Construction Of Haplotype And Copy Number Variations And Genome-wide Association Studies For Carcass Traits In Simmental Cattle

Recently, rapid advances in various high-throughput genotyping technologies provide a chance to perform fine mapping of genes via association studies between complex traits and markers. With taking807Simmental bulls as reference and adopting the Illumina BovineHD genotyping strategy, we construct the haplotype block and copy number variations in cattle genome. Subsequently, Genome-wide association studies was carried out based on the haplotype and single marker analysis to detect the significant genes related to the tenderloin and fore shank. All the study was expected to afford the empirical knowledge and experience of the obtaining genome-wide variations structure for the subsequent molecular scenarios. The results can be summed up as follows.Linkage disequilibrium of population was initially tested by the PLINK software which is based on the EM algorithm. Afterwards, haplotype blocks were constructed based on the calculated r2. Eventually, the whole cattle genome was partitioned into a total of92,553haplotype blocks. The largest haplotype block consists of116SNPs, the smallest block contains only2SNPs and these haplotype blocks cover a total of526,822SNPs from our high density chips. The regions of high LD extend up to-200kb and the size of haplotype blocks ranges from22bp to199.266kb in physical distance, the average size of a block is5.69as well. These haplotype blocks cover1,62Gb of the cattle genome. Then, in the study of Genome-wide association studies based on the haplotype and single marker analysis, seven and three genes were detected respectively for tenderloin and fore shank.Exerting the software of Penncnv, CNVpartition and R package written by myself to identify the copy number variations for individuals, we finally obtained the copy number variation regions for cattle genome. In the end, we identified a total of266CNV regions (CNVRs), including104losses,137gains, and25regions classified as both loss and gain, covering35.49Mb (1.41%) of the bovine genome. The lengths of these CNVRs ranged from1.20kb to1.76Mb, with an average size of133.68kb. In136of these regions, a total of313genes related to biological functions such as transmembrane activity and olfactory transduction activity were identified. To validate the results, we performed quantitative PCR (qPCR) to detect nine randomly selected CNVRs, and successfully confirmed seven (77.6%) of them...