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

Abstract

ObjectiveNon-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.MethodsnsSNPs 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.ResultsTotal 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.ConclusionOur 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.

The effect of the ryanodine receptor gene on the reproductive traits of Welsh sows

“…Regarding the sensitivity to stress of different breeds of pigs, Pietren, Polish-Chinese pigs, Landrace, Hampshire and Yorkshire are considered quite susceptible to stress, while Chester White, Duroc, Large White and Berkshire are considered to be resistant to stress (Nevrkla et al, 2017;Shin et al, 2018;Mote & Rothschild, 2020). In our research, only 8.01% of animals carrying a mutant allele of the RYR1 gene were found, while no animals homozygous for the mutant allele of this gene were found at all.…”

“…In recent decades, precision livestock farming technologies have been introduced, feed rations have been improved, genetic potencial of livestock has been renewed, and a number of other aspects of livestock production have been improved. Further increasing the competitiveness of production in the pig industry on the domestic market requires a transition to a more intensive level of its management (Vranken & Berckmans, 2017;Shin et al, 2018;Gómez et al, 2021). More attention is paid to the conditions of farming pigs (Kanis et al, 2004;López-Vergé et al, 2018;Mylostуva et al, 2022), their balanced feeding and growth intensity (Spring, 2020a(Spring, , 2020b, the latest approaches to meat quality assessment are used (Bankovska et al, 2020;Tarczyński et al, 2021), modern DNAtechnologies are increasingly involved Rudoman et al, 2017).…”

An In Silico Functional Analysis of Non-Synonymous Single-Nucleotide Polymorphisms of Bovine CMAH Gene and Potential Implication in Pathogenesis

“…The fundamental limitation of this study is that most computational methods utilised were optimised for the human genome. However, similar computational techniques have been successfully used for in silico analysis of SNPs in non-human species [67][68][69]. In vitro analysis, for example, site-directed mutagenesis, is recommended for future studies to validate the impacts of these nsSNPs, particularly for c.1271C>T (P424L).…”