Whole-genome resequencing of Ujumqin sheep to investigate the determinants of the multi-vertebral trait

作者：Shuo Li, Rongsong Luo, Defang Lai, Min Ma, Fei Hao, Xuan Qi, Liu Xu, Dongjun Liu · 发表于：Genome · 年份：2018 · DOI：10.1139/gen-2017-0267 · 被引用次数：20 · 研究领域：Genetic and phenotypic traits in livestock、Cancer-related molecular mechanisms research、Molecular Biology Techniques and Applications

The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the "multi-vertebral" phenotype in this breed. Sequencing generated a total of 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98.53% and 99.11%, and the mean depth of coverage relative to the reference genome was between 11.58× and 14.92×. After comparing the differences between the two groups, we identified 21 homozygous single nucleotide polymorphisms (SNPs) in the mutant exons of 14 genes. Nineteen loci of 10 genes contained nonsynonymous mutations, while two loci contained synonymous mutations. Resequencing revealed homozygous mutations comprised of 44 indels located within exons of 19 genes. These indels included 37 frameshift mutations, 6 non-frameshift mutations, and 1 stopgain single nucleotide variation (SNV). Finally, comparisons of genotypic variations revealed 17 genes with homozygous mutations in their coding regions, 5 of which have previously been associated with vertebral development and the remaining 12 genes were newly identified in this study.