P0634 GWAS and beyond: Unravelling Complex Genomic Variation in Boar Taint

Suzanne J. Rowe , The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
Burak Karacaoeren , The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
Dirk-Jan de Koning , The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
Ingela Velander , Danske Slagterier, 1609 KÝbenhavn V, Denmark
Chris S. Haley , The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
Alan L. Archibald , The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
Androstenone and Skatole accumulate in the fat of mature non-castrated male pigs and can be detected as boar taint - an offensive odour affecting the smell and taste of cooked pork. Objectives were to investigate genomic variation shown to exist within Landrace pigs using both genome wide association (GWAS) and a regional heritability approach. Five hundred individuals with high Skatole (>0.3 μg/g) at slaughter were matched with low Skatole litter mates and measured for Androstenone.  Genotyping was done using the Illumina SNP60 porcine beadchip. After QC (call rate >0.95, MAF >0.01), 44,648 SNPs and 936 individuals remained. GWAS was performed using a GRAMMAR approach in GenABEL software fitting effects of herd, abattoir, slaughter age, and meat percentage.  Population substructure was accounted for using multi-dimensional scaling and significance thresholds set by permutation (100,000). For the regional approach, autosomes were fitted simultaneously in a linear mixed model to partition genetic contribution from each chromosome. Considering all SNPs simultaneously captures variation from all effects regardless of significance, and variation missed due to incomplete LD between causal variants and common SNPs. Genome wide significance was reached for a SNP in the region of CYP2E1 on SSC14 explaining 5% of the phenotypic variance for Skatole, and on SSC3 and SSC5 explaining 2 and 4% of phenotypic variance of Androstenone respectively. Interestingly, chromosome 13 explained 20% of the phenotypic variance of Androstenone despite the top SNP only reaching chromosome-wide significance. Further work will involve target regions, prediction using genomic selection approaches and investigation of candidate genes/pathways.