidate gene ABHD6 (c.870C>A p.Asp290Glu; c.987C>A p.Ser329Arg). The missense mutations may have implications for Dehong humped cattle adaptation to hot environments. This study provides valuable genomic resource data at the genome-wide level and paves the way for future genetic breeding work in the Dehong humped cattle.