Genome-wide identification and characterization of the late embryogenesis abundant (LEA) protein-encoding gene family related to water deficit response in Theobroma cacao

Late Embryogenesis Abundant (LEA) proteins play essential roles in plant adaptation to water deficit; however, their genomic organization and stress-responsive regulation remain unexplored in Theobroma cacao . This study represents the first genome-wide identification and characterization of the LEA gene family in cacao and evaluates their involvement in drought response. A total of 30 LEA genes were identified and classified into eight subfamilies based on conserved domains, motif composition, and phylogenetic relationships. Gene structure, chromosomal distribution, and duplication analyses revealed that both tandem and segmental duplication events contributed to family expansion. Promoter analysis showed enrichment of stress- and hormone-responsive cis-acting elements, supporting their regulatory role under abiotic stress. Predicted subcellular localization suggested chloroplast targeting for several LEA-2 members, indicating potential involvement in photosynthetic protection. Expression profiling via RT-qPCR in three cacao clones with contrasting drought tolerance revealed genotype-specific responses. Notably, clone ICS 60 exhibited strong induction of LEA-1, LEA-3, and LEA-5 genes under stress, correlating with greater physiological stress and limited recovery. In contrast, TSH 565 showed moderate induction of SMP and DHN genes, associated with improved recovery, while EET 8 maintained stable expression and physiological parameters. These findings provide new insights into the molecular and physiological mechanisms underlying drought tolerance in cacao and identify candidate genes for breeding climate-resilient cultivars.