Transcriptional regulation reveals potent drought tolerance mechanisms in contrasting genotypes of Cajanus cajan (L.) Millspaugh

Global warming severely impacts crop productivity, particularly in the Global South. Tropical pulse crops are nutritious staples and tolerant to harsh conditions, such as pigeonpea (Cajanus cajan). Two pigeonpea varieties have superior qualities, also with respect to abiotic stress tolerance: drought-tolerant Pusa Arhar 16 (PA16) and moderately drought-sensitive Pusa 992 (PA99). However, both are understudied at the molecular level. This study investigates molecular mechanisms of drought tolerance by investigating their responses to polyethylene glycol-induced drought. Superior drought tolerance in PA16 was characterized by enhanced shoot growth, photosynthetic characteristics and reduced oxidative stress as compared to PA992, while root length showed no significant difference between the varieties. Transcriptomic analysis identified differentially expressed genes among treatments and varieties, significantly upregulated under drought in PA16 versus PA992 with distinct patterns. For example, genes encoding terpenoid biosynthesis were up-regulated only in PA16, while those encoding LATE EMBRYOGENESIS ABUNDANT (LEA) proteins were drought-induced in both, PA16 and PA992. Functional enrichment analyses coupled with Weighted Correlation Network Analysis uncovered co-expression networks regulating drought-related pathways. Hence, the genotype and environment-specific gene regulation patterns suggest molecular and physiological mechanisms related to secondary metabolisms and LEA proteins underlying drought resilience in pigeonpea. This research offers potential targets for breeding drought-tolerant varieties of this important legume crop. - Two pigeonpea (Cajanus cajan) varieties, drought-tolerant Pusa Arhar 16 (PA16) and moderately drought-sensitive Pusa 992 (PA992), were studied under polyethylene glycol (PEG)-induced drought stress. - Both varieties reacted to drought stress, whereby PA16 showed higher tolerance level than PA992. Transcriptomic analysis indicated genotype and environment effects. - Drought-responsive genes in PA16 versus PA992 were associated with secondary metabolite biosynthesis, particularly of terpenoids and flavonoids. Genes encoding LATE EMBRYOGENESIS ABUNDANT (LEA) proteins were significantly upregulated under PEG-induced drought stress in both varieties.