Bryophyte ELIPs as Evolutionary Guardians: Engineering Chloroplast Resilience and ABA‐Enhanced Drought Tolerance in Crops

Early light-induced proteins (ELIPs) are pivotal for plant stress adaptation, yet their evolutionary and functional diversification across land plants remain unclear. Here, 454 ELIPs genes from 15 species (chlorophytes to angiosperms) were analysed using phylogenomics, cis-regulatory element mapping, transcriptomics, and transgenic validation. Phylogenetics classified ELIPs into four groups: Group 1 exclusive to non-seed plants (e.g., Physcomitrium patens), while angiosperms retained only Groups II-IV, reflecting lineage-specific evolutionary trajectories. Gene family expansion in angiosperms primarily occurred via whole-genome duplication, while bryophytes expanded through dispersed/tandem duplication, indicating distinct ecological adaptation strategies. Promoter analysis revealed bryophyte ELIPs uniquely enriched with ABA-responsive (ABRE) and drought-inducible (MBS) motifs, suggesting cis-regulatory innovation for water stress. Dehydration-rehydration transcriptomics revealed transient upregulation of eight P. patens ELIPs during dehydration, contrasting with the sustained AtELIP2 induction in Arabidopsis thaliana. Transgenic Arabidopsis overexpressing PpELIP1/9 exhibited enhanced drought tolerance, delayed chlorophyll degradation, increased lateral root proliferation under ABA treatment, and reduced oxidative damages via chloroplast-localised thylakoid stabilisation. Our results highlight the conserved role of ELIPs in photoprotection and their functional diversification in ABA-mediated drought adaptation, positioning bryophytes as reservoirs of ancestral stress resilience, bridging 450 million years of ELIP evolution and proposing a molecular framework for engineering stress-resilient crops through ELIP manipulation.