济州马是韩国的一种本土马种。然而,对韩国马品种的基因组研究严重缺乏。
这项研究的目的是报告居住在韩国的国内马种群的基因组特征(济州岛,济州杂交,和纯种)和野马品种(Przewalski的马)。
使用马参考基因组组装(EquCab2.0),超过65亿个序列读数被成功映射,整个基因组的平均覆盖率为40.87倍。利用这些数据,我们总共检测到1288万个SNP,其中73.7%被发现是小说。使用RefSeq和Ensemble基因集对所有检测到的SNP进行深度注释以检索基因区域中的SNP。大约27%的SNP位于基因内,而其余的73%在基因间区域发现。使用129,776个编码SNP,我们共检索到12,351个基因中的49,171个非同义SNP。此外,我们共鉴定出10,770个有害的非同义SNP,这些SNP预计会影响蛋白质的结构或功能.
我们展示了来自家养和野马品种的许多基因组变异。这些结果为进一步研究含SNP基因的功能提供了宝贵的资源。并且可以帮助确定马的经济重要性状变异的分子基础。
The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds.
The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski\'s horse).
Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function.
We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.