Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

Abstract

BackgroundBoar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified.ResultsApproximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 μg/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1.ConclusionsDespite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.

A single nucleotide polymorphism in the CYP2E1 gene promoter affects skatole content in backfat of boars of two commercial Duroc-sired crossbred populations

“…Grindflek, Meuwissen, et al (2011) and Grindflek, Lien, et al (2011) mapped QTL regions affecting skatole levels on chromosomes 1, 2, 3, 5, 6, 7, 10, 11, 13, and 14. Finally, Gregersen et al (2012) identified QTL for backfat skatole accumulation on SSC 3 and 9. On the other hand, the functional approach comprises of investigations to estimate gene expression patterns (Lin, Lou, & Squires, 2004a, 2004b and of association studies between SNP within candidate genes supposedly affecting backfat skatole levels (e.g.…”

The MC4R c.893G>A mutation: A marker for growth and leanness associated with boar taint odour in Belgian pig breeds

“…MC4R has not been found under a QTL peak when screening for boar taint or its components (Gregersen et al, 2012;Lee et al, 2005;Ramos et al, 2011;Robic et al, 2011;Varona et al, 2005), but possible negative influence on reproduction is not reported either. In mice, the lack of MC4R results in erectile dysfunction and disturbed sexual behaviour (Van der Ploeg et al, 2002) but this reproductive problem can be overcome by exercise, suggesting it to be merely a consequence of obesity rather than interference with reproductive steroids (Irani, Xiang, Moore, Mandel, & Haskell-Luevano, 2005).…”

“…Recently, genome wide association studies identified several quantitative trait loci (QTL) associated with boar taint components such as skatole (Ramos et al, 2011), androstenone (Robic et al, 2011) or boar taint odour in general (Gregersen et al, 2012;Lee et al, 2005;Varona et al, 2005) in different pig breeds. Grindflek et al examined QTLs simultaneously for boar taint components and fertility traits in order to find QTLs significant for boar taint only .…”

Skatole metabolites in urine as a biological marker of pigs with enhanced hepatic metabolism

“…To identify biomarkers related to boar taint and reproductive traits is still a central requirement so that genetic selections against boar taint can be performed without side effects. There were numerous attempts to identify genetic markers which would allow the selection of free of taint pigs (Duijvesteijn et al, 2010;Gregersen et al, 2012;Gunawan et al, 2013a and2013b). Recently, it was shown that 12 candidate genes in testes of boars with high and low androstenone levels were differentially expressed (Grindflek et al, 2010).…”