Journal article
Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing
PLoS ONE, Vol.8(8), Art. e72298
2013
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.
Details
- Title
- Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing
- Authors/Creators
- A. Gunawan (Author/Creator) - University of BonnS. Sahadevan (Author/Creator) - University of BonnM.U. Çınar (Author/Creator)C. Neuhoff (Author/Creator) - University of BonnC. Große-Brinkhaus (Author/Creator) - University of BonnL. Frieden (Author/Creator) - University of BonnD. Tesfaye (Author/Creator) - University of BonnE. Tholen (Author/Creator) - University of BonnC. Looft (Author/Creator) - University of BonnD.S. Wondim (Author/Creator) - University of BonnM. Hölker (Author/Creator) - University of BonnK. Schellander (Author/Creator) - University of BonnM.J. Uddin (Author/Creator) - University of Bonn
- Publication Details
- PLoS ONE, Vol.8(8), Art. e72298
- Publisher
- Public Library of Science
- Identifiers
- 991005544056507891
- Copyright
- © 2013 Gunawan et al.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
Metrics
19 File views/ downloads
30 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.51 Dairy & Animal Sciences
- 3.51.206 Meat Quality
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics