Genome-wide association analyses for loci controlling boar taint

B. Karacaoren, D.J. de Koning, I. Velander, C.S. Haley, A.L. Archibald

Research output: Contribution to conferenceAbstract


Boar taint, which is an offensive urine-like odour detected in the cooked meat of some mature boar carcasses, is caused by the accumulation of high levels of skatole and/or androstenone in backfat. Levels of these compounds are subject to genetic influence and quantitative trait loci (QTL) with effects on androstenone
and skatole levels have been detected by linkage analysis in Large White x Meishan crosses. The aim of this study was to exploit a SNP (single nucleotide polymorphism) chip with up to 6,500 SNPs to map taint QTL at higher resolution in a commercial population. One thousand pigs comprising 500 pigs with high
skatole levels (>0.3 μg/g) each matched by a litter mate with low skatole levels (a discordant sib-pair, DSP, design) were selected from ~6,000 Danish Landrace pigs recorded for skatole levels at slaughter and genotyped. After quality control to remove uninformative markers and animals with anomalous genotype patterns the data comprised 817 individuals and 2,715 SNPs. We used the GRAMMAR approach to detect association using a linear model, while taking the pedigree structure into account. In addition, we used a case-control design to detect association between sib pairs with 10,000 permutations to deal with multiple
hypothesis testing. We detected possible associations for several six SNPs within and close to the CYP2E1 gene (P=9.999e-05). This locus explains about 5% of phenotypic variance in skatole levels. We further used discordant sip pair test to examine associations based on different allele counting scheme. Whilst
these results should be confirmed in other populations they are consistent with the known role of CYP2E1 in the breakdown of skatole. We are currently undertaking a second scan with the recently developed pig 60K SNP chip which should provided greater genome coverage. These results were obtained through the EC-funded FP6 project ‘SABRE’.
Original languageUndefined/Unknown
Number of pages1
Publication statusPublished - 2009
Event60th Annual Meeting of the European Association for Animal Production - Barcelona, Spain
Duration: 24 Aug 200927 Aug 2009


Conference60th Annual Meeting of the European Association for Animal Production

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