Hunan Institute of Animal and Veterinary Science, Changsha 410131, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712000, China.
Genes (Basel). 2024 Jul 12;15(7):909. doi: 10.3390/genes15070909.
(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed.
（1）背景：马头羊原产于中国湖南和湖北两省，以其卓越的肉质和皮张质量而闻名。然而，关于该品种的遗传结构，基于全基因组的综合研究在文献中却很少见。（2）方法：为了解决这一重大差距，我们使用了 20 只马头羊的全基因组序列，并将其与中国 133 个不同品种的山羊的已发表基因组数据进行了比较。这项综合研究旨在评估遗传多样性、群体结构和基因组选择信号的存在。（3）结果：马头羊群体的全基因组产生了超过 1900 万个单核苷酸多态性（SNP）的大量目录，主要分布在基因间和内含子区域。系统发育树分析揭示了数据集中每个山羊群体的不同分支。值得注意的是，与其他公认的山羊品种相比，该分析将马头羊定位在与贵州白山羊更近的遗传亲缘关系中。主成分分析（PCA）和混合分析也证实了这一点。值得注意的是，马头羊表现出较低的遗传多样性和显著的近亲繁殖程度，表明有效种群规模较小。此外，该研究采用了五种选择性清除检测方法（包括 PI、CLR、PI-Ratio、Fst 和 XP-EHH）来筛选与关键生物学功能相关的顶级信号基因，这些功能包括心肌细胞、免疫、毛色和肉质。（4）结论：总之，本研究显著提高了我们对马头羊当前遗传格局和进化动态的理解。这些发现强调了为这一宝贵品种进行资源保护和遗传增强的重要性。
