Study On Genome Genetic Variation With Vertebral Number Variation In Qinchuan Cattle

Multi-vertebral trait is a beneficial phenotype in livestock. We first found that Qinchuan cattle exist multi-vertebral trait. In order to find the candidate genes that affect vertebral number in Qinchuan cattle, sequencing was used to analyze polymorphism of 12 associated candidate genes in samples with different thoracic and lumbar numbers. This study also used the bovine GeneSeek HD 77 k BeadChip to perform genome-wide association analysis for multi-vertebral trait. In addition, to reveal the genetic variation of Qinchuan cattle, a dataset of Illumina Bovine SNP50 BeadChip of new world cattle was merged into our dataset of 77 k BeadChip with 27 Chinese Qinchuan cattle for the principal component analysis(PCA) and ancestors estimates. And PennCNV was performed to detected copy number variation of Qinchuan cattle, then analyzed gene annotations and functional enrichment analysis of CNVRs. The main results of this study are as follows:(1)There were one, two, two, and one SNPs were detected in NR6A1, NR5A1, VRTN and Hoxd9 genes, respectively. The mutation of Hoxd9 was located in the non-coding sequence region. Both of the two SNPs detected in VRTN gene were synonymous mutations. The SNPs detected in NR6A1 and NR5A1 were missense mutations, causing amino acid changes. But the association analysis showed that these mutations had no obvious correlation with the vertebral number variations.(2)Genome-wide association analysis show that VRTN gene was associated with different number of thoracic. The significant SNP located at 86,060,139 bp on chromosome 10, which was closest of VRTN. The homologous gene had been associated with muti-thoracic traits in pigs. The long-range linkage disequilibrium area(LD) on chromosome 7 might be associated with thoracic-lumbar number variation;the region which associated with total length of the vertebral was found on chromosome 16.(3)Principal component analysis(PCA) revealed significant individual variations in Qinchuan cattle, suggesting a rich genetic variability in this cattle breed. The genetic relationship of Qinchuan cattle is close to that of Turkey cattle, Japanese & Korean cattle, and European cattle, whereas far from Indian cattle and African cattle.. According to the results of ancestors estimates, Qinchuan cattle was hybrid origin, possessing both taurine and indicine ancestry.(4)A total of 255 CNVRs were detected in 281 Qinchuan cattle, containing 215 losses, 31 gains, and 9 mixes. These regions represented 184 Mb on the genome and corresponded to 7.3% of the total length of bovine autosomes.(5)A total of 1503 genes within or partially overlap with 155 of the 255 CNVRs were detected. The function enrichment analysis showed that the genes identified were mainly involved in 46 biological functions. These CNVRs were also related with many economic traits of beef cattle.