In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

<i>In silico</i> approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

Animal Bioscience, March 2018

29514450

Donghyun Shin, Jae-Don Oh, Kyeong-Hye Won, Ki-Duk Song

Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified nsSNPs in Berkshire selective sweep regions and investigated Berkshire-specific nsSNPs to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. NsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using SIFT and Polyphen-2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.