Exploiting whole genome sequence data to fine map and characterize candidate genes within a quantitative trait loci region affecting androstenone on porcine chromosome 5

Abstract

SummaryMale piglets are routinely castrated to eliminate boar taint. However, this treatment is undesirable, and alternative approaches, including genetic strategies to reduce boar taint, are demanded. Androstenone is one of the causative agents of boar taint, and a QTL region affecting this pheromone has previously been reported on SSC5: 22.6–24.8 Mb in Duroc. The QTL region is one of the few reported for androstenone that does not simultaneously affect levels of other sex steroids. The main objective of this study was to fine map this QTL. Whole genome sequence data from 23 Norwegian Duroc boars were analyzed to detect new polymorphisms within the QTL region. A subset of 161 SNPs was genotyped in 834 Duroc sires and analyzed for association with androstenone in adipose tissue and testosterone, estrone sulphate and 17β‐estradiol in blood plasma. Our results revealed 100 SNPs significantly associated with androstenone levels in fat (P < 0.001) with 94 of the SNPs being in strong linkage disequilibrium in the region 23.03–24.27 Mb. This haplotype block contains at least four positional candidate genes (HSD17B6,SDR9C7,RDH16 and STAT6) involved in androstenone biosynthesis. No significant associations were found between any of the SNPs and levels of testosterone and estrogens, confirming previous findings. The amount of phenotypic variance explained by single SNPs within the haplotype block was as high as 5.4%. As the SNPs in this region significantly affect levels of androstenone without affecting levels of other sex steroids, they are especially interesting as genetic markers for selection against boar taint.

Pork Production with Entire Males: Directions for Control of Boar Taint

“…The pathways of synthesis and metabolism of androstenone and skatole metabolism have mostly been described ( Figure 2 and Figure 5 ) and the genes involved in these pathways have been identified through metabolism studies [ 12 , 19 , 95 ]. GWAS studies using large SNP panels for detection of QTL have located several loci throughout the genome [ 93 ] and fine mapping of these loci has identified important candidate genes [ 96 ]. Several expression studies of candidate genes have also been carried out in both testis and liver using microarrays, and mRNA sequencing has been used to identify differentially expressed genes [ 97 ].…”

Genomic background and genetic relationships between boar taint and fertility traits in German Landrace and Large White

“…One of these associated markers (ASGA0103650) was a downgene variant of the gene tachykinin 3 (TAC3). Although this gene seems to have a regulatory function in it was excluded as a candidate gene by van Son et al [45] because amino acid changes did not seem to have an effect on the protein function of TAC3. Nevertheless, significant associations with markers in this QTL and log_AND in fat were already described earlier in the study of Grindflek et al [46] in Duroc.…”

Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis

“…The enzyme is involved in the oxidation of 3␣-hydroxysteroids such as androstanediol and androsterone to dihydrotestosterone and androstanedione (17). RDH16 has been considered a candidate gene together with four genes in the same haplotype block (HSD17B6, SDR9C7, RDH16, and STAT6), which are all involved in androstenone biosynthesis (47).…”