Variant discovery in the sheepmeat odour and flavour in javanese fat tailed sheep using RNA sequencing

M A M Abuzahra,K Listyarini,Jakaria Jakaria,A Gunawan,A Furqon,M J Uddin,C Sumantri

doi:10.1088/1755-1315/157/1/012030

M A M Abuzahra, K Listyarini + Show 5 more

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https://doi.org/10.1088/1755-1315/157/1/012030

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Abstract

High-throughput RNA sequencing (RNA-Seq) reveals new challenges for the detection of transcriptome variants (SNPs) in different tissues and species. The aims of this study was to characterize a SNP discovery analysis in the sheep meat odour and flavour transcriptome using RNA-Seq. Six liver samples from divergent sheep meat odour and flavour were analyzed using the Illumina Genome Hiseq 2500 Analyzer. The SNP detection analysis revealed 142 SNPs in sheep meat samples, and a large number of those corresponded to differences between high and low sheep meat odour and flavour ovis genome assembly OAR v4.0. Among them, about 90.4% of genes had multiple polymorphisms within 12 genes (JAML, ANGPTL8, LOC101103463, SEPW1, SCN5A, LOC101113036, DOCK6, GTSE1, KIF12, KCTD17, KANK2, CYP2A6). Several of the SNPs (JAML, CYP2A6, SEPW1, and KIF12) found in this study could be included as suitable markers in genotyping platforms to perform association analyses in commercial populations and apply genomic selection protocols in the sheep meat production.

Highlights

Generation technologies of modern time for sequencing has been provided new opportunities for maximum output like genome annotation, functional genomic research dividing gene expression, detection and profiling of aberrant transcription and discovery of ncRNA [1]
3.1 Variant Discovery in Javanese fat tailed Sheep In addition to the quantification process of transcriptome, RNA sequencing (RNA-Seq) approach provides valuable information regarding gene polymorphisms which could be directly correlated with the relevant phenotype [2] .The method of variant detection applied to sequence javanese fat tailed sheep was the pooled samples analyses, and it revealed 142 single nucleotide polymorphisms (SNPs) in 37 genes
In the results observation that most of the SNPs were in intergenic region with the maximum number of 142 SNPs, among them, about 90.4% of genes had multiple polymorphisms

Summary

Introduction

Generation technologies of modern time for sequencing has been provided new opportunities for maximum output like genome annotation, functional genomic research dividing gene expression, detection and profiling of aberrant transcription and discovery of ncRNA [1]. It may be used in entire transcriptome to determine the changes in gene expression. RNA sequence provides positive results to identify the splicing events, different transcripts of different family isoforms as well as polymorphism [2]. RNA-Seq has been widely used to detect single nucleotide polymorphisms (SNPs), alternative splicing (AS) events differentially expressed genes (DEGs) between two gene expression patterns and insertion or deletion (InDels). To approach and for better understanding of fat deposition and metabolism in sheep, data of liver transcriptomes from Javanese fat tailed sheep was analyzed

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