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

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

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00901

DOI=10.3389/fgene.2020.00901

ISSN=1664-8021

ABSTRACT=<p>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 &lt; 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 <italic>AP4E1</italic>, <italic>FSHR</italic>, <italic>COL11A2</italic>, and <italic>DYSF</italic>, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide <italic>F</italic><sub>ST</sub> and pooled heterozygosity (<italic>Hp</italic>) 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 (<italic>C2CD3</italic>, <italic>DNAJB13</italic>, <italic>UCP2</italic>, <italic>ZMYND11</italic>, <italic>CEP126</italic>, <italic>SCAPER</italic>, and <italic>TSHR</italic>), growth (<italic>UCP2</italic>, <italic>UCP3</italic>, <italic>TSHR</italic>, <italic>FGFR1</italic>, <italic>ERLIN2</italic>, and <italic>ZNF703</italic>), and coat color (<italic>KITLG</italic>, <italic>ASIP</italic>, <italic>AHCY</italic>, <italic>RALY</italic>, and <italic>MC1R</italic>). 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.</p>