Abstract
BackgroundPrevious studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7–80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons. In order to identify the causal mutation(s) for the QTL and/or identify genetic markers for selection purposes we performed a fine mapping of the SSC7 skatole QTL region.ResultsA dense set of markers on SSC7 was obtained by whole genome re-sequencing of 24 Norwegian Landrace and 23 Duroc boars. Subsets of 126 and 157 SNPs were used for association analyses in Landrace and Duroc, respectively. Significant single markers associated with skatole spanned a large 4.4 Mb region from 75.9–80.3 Mb in Landrace, with the highest test scores found in a region between the genes NOVA1 and TGM1 (p < 0.001). The same QTL was obtained in Duroc and, although less significant, with associated SNPs spanning a 1.2 Mb region from 78.9–80.1 Mb (p < 0.01). The highest test scores in Duroc were found in genes of the granzyme family (GZMB and GZMH-like) and STXBP6. Haplotypes associated with levels of skatole were identified in Landrace but not in Duroc, and a haplotype block was found to explain 2.3% of the phenotypic variation for skatole. The SNPs in this region were not associated with levels of sex steroids.ConclusionsFine mapping of a QTL for skatole on SSC7 confirmed associations of this region with skatole levels in pigs. The QTL region was narrowed down to 4.4 Mb in Landrace and haplotypes explaining 2.3% of the phenotypic variance for skatole levels were identified. Results confirmed that sex steroids are not affected by this QTL region, making these markers attractive for selection against boar taint.
Highlights
Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7–80.5 Mb on SSC7
Results confirmed that sex steroids are not affected by this QTL region, making these markers attractive for selection against boar taint
Whole genome re-sequencing was performed on 24 Landrace and 23 Duroc pigs, and provided a total of 10.1 billion paired-end reads (PE; 2 × 100 base pairs) with a per-animal genome coverage ranging from 9-17X
Summary
Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7–80.5 Mb on SSC7. Our previous studies found very high genetic correlations of boar taint compounds to testosterone and estrogens (0.8–0.9 for androstenone and 0.4–0.6 for skatole, respectively) [7]. Some studies have suggested that selection for low levels of boar taint should be feasible as they found no negative correlations between boar taint and male fertility [13] or production traits [14,15,16,17]. Genetic markers breaking unfavorable correlations between boar taint compounds and sex steroids may be potent selection candidates
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