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

Jun Gao; Yuhua Lyu; Defu Zhang; Kiran Kumar Reddi; Fengping Sun; Jianzhong Yi; Chengqian Liu; Hong Li; Huijuan Yao; Jianjun Dai; Fuyi Xu

doi:10.3389/fgene.2020.00901

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

Front Genet. 2020 Aug 21:11:901. doi: 10.3389/fgene.2020.00901. eCollection 2020.

Authors

Jun Gao^{1

2}, Yuhua Lyu¹, Defu Zhang¹, Kiran Kumar Reddi³, Fengping Sun¹, Jianzhong Yi¹, Chengqian Liu¹, Hong Li¹, Huijuan Yao¹, Jianjun Dai¹, Fuyi Xu²

Affiliations

¹ Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China.
² Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States.
³ Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, Memphis, TN, United States.

Abstract

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 14-20× 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, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F _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, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). 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.

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