Copy number variations identified in the chicken using a 60K SNP BeadChip |
| |
Authors: | H. Zhou D. Li W. Liu N. Yang |
| |
Affiliation: | 1. Department of Animal Science, University of California at Davis, , Davis, CA, 95616 USA;2. Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, , Beijing, 100193 China |
| |
Abstract: | Copy number variation (CNV) is considered an important genetic variation, contributing to many economically important traits in the chicken. Although CNVs can be detected using a comparative genomic hybridization array, the high‐density SNP array has provided an alternative way to identify CNVs in the chicken. In the current study, a chicken 60K SNP BeadChip was used to identify CNVs in two distinct chicken genetic lines (White Leghorn and dwarf) using the penncnv program. A total of 209 CNV regions were identified, distributing on chromosomes 1–22 and 24–28 and encompassing 13.55 Mb (1.42%) of chicken autosomal genome area. Three of seven selected CNVs (73.2% individuals) were completely validated by quantitative PCR. To our knowledge, this is the first report in the chicken identifying CNVs using a SNP array. Identification of 190 new identified CNVs illustrates the feasibility of the chicken 60K SNP BeadChip to detect CNVs in the chicken, which lays a solid foundation for future analyses of associations of CNVs with economically important phenotypes in chickens. |
| |
Keywords: | 60K SNP array chicken genome copy number variations genetic variation |
|
|