Abstract
BackgroundChickpea, 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.ResultsIn 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.ConclusionAs 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.
Highlights
Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress
Identification and genomic distribution of NAC proteins/ genes in chickpea, pigeonpea, and groundnut NAC protein sequences from other plant species and NAC Hidden Markov model (HMM) profiles were searched against chickpea [5], pigeonpea [7], and groundnut [8] gene models
Prediction of subcellular localization based on significant similarity in potential location/location DB indicated 73.16 and 64.5% of the identified NAC genes were potentially located in the nucleus of chickpea and pigeonpea, respectively, while in the case of groundnut, only 57.83% of genes were potentially located in the nucleus
Summary
Pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. A diploid legume crop species (2n = 2x = 16; genome size of 738.09 Mb), is the second most extensively grown legume with an annual production of ~ 17.19 Mt [3] globally after soybean and provides a rich source of proteins, carbohydrates, vitamins, and minerals for human consumption [4, 5]. On the other hand, is one of the leading legumes and oilseed crops with high protein content It is grown widely in the tropics and subtropics with an annual production of ~ 45.95 Mt [3]. An in-depth understanding of the underlying mechanisms of drought stress tolerance is required to improve the yield potential of these crops
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