Functional genomics to study stress responses in crop legumes: progress and prospects

Abstract

Abstract. Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stressresponsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.

Molecular Approaches in Deciphering Abiotic Stress Signaling Mechanisms in Plants

“…The use of SuperSAGE technique in plant has been widely implemented for studying responses of genes under various biotic and abiotic stresses across different species, such as banana, tobacco, capsicum, chickpea, etc. Utilization of this technique for elucidating role of genes in abiotic stress response has helped in the elucidation of 3,000 stress-related transcripts from 360,000 transcripts of salt-and drought-related transcriptome of chickpea and lentil (Kudapa et al 2013 ). The amenability of SuperSAGE with integrative transcriptome, SuperSAGE microarray, and next-generation sequencing has also led to an increase in its effi ciency towards gene expression profi ling (Matsumura et al 2005 ).…”

“…In legumes, high-density cDNA-based arrays have been employed to study 27,513 unigene sets from various developmental stages and stress-exposed tissues of soybean. The result thus obtained identifi ed a large number of genes involved during different biotic (herbicide and pathogen) and abiotic stresses (drought, heat, fl ooding) (Vodkin et al 2004 ) reviewed by Kudapa et al ( 2013 ). Other legumes such as chickpea have also been subjected to global gene expression analysis by various researchers, and in the year 2010 Mantri et al ( 2010 ) identifi ed differentially expressed genes in varying genotypes, in response to various abiotic stresses by comparing a 768 feature microarray of chickpea cDNA (559), grass pea cDNA (156), lentil resistance gene analogue cDNA (41), and control (12).…”

“…siRNAmediated DNA methylation and heterochromatin formation through epigenetic modulation are also one of the key approaches of transcriptional inhibition of the desired gene (Verdel et al 2009 ) reviewed by McGinnis ( 2010 ). The technology fi nds its relevance in areas where antisense technologies fail to perform (Kudapa et al 2013 ). The use of a single copy of transgene-induced RNAi, to effi ciently block genes belonging to gene families or expressing during various time and places of developing tissues (Kudapa et al 2013 ), helps in simplifi cation of several phenotypic assays (such as several generation crosses for marker-assisted silencing) in a functional genomics project (McGinnis 2010 ).…”

“…The technology fi nds its relevance in areas where antisense technologies fail to perform (Kudapa et al 2013 ). The use of a single copy of transgene-induced RNAi, to effi ciently block genes belonging to gene families or expressing during various time and places of developing tissues (Kudapa et al 2013 ), helps in simplifi cation of several phenotypic assays (such as several generation crosses for marker-assisted silencing) in a functional genomics project (McGinnis 2010 ). However, early attempts of homologous recombination-based gene silencing in rice showed minimal success rate with very low effi ciency rate (Hanin and Paszkowski 2003 ).…”

Genomics-assisted breeding for drought tolerance in chickpea

“…However, gene discovery has been very limited in chickpea. Hence, only a few candidate genes have been cloned and functionally validated (Kaur et al 2008;Shukla et al 2009;Tripathi et al 2009;Peng et al 2010;Kudapa et al 2013). By studying two chickpea varieties (PUSABGD 72 and ICCV 2) for differences in transcript profiling during drought stress treatment by withdrawal of irrigation at different time points, Jain and Chattopadhyay (2010) reported that most of the highly expressed ESTs in the tolerant cultivar predicted that most of them encoded proteins involved in cellular organisation, protein metabolism, signal transduction and transcription.…”