全基因组纯合片段揭示了不同绵羊品种的近交水平和性状相关候选基因。

Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds.

作者信息

Ma Rui, Liu Jiaxin, Ma Xiao, Yang Ji

机构信息

Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.

出版信息

Genes (Basel). 2025 Mar 7;16(3):316. doi: 10.3390/genes16030316.

DOI:10.3390/genes16030316

PMID:40149467

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11942120/

Abstract

BACKGROUND

Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale.

METHODS

Here, we analyzed high-depth genomes of 210 sheep from 20 worldwide breeds to identify the pattern and distribution of genome-wide runs of homozygosity (ROH) and detect candidate selected genes in ROH islands for agronomic and phenotypic traits.

RESULTS

Leveraging whole-genome sequencing data, we found a large number of short ROH (e.g., <1.0 Mb) in all breeds and observed the overall higher values of ROH statistics and inbreeding coefficient in European breeds than in Asian breeds and Dorper sheep. We identified some well-known candidate genes (e.g., , gene family, , , and ) and 40 novel genes (e.g., , , , , and ) that are functionally associated with fecundity, body size, and wool-related traits in sheep. Based on the candidate genes, we revealed different genetic bases for the fecundity traits of European and Asian sheep.

CONCLUSIONS

This study improves the resolution of ROH detection and provides new insights into genomic inbreeding and trait architecture in sheep as well as useful markers for future breeding practice.

摘要

背景

量化和控制家畜群体的近交水平对于畜牧业的长期可持续发展至关重要。然而，全球范围内绵羊群体的近交程度尚未得到充分了解。

方法

在此，我们分析了来自全球20个品种的210只绵羊的高深度基因组，以确定全基因组纯合片段（ROH）的模式和分布，并检测ROH岛中与农艺和表型性状相关的候选选择基因。

结果

利用全基因组测序数据，我们在所有品种中发现了大量短ROH（例如，<1.0 Mb），并观察到欧洲品种的ROH统计值和近交系数总体高于亚洲品种和杜泊羊。我们鉴定了一些与绵羊繁殖力、体型和羊毛相关性状功能相关的知名候选基因（例如，基因家族、、、和）以及40个新基因（例如，、、、、和）。基于这些候选基因，我们揭示了欧洲和亚洲绵羊繁殖力性状的不同遗传基础。