Chapter 2 - Emerging approach of transcriptomics for crop plants improvements

Abstract

The discovery of RNA has always been a source of interest because of the interactions between DNA and protein. RNAs are molecules that control complex gene expression networks, establish relationships between biological and physiological reactions and phenotype, and provide adaptation between the environment and biological systems. Transcriptome is a technique that generally includes next-generation sequencing-based approaches that enable transcriptome profiling of a tissue or cell, determination of ploidy level, molecular marker development, determination of genetic mechanism against biotic and abiotic stressors, and mRNA profiling. Transcriptome analysis is very important in elucidating the genetic and molecular mechanisms associated with all biological processes. Northern blot, RT-PCR, qRT-PCR, SAGE, microarray, and RNA-seq methods are used in transcriptome analysis. Northern blot is a legacy technique based on hybridization, while RT-PCR and qRT-PCR are techniques that can determine the expression level of a limited number of genes. Microarray, on the other hand, is an advanced technique that enables the determination of the expression level of many genes, but it needs sequence information (genome information) of the genes whose expression level is determined. With the RNA-seq method, the expression level of all transcripts (transcriptome) of a cell can be determined without the need for any reference genome, and new genes with unknown functions can be identified. Therefore, most of the gene expression studies in recent years have been carried out using RNA-seq technology.