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Permanent link (DOI): https://doi.org/10.7939/R3TX35977

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Genome wide association studies (GWAS) identify QTL on SSC2 and SSC17 affecting loin peak shear force in crossbred commercial pigs Open Access

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Author or creator
Zhang, Chunyan
Bruce, Heather
Yang, Tianfu
Charagu, Patrick
Kemp, Robert A.
Boddicker, Nicholas
Miar, Younes
Wang, Zhiquan
Plastow, Graham
Additional contributors
Subject/Keyword
Meat
Genome-Wide Association Studies
Pork
Swine
Introns
Haplotypes
Genomic Databases
Muscle Proteins
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
Of all the meat quality traits, tenderness is considered the most important with regard to eating quality and market value. In this study we have utilised genome wide association studies (GWAS) for peak shear force (PSF) of loin muscle as a measure of tenderness for 1,976 crossbred commercial pigs, genotyped for 42,721 informative SNPs using the Illumina PorcineSNP60 Beadchip. Four 1 Mb genomic regions, three on SSC2 (at 4 Mb, 5 Mb and 109 Mb) and one on SSC17 (at 20 Mb), were detected which collectively explained about 15.30% and 3.07% of the total genetic and phenotypic variance for PSF respectively. Markers ASGA0008566, ASGA0008695, DRGA0003285 and ASGA0075615 in the four regions were strongly associated with the effects. Analysis of the reference genome sequence in the region with the most important SNPs for SSC2_5 identified FRMD8, SLC25A45 and LTBP3 as potential candidate genes for meat tenderness on the basis of functional annotation of these genes. The region SSC2_109 was close to a previously reported candidate gene CAST; however, the very weak LD between DRGA0003285 (the best marker representing region SSC2_109) and CAST indicated the potential for additional genes which are distinct from, or interact with, CAST to affect meat tenderness. Limited information of known genes in regions SSC2_109 and SSC17_20 restricts further analysis. Re-sequencing of these regions for informative animals may help to resolve the molecular architecture and identify new candidate genes and causative mutations affecting this trait. These findings contribute significantly to our knowledge of the genomic regions affecting pork shear force and will potentially lead to new insights into the molecular mechanisms regulating meat tenderness.
Date created
2016/02/22
DOI
doi:10.7939/R3TX35977
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Attribution 4.0 International
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Citation for previous publication
Zhang, C., Bruce, H., Yang, T., Charagu, P., Kemp, R.A., Boddicker, N., Miar, Y., Wang, Z., Plastow, G. (2016) Genome wide association studies (GWAS) identify QTL on SSC2 and SSC17 affecting loin peak shear force in crossbred commercial pigs. PLoS ONE 11(2), e0145082. doi: 10.1371/journal.pone.0145082
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File title: Genome Wide Association Studies (GWAS) Identify QTL on SSC2 and SSC17 Affecting Loin Peak Shear Force in Crossbred Commercial Pigs
File author: Chunyan Zhang, Heather Bruce, Tianfu Yang, Patrick Charagu, Robert Alan Kemp, Nicholas Boddicker, Younes Miar, Zhiquan Wang, Graham Plastow
Page count: 16
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