Dataset Information

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.

SUBMITTER: Gunawan A

PROVIDER: S-EPMC3753299 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing.

Gunawan Asep A Sahadevan Sudeep S Cinar Mehmet Ulas MU Neuhoff Christiane C Große-Brinkhaus Christine C Frieden Luc L Tesfaye Dawit D Tholen Ernst E Looft Christian C Wondim Dessie Salilew DS Hölker Michael M Schellander Karl K Uddin Muhammad Jasim MJ

PloS one 20130826 8

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 1 ...[more]

PMID: 23991084

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Project description:BackgroundPrevious studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7-80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons. In order to identify the causal mutation(s) for the QTL and/or identify genetic markers for selection purposes we performed a fine mapping of the SSC7 skatole QTL region.ResultsA dense set of markers on SSC7 was obtained by whole genome re-sequencing of 24 Norwegian Landrace and 23 Duroc boars. Subsets of 126 and 157 SNPs were used for association analyses in Landrace and Duroc, respectively. Significant single markers associated with skatole spanned a large 4.4 Mb region from 75.9-80.3 Mb in Landrace, with the highest test scores found in a region between the genes NOVA1 and TGM1 (p < 0.001). The same QTL was obtained in Duroc and, although less significant, with associated SNPs spanning a 1.2 Mb region from 78.9-80.1 Mb (p < 0.01). The highest test scores in Duroc were found in genes of the granzyme family (GZMB and GZMH-like) and STXBP6. Haplotypes associated with levels of skatole were identified in Landrace but not in Duroc, and a haplotype block was found to explain 2.3% of the phenotypic variation for skatole. The SNPs in this region were not associated with levels of sex steroids.ConclusionsFine mapping of a QTL for skatole on SSC7 confirmed associations of this region with skatole levels in pigs. The QTL region was narrowed down to 4.4 Mb in Landrace and haplotypes explaining 2.3% of the phenotypic variance for skatole levels were identified. Results confirmed that sex steroids are not affected by this QTL region, making these markers attractive for selection against boar taint.

Dataset Information

Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing.

Publications

Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing.

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