Copy number variations identified in the chicken using a 60K SNP BeadChip

作者：Xinzheng Jia, S. Chen, Huaijun Zhou, D. Li, Wei Liu, Ning Yang · 发表于：Animal Genetics · 年份：2012 · DOI：10.1111/age.12009 · 被引用次数：49 · 研究领域：Genomic variations and chromosomal abnormalities、Chromosomal and Genetic Variations、RNA and protein synthesis mechanisms

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.