Effects of the porcine 384-SNP assay system using selected SNPs for meat quality

Three hundred and eighty-four single nucleotide polymorphisms for meat quality traits were selected from the Illumina Porcine SNP 60K Chip association assay using Berkshire breed. This study was aimed to make a selected SNPs Chip for meat quality and confirm the extensive usage with various breeds. Five hundred and sixty-five pigs (204 Berkshire, 136 Landrace and 225 Yorkshire) were genotyped with the custom 384-SNP Illumina GoldenGate assay and 308 SNPs from 565 animals were analysed for 7 meat quality traits after filtering by quality control. The number of SNPs significantly associated with backfat thickness was 134 (P<0.05) or 80 (P<0.01) among 308 SNPs. Over the half number of SNPs had significant effects (P<0.05) on lightness (176 SNPs), bag driploss percentage (183 SNPs) and filter-fluid uptake (170 SNPs) traits. However, the pH value was only significantly associated with 36 (P<0.05) or 16 SNPs (P<0.01). Seventy-seven SNPs (25 %, P<0.05) or fourty-three SNPs (14 %, P<0.01) were significant effects on over 5 number of meat quality traits. Especially, five SNPs were associated with all of 7 meat quality traits. The porcine 384 SNP Chip for meat quality was quite effective in our current population. However, the estimation of additive genetic effects of selected markers would be required to fine confirm the effectiveness. And more breeds and bigger size of populations would be also required to reduce SNPs treated false-negative.