Stress regulatory capabilities discovered in late embryogenesis abundant (LEA) proteins expressed during pecan (Carya illinoinensis) kernel development

Authors: PULICHERLA, SAHITHI - New Mexico State University; CLERMONT, KRISTEN - Oak Ridge Institute For Science And Education (ORISE); PRESTENBURG, ERIC - Oak Ridge Institute For Science And Education (ORISE); Mattison, Christopher; RANDALL, JENNIFER - New Mexico State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2025
Publication Date: 9/29/2025
Citation: Pulicherla, S., Clermont, K., Prestenburg, E.C., Mattison, C.P., Randall, J.J. 2025. Stress regulatory capabilities discovered in late embryogenesis abundant (LEA) proteins expressed during pecan (Carya illinoinensis) kernel development. BMC Genomics. https://doi.org/10.1186/s12864-025-12040-8.
DOI: https://doi.org/10.1186/s12864-025-12040-8

Interpretive Summary: Pecan nuts are a major American tree nut crop. A lack of precipitation can decrease tree growth and nut production. Pecan trees are also susceptible to increased salt in the soil, and this can also harm the tree and reduce nut production. To deal with a lack of water or increased salt, pecans can produce Late Embryogenesis Abundant (LEA) proteins to assist the tree in dealing with these stresses. This study identified 43 LEA proteins in two pecan tree cultivars and highlighted some of their properties important for pecan tree survival under stress. Gene expression studies indicated that LEA#3 and LEA#4 proteins were highly expressed during nut development. Using a model system, LEA#3 and LEA#4 proteins were expressed in microbes, and they improved the survival of the microbes when grown in conditions with increased salt or decreased water. When miniature pecan trees were grown in conditions of high salt expression of the LEA#4 gene was increased indicating it’s possible role in adapting to high salt. This is the first large scale study of pecan LEA proteins and the results provide key targets to improve drought and salt tolerance in pecan trees and post-harvest storage protocols for pecan nuts.

Technical Abstract: Background Pecan (Carya illinoinensis), a major North American tree nut crop, faces yield losses due to abiotic stressors like drought and salinity. Late embryogenesis abundant (LEA) proteins, known for stabilizing cellular components under desiccation, remain uncharacterized in pecans. This study bridges this gap by analysing LEA proteins during kernel development in 'Sumner' and 'Pawnee' cultivars, combining phylogenetics, structural modelling, and functional assays to elucidate their roles in stress adaptation. Results We identified 43 LEA proteins across seven subfamilies, with LEA2 as the largest subgroup (30 members). Phylogenetic analysis revealed strong conservation with Arabidopsis homologs. Structural characterization highlighted hydrophilic properties in LEA4 and dehydrins, critical for stress mitigation. Transcriptomic profiling revealed cultivar-specific expression patterns, with 'Sumner' nuts displaying high CiPLEA1.1 and CiPLEA4.1 gene expression, while 'Pawnee' upregulated CiPLEA4.1 and CiPLEA3.1. Heterologous expression in E. coli demonstrated that LEAP3 and LEAP4 conferred enhanced tolerance to osmotic stress (0.4 M NaCl/sorbitol) and desiccation, with LEAP4 expressing cells showing a 2.5-fold growth advantage under salinity. In micropropagated pecan plants, LEAP4 expression surged transiently under 75 mM NaCl, peaking at 48 hours, indicating its role as an early stress responder. Conclusion This is the first comprehensive study of pecan LEA proteins and underscores LEAP4’s dual role in osmotic adjustment and desiccation tolerance, positioning it as a key candidate for improving abiotic stress resilience. The conserved yet diverse LEA family in pecan kernels provides molecular insights into stress adaptation mechanisms, with implications for breeding programs and postharvest storage protocols. Future work will explore LEA-mediated regulatory networks across diverse abiotic stress conditions to mitigate crop losses in perennial tree crops.