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Background  Androstenone 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.    Results  Haplotypes 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.    Conclusions  Differential 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.

bmc genomic data

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