Waterlogging tolerance in pigeonpea: current understanding of physiological responses, genetic resources, and genomic...

Waterlogging is an escalating threat to pigeonpea (Cajanus cajan L. Millsp.) production in tropical and subtropical regions, where increasingly erratic monsoon rainfall and poorly drained Vertisols frequently expose crops to root-zone hypoxia during germination and early vegetative growth. Waterlogging in pigeonpea has historically been associated with substantial production losses in affected areas; however, the magnitude of these losses depends on stress duration, developmental stage, genotype, environmental conditions, and post-stress recovery. Oxygen deprivation disrupts root respiration, energy metabolism, and symbiotic nitrogen fixation, yet the mechanistic basis of tolerance remains poorly resolved. This review distinguishes experimentally supported physiological and anatomical responses from transcriptome-derived molecular hypotheses through a five-tier evidence-classification framework (Categories I-V). Experimental studies provide Category I evidence for traits associated with waterlogging tolerance, including cortical aerenchyma formation, hypertrophied lenticels, adventitious rooting, enhanced fermentative metabolism, and antioxidant enzyme activity in tolerant genotypes. Transcriptomic and genomic resources identify putative candidate gene families, but no candidate gene has been functionally validated in pigeonpea through gene editing, transgenic analysis, or expression quantitative trait locus (eQTL) mapping. Phenotypic screening has identified promising tolerant germplasm, including ICPL 20241, ICP 5028, and ICPH 2740, providing resources for breeding. We propose priorities for strengthening the evidence base: standardized multi-stage phenotyping, temporally resolved transcriptomics, QTL mapping, functional validation of candidate genes, and integrated multi-omics approaches. This evidence-based framework provides a roadmap for moving from observed tolerance mechanisms toward experimentally validated molecular targets and their deployment in climate-resilient pigeonpea breeding.