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


Gunawan A., Sahadevan S., Cinar M. U. , Neuhoff C., Grosse-Brinkhaus C., Frieden L., ...Daha Fazla

PLOS ONE, cilt.8, 2013 (SCI İndekslerine Giren Dergi) identifier identifier identifier

Özet

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.
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.