Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Anim Genet. 2013 Jun;44(3):276-84. doi: 10.1111/age.12009. Epub 2012 Nov 23.
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.
拷贝数变异 (CNV) 被认为是一种重要的遗传变异，对鸡的许多经济重要性状有贡献。虽然可以使用比较基因组杂交阵列来检测 CNV，但高密度 SNP 阵列为在鸡中识别 CNV 提供了另一种方法。在本研究中，使用 PENNCNV 程序，使用鸡 60K SNP BeadChip 在两个不同的鸡遗传系（白来航鸡和矮脚鸡）中识别 CNV。总共鉴定出 209 个 CNV 区域，分布在染色体 1-22 和 24-28 上，包含鸡常染色体基因组区域的 13.55 Mb（1.42%）。通过定量 PCR 完全验证了七个选定 CNV 中的三个（73.2%的个体）。据我们所知，这是首次使用 SNP 阵列在鸡中鉴定 CNV 的报告。鉴定出的 190 个新鉴定的 CNV 说明了鸡 60K SNP BeadChip 检测鸡中 CNV 的可行性，为未来分析 CNV 与鸡的经济重要表型之间的关联奠定了坚实的基础。
