On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis

Abstract

BackgroundAndrostenone is one of the major compounds responsible for boar taint, a pronounced urine-like odor produced when cooking boar meat. Several studies have identified quantitative trait loci (QTL) for androstenone level on Sus scrofa chromosome (SSC) 6. For one of the candidate genes in the region SULT2A1, a difference in expression levels in the testis has been shown at the protein and RNA level.ResultsHaplotypes were predicted for the QTL region and their effects were estimated showing that haplotype 1 was consistently related with a lower level, and haplotype 2 with a higher level of androstenone. A recombinant haplotype allowed us to narrow down the QTL region from 3.75 Mbp to 1.94 Mbp. An RNA-seq analysis of the liver and testis revealed six genes that were differentially expressed between homozygotes of haplotypes 1 and 2. Genomic sequences of these differentially expressed genes were checked for variations within potential regulatory regions. We identified one variant located within a CpG island that could affect expression of SULT2A1 gene. An allele-specific expression analysis in the testis did not show differential expression between the alleles of SULT2A1 located on the different haplotypes in heterozygous animals. However a synonymous mutation C166T (SSC6: 49,117,861 bp in Sscrofa 10.2; C/T) was identified within the exon 2 of SULT2A1 for which the haplotype 2 only had the C allele which was higher expressed than the T allele, indicating haplotype-independent allelic-imbalanced expression between the two alleles. A phylogenetic analysis for the 1.94 Mbp region revealed that haplotype 1, associated with low androstenone level, originated from Asia.ConclusionsDifferential expression could be observed for six genes by RNA-seq analysis. No difference in the ratio of C:T expression of SULT2A1 for the haplotypes was found by the allele-specific expression analysis, however, a difference in expression between the C over T allele was found for a variation within SULT2A1, showing that the difference in androstenone levels between the haplotypes is not caused by the SNP in exon 2.

Asian low‐androstenone haplotype on pig chromosome 6 does not unfavorably affect production and reproduction traits

“…Two major haplotype groups (low and high androstenone), spanning this entire region, can be distinguished (Hidalgo et al . ). Other genome scans also reported this quantitative trait loci (QTL) region on SSC6 (Lee et al .…”

“…), which does not overlap but is near (2.5 Mbp downstream) the androstenone QTL identified by Hidalgo et al . (). The Meishan alleles were reported to increase the NTEAT, in accordance with the Asian origin of the haplotypes increasing NTEAT in this study.…”

“…The three lines studied were also included in the study of Hidalgo et al . () in which the Dutch Landrace corresponds to population 3, Large White corresponds to population 6 and Pietrain corresponds to population 4. Phenotypes were available for eight traits: growth rate (g/day), backfat thickness (mm), litter birth weight (kg), total number of piglets born, birth weight (kg), number of teats, sperm motility (% of motile cells) and number of spermatozoa per ejaculation (billions).…”

“…Based on the haplotypes of our previous study (Hidalgo et al . ), we selected single nucleotide polymorphism (SNP) marker rs81308021 to test the trait associations. This marker is a tag SNP that distinguishes between the low‐ and high‐androstenone haplotype groups.…”

Omics and bioinformatics approaches to target boar taint

“…In one of the recent boar taint studies, whole genome sequencing of 55 animals including European and Asian pig breeds was performed to find out SNPs within regulatory regions of six differential candidate genes (SPACA4, SYNGR4, TULP2, FTL, GLTSCR1 and SULT2A1) identified by using mRNA sequencing, and within coding region of all of the possible candidate genes located on porcine chromosome 6 (SSC6) in position between 48,585,961 bp and 52,336,598 bp (according to Sscrofa10.2 assembly) underlying androstenone in fat tissue ( Hidalgo, André M., et al, 2014). From this data, they identified single SNP (C/G at position 49,110,873 bp) reside inside a CpG island (49,110,687 bp -49,110,889 bp) that could play important role in differential expression of SULT2A1 gene (Hidalgo, André M., et al, 2014). This SULT2A1 gene encodes the sulfotransferase enzyme to perform sulfoconjugation of α -androstenone in testis.…”