Identification of the Novel Candidate Genes and Variants in Boar Liver Tissues with Divergent Skatole Levels Using RNA Deep Sequencing

Abstract

Boar taint is the unpleasant odour of meat derived from non-castrated male pigs, caused by the accumulation of androstenone and skatole in fat. Skatole is a tryptophan metabolite produced by intestinal bacteria in gut and catabolised in liver. Since boar taint affects consumer’s preference, the aim of this study was to perform transcriptome profiling in liver of boars with divergent skatole levels in backfat by using RNA-Seq. The total number of reads produced for each liver sample ranged from 11.8 to 39.0 million. Approximately 448 genes were differentially regulated (p-adjusted <0.05). Among them, 383 genes were up-regulated in higher skatole group and 65 were down-regulated (p<0.01, FC>1.5). Differentially regulated genes in the high skatole liver samples were enriched in metabolic processes such as small molecule biochemistry, protein synthesis, lipid and amino acid metabolism. Pathway analysis identified the remodeling of epithelial adherens junction and TCA cycle as the most dominant pathways which may play important roles in skatole metabolism. Differential gene expression analysis identified candidate genes in ATP synthesis, cytochrome P450, keratin, phosphoglucomutase, isocitrate dehydrogenase and solute carrier family. Additionally, polymorphism and association analysis revealed that mutations in ATP5B, KRT8, PGM1, SLC22A7 and IDH1 genes could be potential markers for skatole levels in boars. Furthermore, expression analysis of exon usage of three genes (ATP5B, KRT8 and PGM1) revealed significant differential expression of exons of these genes in different skatole levels. These polymorphisms and exon expression differences may have impacts on the gene activity ultimately leading to skatole variation and could be used as genetic marker for boar taint related traits. However, further validation is required to confirm the effect of these genetic markers in other pig populations in order to be used in genomic selection against boar taint in pig breeding programs.

Preliminary study of FMO1, FMO5, CYP21, ESR1, PLIN2 and SULT2A1 as candidate gene for compounds related to boar taint

“…But in this study we could not find association between polymorphism and androstenone which coincided with a previous study (Arasta et al, 2007). Recently using RNA deep sequencing, we have identified several polymorphisms in CYPA25, CYP4A24 and CYP4B24 but a variant in CYP4A25 (A NCg.152197351) failed to be associated with skatole level (Gunawan, Sahadevan, Cinar, et al, 2013;. Several QTL for androstenone and skatole are reported in the region on SSC7 which embraces the candidate gene CYP21 (Grindflek, Lien, et al, 2011).…”

“…A number of candidate genes have been identified for reducing boar taint compound in different populations (Duijvesteijn et al, 2010;Moe et al, 2009) with the final goal to utilize this genetic information in the breeding scheme. A recent study by our group using RNA deep sequencing technology identified a number of genes including flavin-containing monooxygenases (FMO1 and FMO5), Cytochrome P450 steroid, 21 Hydroxylase (CYP21), Estrogen receptor 1 (ESR1), Perilipin (PLIN2) and Hydroxysteroid sulphotransferase (SULT2A1) that were expressed differentially in boars with divergent levels of boar taint compounds (Gunawan, Sahadevan, Cinar, et al, 2013;. Additionally, FMO1, FMO5, CYP21, ESR1, PLIN2 and SULT2A1 genes are reported to be functionally involved in boar taint, reproduction and meat quality trait (Davoli et al, 2011;Glenn, Ramos, & Rothschild, 2007;Gunawan et al, 2011).…”

Skatole metabolites in urine as a biological marker of pigs with enhanced hepatic metabolism

“…To identify biomarkers related to boar taint and reproductive traits is still a central requirement so that genetic selections against boar taint can be performed without side effects. There were numerous attempts to identify genetic markers which would allow the selection of free of taint pigs (Duijvesteijn et al, 2010;Gregersen et al, 2012;Gunawan et al, 2013a and2013b). Recently, it was shown that 12 candidate genes in testes of boars with high and low androstenone levels were differentially expressed (Grindflek et al, 2010).…”

Reduced Concentration of Androstenone and Up-Regulation of 3β-Hydroxysteroid Dehydrogenase and 17β-Hydroxysteroid Dehydrogenase mRNA Levels by Active Immunisation Against Gonadotropin Releasing Hormone I

“…The unpleasant odour of meat is caused by the accumulation of androstenone and skatole (3-methylindole) in fat (Gunawan et al, 2013). Androstenone is a testicular steroid that accumulates in fat tissue (Kantas et al, 2014).…”

“…Androstenone is a testicular steroid that accumulates in fat tissue (Kantas et al, 2014). Skatole is a tryptophan metabolite produced by intestinal bacteria in gut and catabolised in liver (Gunawan et al, 2013).…”