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

Content Provider	PubMed Central
Author	Gunawan, Asep Sahadevan, Sudeep Cinar, Mehmet Ulas Neuhoff, Christiane Christine, Große-brinkhaus Frieden, Luc Tesfaye, Dawit Tholen, Ernst Looft, Christian Wondim, Dessie Salilew Michael, Hölker Schellander, Karl Uddin, Muhammad Jasim
Editor	Calogero, Raffaele A.
Copyright Year	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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0072298
Starting Page	72298
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	8
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-08-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

RNA Deep Sequencing Reveals Novel Candidate Genes and Polymorphisms in Boar Testis and Liver Tissues with Divergent Androstenone Levels

Exomic Sequencing of Immune-Related Genes Reveals Novel Candidate Variants Associated with Alopecia Universalis

Identification of Sequence Variants in Genetic Disease-Causing Genes Using Targeted Next-Generation Sequencing

Exome Sequencing Identifies Three Novel Candidate Genes Implicated in Intellectual Disability

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

Identification of Novel and Differentially Expressed MicroRNAs of Dairy Goat Mammary Gland Tissues Using Solexa Sequencing and Bioinformatics

Identification of KIF3A as a Novel Candidate Gene for Childhood Asthma Using RNA Expression and Population Allelic Frequencies Differences

Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing

Detection Theory in Identification of RNA-DNA Sequence Differences Using RNA-Sequencing

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

Similar Documents

RNA Deep Sequencing Reveals Novel Candidate Genes and Polymorphisms in Boar Testis and Liver Tissues with Divergent Androstenone Levels

Exomic Sequencing of Immune-Related Genes Reveals Novel Candidate Variants Associated with Alopecia Universalis

Identification of Sequence Variants in Genetic Disease-Causing Genes Using Targeted Next-Generation Sequencing

Exome Sequencing Identifies Three Novel Candidate Genes Implicated in Intellectual Disability

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

Identification of Novel and Differentially Expressed MicroRNAs of Dairy Goat Mammary Gland Tissues Using Solexa Sequencing and Bioinformatics

Identification of KIF3A as a Novel Candidate Gene for Childhood Asthma Using RNA Expression and Population Allelic Frequencies Differences

Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing

Detection Theory in Identification of RNA-DNA Sequence Differences Using RNA-Sequencing

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