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Background  Boar taint is an unpleasant odour and flavour of the meat from some uncastrated male pigs primarily caused by elevated levels of androstenone and skatole in adipose tissue. Androstenone is produced in the same biochemical pathway as testosterone and estrogens, which represents a particular challenge when selecting against high levels of androstenone in the breeding programme, without simultaneously decreasing levels of other steroids. Detection of single nucleotide polymorphisms (SNPs) associated with compounds affecting boar taint is important both for gaining a better understanding of the complex regulation of the trait and for the purpose of identifying markers that can be used to improve the gain of breeding. The beneficial SNPs to be used in breeding would have the combinational effects of reducing levels of boar taint without affecting fertility of the animals. The aim of this study was to detect SNPs in boar taint candidate genes and to perform association studies for both single SNPs and haplotypes with levels of boar taint compounds and phenotypes related to reproduction.    Results  An association study involving 275 SNPs in 121 genes and compounds related to boar taint and reproduction were carried out in Duroc and Norwegian Landrace boars. Phenotypes investigated were levels of androstenone, skatole and indole in adipose tissue, levels of androstenone, testosterone, estrone sulphate and 17β-estradiol in plasma, and length of bulbo urethralis gland. The SNPs were genotyped in more than 2800 individuals and several SNPs were found to be significantly (LRT > 5.4) associated with the different phenotypes. Genes with significant SNPs in either of the traits investigated include cytochrome P450 members  CYP2E1 ,  CYP21 ,  CYP2D6  and  CYP2C49 , steroid 5α-reductase  SRD5A2 , nuclear receptor  NGFIB , catenin  CTNND1 , BRCA1 associated protein  BAP1  and hyaluronoglucosaminidase  HYAL2 . Haplotype analysis provided additional evidence for an effect of  CYP2E1  on levels of skatole and indole, and for  BAP1 ,  HYAL2  and  SRD5A2  on levels of androstenone.    Conclusion  The findings in this study indicate that polymorphisms in  CYP2E1, CYP21, CYP2D6, CYP2C49, NGFIB  and  CTNND1  might be used to reduce levels of boar taint without affecting levels of testosterone, estrone sulphate, 17β-estradiol or length of bulbo urethralis gland.

Association between SNPs within candidate genes and compounds related to boar taint and reproduction