Comparative transcriptome analysis reveals terminal drought-responsive genes in chickpea (Cicer arietinum L.)

Drought at the reproductive phase, referred to as terminal drought is a major constraint which severely limits seed yield in chickpea. Development of drought tolerant cultivars entails identification of key genes which govern drought tolerance.

In order to identify such genes, two different genotypes, which contrast for drought stress tolerance were analysed under terminal drought. The drought tolerant (DT) variety, ICC 4958 and the drought sensitive (DS) variety, ICC 1882 responded differently to terminal drought stress. To identify the drought-induced changes in gene expression, the root transcriptomes of both genotypes were analysed. Two genes belonging to the SPL (SQUAMOSA promoter binding protein-like) transcription factor (TF) family, CarSPL1 and CarSPL9 were significantly (p < 0.05) upregulated, by a fold change of more than 8, in the sensitive genotype relative to the tolerant genotype. Many stress responsive genes like HKT1;3-like, NAC57, GolS3, WSD11, LTP4, etc. were downregulated in the sensitive genotype compared to the tolerant genotype. The CarSPL1 and CarSPL9 proteins shared a high degree of homology with the CaSBP13 and OsSPL6 of pepper and rice, respectively, which are known negative regulators of drought stress response in these crops. In silico analysis revealed a high amenability of the two genes for gene editing as high-efficiency sgRNAs (single guide RNAs) with high (> 66) out-of-frame scores, could be designed.

The findings suggest that the identified CarSPLs act as negative regulators of drought tolerance in chickpea, allowing their utilization as potential targets for gene editing to engineer drought stress tolerance.