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Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs
BACKGROUND: Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide ass...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426056/ https://www.ncbi.nlm.nih.gov/pubmed/28494783 http://dx.doi.org/10.1186/s12864-017-3752-0 |
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author | van Son, Maren Enger, Eli Gjerlaug Grove, Harald Ros-Freixedes, Roger Kent, Matthew P. Lien, Sigbjørn Grindflek, Eli |
author_facet | van Son, Maren Enger, Eli Gjerlaug Grove, Harald Ros-Freixedes, Roger Kent, Matthew P. Lien, Sigbjørn Grindflek, Eli |
author_sort | van Son, Maren |
collection | PubMed |
description | BACKGROUND: Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace. RESULTS: Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7. CONCLUSIONS: This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3752-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5426056 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-54260562017-05-12 Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs van Son, Maren Enger, Eli Gjerlaug Grove, Harald Ros-Freixedes, Roger Kent, Matthew P. Lien, Sigbjørn Grindflek, Eli BMC Genomics Research Article BACKGROUND: Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace. RESULTS: Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7. CONCLUSIONS: This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3752-0) contains supplementary material, which is available to authorized users. BioMed Central 2017-05-11 /pmc/articles/PMC5426056/ /pubmed/28494783 http://dx.doi.org/10.1186/s12864-017-3752-0 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article van Son, Maren Enger, Eli Gjerlaug Grove, Harald Ros-Freixedes, Roger Kent, Matthew P. Lien, Sigbjørn Grindflek, Eli Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title | Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title_full | Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title_fullStr | Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title_full_unstemmed | Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title_short | Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs |
title_sort | genome-wide association study confirm major qtl for backfat fatty acid composition on ssc14 in duroc pigs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426056/ https://www.ncbi.nlm.nih.gov/pubmed/28494783 http://dx.doi.org/10.1186/s12864-017-3752-0 |
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