Methods of gene expression profiling to understand abiotic stress perception and response in legume crops

Abstract

Legume crops offer a wide genetic diversity that can be exploited to raise improved crop varieties with higher tolerance against adverse climatic conditions. In order to achieve food and nutritional security, legume breeding programs should also incorporate advanced genomics tools. Genomes of many model and nonmodel legume crops have been sequenced, which provide opportunities to identify and characterize candidate genes to develop abiotic stress tolerant crops. Gene expression profiling is a powerful tool to identify candidate genes and understand their function. The present chapter describes two such strategies, that is, candidate gene expression profiling approach and global transcriptome profiling approach. The methods like RT-PCR and qRT-PCR that are being traditionally used to study expression of target genes under defined experimental conditions are discussed. In addition, global transcriptome analysis approach and its advancements are discussed. Details of next-generation sequencing (NGS) based RNA-sequencing (RNA-seq) and associated advanced bioinformatics tools to identify differentially expressing genes at a global level are also described.