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

Gunawan, Asep, Sahadevan, Sudeep, Cinar, Mehmet Ulas, Neuhoff, Christiane, Grosse-Brinkhaus, Christine, Frieden, Luc, Tesfaye, Dawit, Tholen, Ernst, Looft, Christian, Wondim, Dessie Salilew, Hoelker, Michael, Schellander, Karl and Uddin, Muhammad Jasim (2013) Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing. PLoS One, 8 8: e72298.1-e72298.19. doi:10.1371/journal.pone.0072298


Author Gunawan, Asep
Sahadevan, Sudeep
Cinar, Mehmet Ulas
Neuhoff, Christiane
Grosse-Brinkhaus, Christine
Frieden, Luc
Tesfaye, Dawit
Tholen, Ernst
Looft, Christian
Wondim, Dessie Salilew
Hoelker, Michael
Schellander, Karl
Uddin, Muhammad Jasim
Title Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2013-08-01
Sub-type Article (original research)
DOI 10.1371/journal.pone.0072298
Open Access Status DOI
Volume 8
Issue 8
Start page e72298.1
End page e72298.19
Total pages 19
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Veterinary Science Publications
 
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