A Genome-wide Detection Of Copy Number Variation And Its Association With Some Immune Traits In Beijing-You Chickens

Copy number variation (CNV) is one source of genomic variation associated with animal disease or resistance, including intermediately sized DNA segments which have undergone submicroscopic insertion, deletion, segmental duplication and complex changes of greater than1kb to several Mb in size. In this paper, a genome-wide CNV detection system based on the SNP BeadChip was used on in Beijing-You chickens. The polymorphism of Copy Number Variation (CNV) were analyzed and its association with AI tite and IgG level. This approach may facilitate the application of marker-assisted selection in breeding programs for disease resistance in chickens.A total of1310Beijing-You chickens were used from IAS-CAAS. After quality control of the raw SNP genotyping data and the raw CNVs,1005CNVRs (155Loss events,778Gain events,72Loss-Gain events) and319Trio CNVRs (67Loss events,224Gain events,28Loss-Gain events) were found which covered91.64Mb to179Mb of the chicken genome and correspond to8.9%to17.3%of the autosomal genomic sequence. CNVR in three or more animals overlapped on a chromosome they were considered to be high confidence CNVR. There were141high confidence CNVRs detected here. Among these,121involved known genes or coding sequences were identified including some immunity genes:RHACD8, MHC class I antigen, IL11RA, VAV2and zinc finger protein.13birds were chosen randomly for Q-PCR. Results were showed that copy number of genes such as RHACD, MHC B-G and ZFP varied between individual chickens, which supported the reliability of chip-detection of the CNVs.According to the result of GWAS, CNVRs in GGA4, GGA16and Z were chosen for analyzing polymorphism and its association with AI tite and IgG level. The three CNVs were thought to be high polymorphism. And GGA16(201882-299166) were thought to be significantly association with IgG level (P<0.05), while others were on the contray.Five SNPs assocatied with IgG level were found on GGA16, so GGA16were chosen here for further research. Haploview4.1and PHASE2.0were used for Linkage Disequilibrium (LD), haplotype ananlysis and association with IgG level. This study presented two Blocks. IgG level of H2was1.06times of H3and H1H2was1.45times H3H3in IgG level (P<0.05). Eghit SNP markers were chosen here for analysis. The markers rs16057310, Gga_rs15788237and Gga_rs15788101were significant difference in genotypes (P<0.05).In this study,141high confidence CNVRs and some associated immunity genes such as RHACD8were found. rs16057310, Gga_rs15788101, Gga_rsl5788237, CNV1(6471-59984bp) and CNV2(201882-299166bp) may have an effect on IgG level, the genes in the regions CD1b, CD1c, TRIM27, ZNF692and MHC have an strong association with disease.