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

Asian-Australasian Journal of Animal Sciences

Donghyun Shin¹  Kyeong-Hye Won¹  Jae-Don Oh¹  Ki-Duk Song¹ 

[1] Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea;

关键词: Berkshire;    Functional Annotation;    Next Generation Sequencing;    Non-synonymous Single Nucleotide Polymorphisms;    Selective Sweep;   

DOI  :  10.5713/ajas.17.0211

来源: DOAJ

【 摘 要 】

Objective Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated 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. Methods 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. Results 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 sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are 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.

【 授权许可】

Unknown