Flowchart of the steps taken in the current study. We started the analysis with a region associated with androstenone level previously found on SSC6. The position of the markers were adjusted to the Sscrofa10.2 assembly of the reference genome. Afterwards, haplotypes for the region were identified and their effects were estimated. The region was narrowed down using information from a recombinant haplotype. RNA-seq analysis, within the narrowed region, was performed in the liver and testis. For candidate genes that were differentially expressed, we used whole genome sequence data to look for variations within regulatory regions and also to look for variations within coding regions for all genes within the narrowed region. Allele-specific expression analysis in the testis was performed for SULT2A1 gene because a variation is located within a regulatory region. Finally, we analyzed genomic sequence data to assess the origin of the haplotypes.