Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis

被引:0
|
作者
Huangfu, Ruiyao [1 ,2 ]
Li, Haobang [1 ]
Luo, Yang [1 ]
He, Fang [1 ]
Huan, Cheng [1 ]
Ahmed, Zulfiqar [3 ]
Zhang, Baizhong [1 ]
Lei, Chuzhao [2 ]
Yi, Kangle [1 ]
机构
[1] Hunan Inst Anim & Vet Sci, Changsha 410131, Peoples R China
[2] Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712000, Peoples R China
[3] Univ Poonch Rawalakot, Fac Vet & Anim Sci, Rawalakot 12350, Pakistan
关键词
genetic diversity; Matou goat; selection signature; whole genome; CAPRA-HIRCUS; C-KIT; LONGEVITY; FAMILY; METABOLISM; EXPRESSION; PATHWAY; SYSTEM; GROWTH; SCANS;
D O I
10.3390/genes15070909
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
(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.
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页数:16
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