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

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...

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Autores principales: Shin, Donghyun, Oh, Jae-Don, Won, Kyeong-Hye, Song, Ki-Duk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043433/
https://www.ncbi.nlm.nih.gov/pubmed/29514450
http://dx.doi.org/10.5713/ajas.17.0211
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author Shin, Donghyun
Oh, Jae-Don
Won, Kyeong-Hye
Song, Ki-Duk
author_facet Shin, Donghyun
Oh, Jae-Don
Won, Kyeong-Hye
Song, Ki-Duk
author_sort Shin, Donghyun
collection PubMed
description 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.
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spelling pubmed-60434332018-08-01 In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome Shin, Donghyun Oh, Jae-Don Won, Kyeong-Hye Song, Ki-Duk Asian-Australas J Anim Sci Article 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. Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) 2018-08 2018-03-02 /pmc/articles/PMC6043433/ /pubmed/29514450 http://dx.doi.org/10.5713/ajas.17.0211 Text en Copyright © 2018 by Asian-Australasian Journal of Animal Sciences This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Shin, Donghyun
Oh, Jae-Don
Won, Kyeong-Hye
Song, Ki-Duk
In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title_full In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title_fullStr In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title_full_unstemmed In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title_short In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome
title_sort in silico approaches to identify the functional and structural effects of non-synonymous snps in selective sweeps of the berkshire pig genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043433/
https://www.ncbi.nlm.nih.gov/pubmed/29514450
http://dx.doi.org/10.5713/ajas.17.0211
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