RNA-Sequencing: A tool to explore new frontiers in animal genetics

•RNA-Seq has revolutionize gene expression analysis by next generation sequencing.•Provides transcript quantification, mapping boundaries of mRNA and introns.•Identifies novel exons, allele-specific expression, SNP discovery, non-coding RNAs.•RNA-Seq in livestock is the method of choice for transcriptome analysis.

Global gene expression profiling by RNA-Sequencing (RNA-Seq) was introduced in 2004 with the advent of next generation sequencing technologies and has made a revolutionary impact on transcriptome analysis. When compared to the traditional microarray technologies, RNA-Seq has major advantages such as a higher dynamic range, a precise unbiased quantification of transcripts and a comprehensive coverage of all expressed sequences in a given tissue. Besides transcript quantification, RNA-Seq is utilized for comparison of transcriptomes, mapping the 5′ and 3′ boundaries of mRNA and introns, finding of novel exons, study of allele-specific expression, SNP discovery, study of non-coding RNA and de novo gene model building. Two major challenges faced with the RNA-Seq are the differences in sequencing technologies and bioinformatics analysis. Recently, RNA-Seq technology has increasingly been used in livestock, wild and aquatic animal studies to measure gene expression analysis and SNP discovery. This review summarizes the capabilities and challenges of RNA-Seq and the impact of this technology on animal genetics research.