Whole genome sequencing of the Chinese cattle breeds (Nanyang and Qinchuan)

Cattle have drawn so much attention due to being domesticated with a long history of accompanying human being for beef or dairy, and there are abundant cattle resources in China, whose population genomic background is still unclear. Nanyang and Qinchuan are two indigenous cattle breeds. In our study, we sequenced the whole genomes of Nanyang and Qinchuan cattle, and found that all the genetic sequence variations and their referring genes established the fact that the Nanyang genome showed a higher degree of genetic diversity than that of Qinchuan, including non-synonymous SNPs, frame-shift, and indels (NS/FS/Indel). In addition, among the detected 495 Ensembl genes in CNV region, the bovine LEPR gene was identified and considered as one of the phenotype-altering genes, and the higher copy number of LEPR gene could lead to fat deposition, thus ultimately improving the meat-related traits of Qinchuan breed. Our results generated a valuable genome-wide data resource for cattle genomic researches, and are expected to draw a lot of interests from scientists over the world.