The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, Scotland EH25 9RG, UK.
BMC Genomics. 2014 Jun 3;15(1):424. doi: 10.1186/1471-2164-15-424.
Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint.A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a 'regional heritability approach' combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes.
A highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS.
Significant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance.
公猪异味是一种令人不快的尿液或粪便样气味，会影响部分未去势成熟公猪所产猪肉的气味和味道。公猪异味的产生与脂肪中的雄烯酮和粪臭素有关。在大多数养猪生产体系中，为了降低公猪异味的风险，雄性仔猪通常会在出生后不久被去势。公猪异味易感性存在遗传变异。本研究进行了全基因组关联研究（GWAS），以鉴定与公猪异味相关的基因座。500 头丹麦长白猪脂肪中粪臭素含量较高（>0.3μg/g），每头与脂肪中粪臭素含量较低的同窝仔猪匹配，并测量雄烯酮含量。使用 Illumina PorcineSNP60 Beadchip 对这 1000 头未去势公猪的 DNA 进行基因分型。经过质量控制，对 938 头表型个体和 44648 个 SNP 进行了与公猪异味相关的 SNP 检测。通过置换（100000 次）确定了经验显著性阈值。对于雄烯酮，采用结合多个 SNP 信息的“区域遗传力方法”来估计个体常染色体归因于个体常染色体的遗传变异。
在 CYP2E1 基因（14 号染色体 SSC14）内的 SNP 与粪臭素水平之间发现了高度显著的关联，该基因编码一种参与粪臭素降解的酶。与粪臭素相关的其他 4 个 SNP 包括之前报道的 SSC6 上的一个区域，也检测到了显著的效应。在 SSC5 上的 SNP 与雄烯酮水平之间发现了与 GWAS 相关的显著关联，在 SSC13 和 SSC17 上的 SNP 也发现了名义上的显著关联。区域分析证实了 SSC5 上与雄烯酮的显著关联，并表明 SSC5 解释了雄烯酮遗传变异的 23%。常染色体遗传力分析还表明，在 SSC2 上与雄烯酮相关的存在一个较大的效应，这在 GWAS 中没有检测到。
在长白猪中，发现了 SSC14 上粪臭素和 SSC5 上雄烯酮的 SNP 显著关联。该研究证实了 CYP2E1 基因对肝脏中粪臭素分解的影响。常染色体遗传力估计可以揭示出较小遗传效应的聚类，这些效应单独没有超过 GWAS 显著性的阈值。
