NGS based molecular characterization of a region affecting 5alphaandrost-16-en-3-one

Background: Castration of male piglets is performed by the pig industry to eliminate an undesirable smell and taste (boar taint) generated during the cooking of meat from intact male pigs, however this practice is ineffiecent and alternative strategies including genetic improvement are being investigated. Androstenone is a major contributor responsible for boar taint, and a significant quantitative trait loci (QTL) for this sex hormone has been reported on SSC5, the main objective of this study was to fine map this QTL and explore the relationship between androstone levels and the seven candidate genes [1] found within this region. We began by identifying novel single nucleotide polymorphisms (SNPs) using whole genome resequencing of 23 Norwegian Duroc pigs. This was followed by genotyping 192 SNPs in 834 animals and performing association studies to better define the QTL region. A large, significant haplotype block was identified that included three candidate genes. By improving our understanding of the molecular pathways connected to androstenone and identifying mutations showing significant associations it is hoped that this information can be used by industy in selection programs for reducing boar taint. Results: Whole genome resequencing of 23 Norwegian Duroc boars produced ~4.9 billion 2x100bp paired-end (PE) Illumina reads. The reads were subsequently mapped to a latest Sus scrofa build 10.2 reference sequence embracing the QTL region (22.6 - 24.8 Mb of SSC5). Using a variety of filters 64,117 putative SNPs were reduced to a more manageable subset of 192 which were genotyped in 834 Norwegian Duroc sires with known phenotypes. Of these, 168 (87%) were successfully assayed, and 132 were significantly associated with androstenone levels in fat (p<0.001). Due to extensive linkage disequilibrium (LD) among the significantly associated SNPs we were unable to detect single mutations with large effects, but a large and significantly associated haplotype block (p<0.001) composed of 69 SNPs was identified. This block includes three interesting candidate genes; (i) all trans retinol dehydrogenase 16 (RDH16/SRD9C8), (ii) short chain dehydrogenase/reductase family 9C, member 7 (SDR9C7) and (iii) 17 beta hydroxysteroid dehydrogenase 6 homolog (HSD17B6). A SNP of RDH16 and SDR9C7 genes was predicted to be non-synonymous. Finally, a single non-synonymous SNP and two synonymous SNPs in 11-cis/9-cis retinol dehydrogenase 5 (RDH5), located outside the block, were found to be highly significant during SNP association mapping. Conclusions: Close examination of the QTL revealed a number of highly significant nonsynonymous and synonymous SNPs in four of seven candidate genes. A large and significant haplotype block of 69 SNPs for fat androstenone levels in Norwegian Duroc boars was identified and the amount of the phenotypic variance explained by single non-synonymous SNPs within this block ranged from 5.3-5.4 %. These finding have particular value since this QTL has been reported to not significantly affect other important sex hormones, estrogens or testosterone