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Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

文献类型： 外文期刊

作者： Gao, Jun 1 ; Lyu, Yuhua 1 ; Zhang, Defu 1 ; Reddi, Kiran Kumar 3 ; Sun, Fengping 1 ; Yi, Jianzhong 1 ; Liu, Chengqian; 1 ;

作者机构： 1.Shanghai Acad Agr Sci, Inst Anim Husb & Vet Sci, Shanghai, Peoples R China

2.Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA

3.Univ Tennessee, Coll Dent, Hlth Sci Ctr, Dept Biosci Res, Memphis, TN USA

关键词： chongming white goat; whole-genome re-sequencing; genomic characteristics; selection signature; Capra hircus

期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）

ISSN：

年卷期： 2020 年 11 卷

页码：

收录情况： SCI

摘要： The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14-20x coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, includingAP4E1,FSHR,COL11A2, andDYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wideF(ST)and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3,DNAJB13,UCP2,ZMYND11,CEP126,SCAPER, andTSHR), growth (UCP2,UCP3,TSHR,FGFR1,ERLIN2, andZNF703), and coat color (KITLG,ASIP,AHCY,RALY, andMC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

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