Weighted genome-wide association study reveals new candidate genes related to boar taint compounds

The weighted single-step genome-wide association study (WssGWAS) and post-GWAS analysis may be a useful tool to identify quantitative trait loci (QTL) and candidate genes linked to economically important phenotypes, such as boar taint in pigs. The boar taint is an unpleasant taste and smell observable at uncastrated pork cooking. Therefore, we aimed to identify QTL regions and pinpoint candidate genes associated with boar taint compounds applying a WssGWAS. In this study, we analyzed phenotypic records of androstenone, skatole and indole levels (AND, SKA and IND, respectively) recorded on 4,922 animals from three pig sire lines. From these animals, a total of 3,749 were genotyped. This dataset was used to perform a WssGWAS analysis. A total of 16 windows, explaining 0.5% or more of the genetic variance of boar taint compounds, were identified (5, 4 and 7 for AND, SKA and IND, respectively) at Sus scrofa chromosomes 1, 2, 3, 5, 6, 10 12, 15 and 17. Together, these windows explained 2.90%, 2.15% and 4.47% of the genetic variance of AND, SKA or IND, respectively. A total of 128 genes located in the significant QTL regions were identified. Five new candidate genes (CDK4, CRHBP, CTDSP2, CYP27B1 and SDR4E1) were identified as linked to boar taint compounds. In addition, we also find the HSD17B2 gene, which has already been described in literature as associated with the studied traits. These genes should be better studied looking to understand the boar taint occurrence and selection against that.