西门塔尔牛全基因组测序用于 SNP 和 CNV 发现。
Whole genome sequencing of simmental cattle for SNP and CNV discovery.
机构信息
State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
出版信息
BMC Genomics. 2023 Apr 5;24(1):179. doi: 10.1186/s12864-023-09248-x.
BACKGROUD
The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity.
RESULTS
In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility.
CONCLUSIONS
In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
背景
单核苷酸多态性（SNPs）和拷贝数变异（CNVs）是两种主要的基因组变异，它们在进化和表型多样性中起着至关重要的作用。
结果
在这项研究中，我们使用高覆盖（25×）短读长下一代测序和单分子长读测序数据，对高精子活力（HSM）和低精子活力（PSM）西门塔尔公牛的遗传变异（SNP 和 CNV）进行了全面分析。在西门塔尔公牛中检测到约 1500 万个 SNPs 和 2944 个 CNV 区域（CNVRs），并发现一组阳性选择基因（PSGs）和 CNVRs与涉及免疫、肌肉发育、生殖等的数量性状基因座（QTLs）重叠。此外，我们在 LEPR 中检测到两个新的变异体，这可能与人工选育以提高重要经济性状有关。此外，还鉴定出一组与男性生育力功能相关的基因和途径。值得注意的是，SPAG16 上的一个 CNV（chr2:101,427,468-101,429,883）在所有低精子活力（PSM）公牛和一半高精子活力（HSM）公牛中完全缺失，这可能在公牛的生育能力中起着关键作用。
结论
总之，本研究为牛的选育和选择计划提供了有价值的遗传变异资源。
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