Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

Abstract

Background: Chickpea, pigeonpea, and groundnut are the primary crop legumes of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. – Results: In this study, genome-wide NAC proteins – 72, 96, and 166 – have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). On exploring the available transcriptome data of each of these legumes, putative stress-responsive NACs at various developmental stages revealed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, 10/14 Ca_NACs (Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186); 6/15 Cc_NACs (Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430); 5/14 Ah_NACs (Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1) were identified as potential drought stress-responsive candidate genes. Conclusion: In the present study, comprehensive genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. Based on the genome sequence, we analyzed phylogenetic association, structural characteristics, promoter analysis, gene interaction networks, and expression profiles of NAC genes among these three legumes. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. The identified candidate genes would serve as a useful resource for molecular breeding for developing drought-tolerant legume varieties with improved productivity.