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Genome-wide association study for meat quality traits in an F2 Duroc x Pietrain population
Meat quality is essential for consumer acceptance and ultimately impacts pork production profitability, and it is subject to genetic control. We performed genome-wide association analysis of pork quality traits to increase our understanding of the genetic basis of variation in these traits. Thirty eight meat quality and carcass traits were recorded in 948 F2 pigs from the Michigan State University Duroc x Pietrain F2 resource population. The F0, F1 and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 beadchip, and the remaining F2 animals were genotyped with the GeneSeek Genomic Profiler for Porcine LD chip. Monomorphic SNP and low quality genotypes where discarded and the remaining missing genotypes where imputed (accuracy = 0.968). A total of 44,911 SNP remained for analysis. Analysis was performed using linear mixed effects models using the R gwaR package. Fixed effects of sex, contemporary group and age at slaughter, and a random polygenic effect with variance proportional to marker relationship matrix G were included. Type I error rate was controlled at FDR = 5%. Ten putative QTL regions were found for 16 meat quality and carcass traits. The table shows for each trait the chromosomal location for the QTL, the physical peak position, the qvalue and the total number of annotated genes found in the region. These regions can now be further evaluated in order to search for functional candidate genes. For instance, a QTL associated with backfat thickness was identified on chromosome 6. This region includes genes that encode the enzymes phosphoglucomutase 1 and acyl-CoA dehydrogenase C4 to C12 straight chain, which are involved in pathways for glycogenolysis and lipolysis, respectively. The QTL and genes in the regions should be further investigated to assess their potential to improve pork quality.
Trait |
Chromosome |
Peak position megabase |
qvalue |
Region genes |
Carcass Backfat 10th Rib (CBF10) |
1 |
304.96 |
0.0025 |
48 |
Warner-Bratzler shear force (WBS) |
2 |
2.92 |
0.0003 |
36 |
Tenderness/ Overall Tenderness (OT) |
2 |
58.8 |
0.0001 |
116 |
Tenderness/ OT |
3 |
136.52 |
0.045 |
9 |
Tenderness/ OT |
5 |
68.19 |
0.027 |
67 |
Last Lumbar Backfat / CBF10 / Loin Muscle weight |
6 |
104 |
0.029 |
104 |
Loin Muscle Area / Dressing Percentage |
7 |
35 |
0.041 |
14 |
Number of Ribs/ Carcass length |
7 |
103 |
0.009 |
153 |
Belly weight |
11 |
84.39 |
0.006 |
11 |
Tenderness/ OT / WBS/ Juiciness/ Driploss/ pH Ultimate/ Cook Yield/ Protein percentage |
15 |
135 |
0.0026 |
206 |
Keywords: GWAS, meat quality, swine