Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75 Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds. China’s northwest provinces, particularly Gansu province, have breeding populations that include Dorper, Poll Dorset, Texel, Suffolk, South African Mutton Merino, Borderdale, Gansu Alpine Merino, and Gansu Morden varieties of sheep. These are widely farmed in the foothills of the Hindu Kush and Himalaya as well as on the Qinghai/Tibetan Plateau, all regions ranging from 1000m to 5500m above sea level. In order to better adapt to these climates and environments, the Gansu Morden sheep breed was hybridized with Dorper, Poll Dorset and Small-Tail Han sheep. The resulting hybrids, which contain 75.0% foreign high-quality sheep genetics, were selected for planned crossbreeding. This new breed and other sheep breeds were selected and used for the present analysis of copy number variations by SNP50 BeadChip array, with the aim of generating a fuller understanding of sheep genetic resources.