Abstract
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
Highlights
Boar taint is an offensive odour and/or taste observed in cooked meat from a proportion of non-castrated male pigs undergoing sexual maturity and is primarily related to two compounds: skatole (3-methylindole) from the hindgut and androstenone (5α-androst-16-ene3-one) from the testis [1]
The aims of this study were to i) identify and analyse single- and multi-tissue eQTLs significantly associated with estimated breeding values (EBVs) of skatole and human nose scores in Danish Landrace pigs, ii) functionally characterise the single-nucleotide polymorphism (SNP) and genes of eQTLs and iii) find candidate eQTLs associated with low-EBV genotypes and evaluate any possible selection effects by comparison of genomic loci with those of important production traits
All RNA sequencing (RNA-Seq) data was obtained from a previous study on differentially expressed genes (DEG) associated with the summarised estimated breeding values (EBVs) of skatole and human nose scores (HNS) [41]
Summary
Boar taint is an offensive odour and/or taste observed in cooked meat from a proportion of non-castrated male pigs undergoing sexual maturity and is primarily related to two compounds: skatole (3-methylindole) from the hindgut and androstenone (5α-androst-16-ene3-one) from the testis [1]. As an alternative to castration, gene-based selection [9] through large-scale breeding programmes using predictive biomarkers for reduced boar taint in non-castrated male pigs has been proposed [10,11,12,13,14,15]. Skatole and androstenone are moderate to highly heritable traits [16,17,18] depending on the breed [4], and previous work has established low and mostly favourable genetic correlations between boar taint compounds and production traits such as meat quality [19]. Gene-based selection should be possible without negatively affecting important male fertility traits [19] or sexual maturation [6]
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