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Background  Chickpea, pigeonpea, and groundnut are the primary legume crops 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. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops.    Results  In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. 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). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed 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,  Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186 ;  Cc_26125 ,  Cc_43030 ,  Cc_43785 ,  Cc_43786 ,  Cc_22429 , and  Cc_22430 ;  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  As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07602-5.

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