The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars

The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome.This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigsBoar taint is characterized as the unpleasant odour and flavour that is released from pork when it is heated. This undesirable condition in meat from a certain proportion of finishing boars is perceived as offensive by consumers and leads to economic losses through the rejection of tainted carcasses. The most common practice to prevent boar taint is castration of male piglets. However, this is an objectionable practice because of animal welfare concerns and a ban on castration is viewed as a likely measure to be adopted by the European Union [1]. In addition, castrated males have inferior productive performances when compared with un-castrated males, namely worse feed conversion and lower lean content [2]. Hence, there is considerable interest in developing a solution for boar taint that does not involve castration.Boar taint is mainly caused by abnormally elevated levels of androstenone an