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Open Access Research article

Analysis of the genetics of boar taint reveals both single SNPs and regional effects

Suzanne J Rowe17*, Burak Karacaören12, Dirk-Jan de Koning13, Boris Lukic4, Nicola Hastings-Clark1, Ingela Velander5, Chris S Haley16 and Alan L Archibald1

Author Affiliations

1 The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, Scotland EH25 9RG, UK

2 Faculty of Agriculture, Department of Animal Science, Section of Biometry and Genetics, University of Akdeniz, Antalya 07059, Turkey

3 The Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden

4 Faculty of Agriculture, University of J.J.Strossmayer in Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia

5 Pig Research Centre, Danish Agriculture & Food Council, Axeltorv 3, København V 1609, Denmark

6 MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, Scotland EH4 2XU, UK

7 AgResearch, Dept of Animal Genomics, Invermay Agricultural Centre, Private Bag 50034, Puddle Alley, Mosgiel 9053, New Zealand

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BMC Genomics 2014, 15:424  doi:10.1186/1471-2164-15-424

Published: 3 June 2014

Abstract

Background

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.

Results

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.

Conclusions

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.

Keywords:
Boar taint; Skatole; Androstenone; Regional heritability; Genome-wide association