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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.

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