A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6

Abstract

Background: In many countries, male piglets are castrated shortly after birth because a proportion of un-castrated male pigs produce meat with an unpleasant flavour and odour. Main compounds of boar taint are androstenone and skatole. The aim of this high-density genome-wide association study was to identify single nucleotide polymorphisms (SNPs) associated with androstenone levels in a commercial sire line of pigs. The identification of major genetic effects causing boar taint would accelerate the reduction of boar taint through breeding to finally eliminate the need for castration.

Results: The Illumina Porcine 60K+SNP Beadchip was genotyped on 987 pigs divergent for androstenone concentration from a commercial Duroc-based sire line. The association analysis with 47,897 SNPs revealed that androstenone levels in fat tissue were significantly affected by 37 SNPs on pig chromosomes SSC1 and SSC6. Among them, the 5 most significant SNPs explained together 13.7% of the genetic variance in androstenone. On SSC6, a larger region of 10 Mb was shown to be associated with androstenone covering several candidate genes potentially involved in the synthesis and metabolism of androgens. Besides known candidate genes, such as cytochrome P450 A19 (CYP2A19), sulfotransferases SULT2A1, and SULT2B1, also new members of the cytochrome P450 CYP2 gene subfamilies and of the hydroxysteroid-dehydrogenases (HSD17B14) were found. In addition, the gene encoding the ss-chain of the luteinizing hormone (LHB) which induces steroid synthesis in the Leydig cells of the testis at onset of puberty maps to this area on SSC6. Interestingly, the gene encoding the alpha-chain of LH is also located in one of the highly significant areas on SSC1.

Conclusions: This study reveals several areas of the genome at high resolution responsible for variation of androstenone levels in intact boars. Major genetic factors on SSC1 and SSC6 showing moderate to large effects on androstenone concentration were identified in this commercial breeding line of pigs. Known and new candidate genes cluster especially on SSC6. For one of the most significant SNP variants, the difference in the proportion of animals surpassing the threshold of consumer acceptance between the two homozygous genotypes was as much as 15.6%.

Figure 1

Distribution of androstenone for the full dataset (N = 1663) and after selective genotyping was applied (N = 987).

Figure 2

Association between ln-androstenone and 40,525 mapped SNPs across 18 autosomes using an additive model. Each dot represents one SNP. On the y-axis are -log10 (p-values), and on the x-axis are the physical positions of the SNPs by chromosome. Cut-off value is 4.35 which equals a FDR q-value ≤ 0.05.

Figure 3

Box plots of the distribution of the untransformed androstenone concentrations for the SNP MARC0049189 (nr 15). The mean is given in bold.

Figure 4

Linkage disequilibrium plot for the region between 36.9 Mb and 39.7 Mb on SSC6. All 31 significant SNPs (p ≤ 0.05 after FDR) and intervening SNPs for all animals (N = 943) are shown (A). The values in the boxes are pair wise SNP correlations (r²) and the box colour reflects the degree of correlation. B Haplotypes with all SNPs from the LD block are shown. Each line represents a haplotype and the frequency of the haplotype in this population is given at the end of the line. Haplotypes with a frequency below 2% are not included. Two SNPs are tagged and the SNP names are given in C.

Figure 5

Location of the QTL from PigQTLdb for boar taint traits on the physical map of Sus scrofa build9 SSC6. The references and traits of the QTLs are given in Table 3. Positions in Mb were deduced from a BLAST alignment with the microsatellite markers. The green bar indicates the region found in this GWA study between 33 Mb and 45 Mb.