Hot, humid environments induce the expression of cell wall remodeling genes in whole mature dry beans (Phaseolus vulgaris L.)

Dry bean (Phaseolus vulgaris L.) cooking time is under genetic and environmental control. High temperature, high relative humidity (i.e., tropic-like) environments are thought to influence cooking times in dry beans by causing a phenomenon known as hard-to-cook (HTC). The goal of this work was to understand how different dry bean germplasm responds to high temperature and high humidity storage, thereby facilitating the development of varieties that are less sensitive to the effects of HTC. This study compared gene expression in four dry bean genotypes with contrasting market classes and cooking times by subjecting mature seeds to one of two soaking treatments (raw and a 12-hour soak) and one of three environmental treatments: 1) no storage, 2) storage for 3 days in a temperate (25C/50% RH) environment, or 3) storage for 3 days in a tropical (35C/75% RH) environment. The physiochemical properties of these seeds were then measured, including raw seed weight, water uptake percentage, cooking time, cell wall thickness, nutrient content, phytate content, and germination rate. RNA-seq was also performed, and reads were subjected to DESeq2, WGCNA, and topGO analysis. Genotypes that cooked faster prior to storage also cooked faster following tropical storage and 12 hours of soaking, although the cooking times of each genotype did increase on average by ~7 minutes. Cell wall thickness decreased on average in tropical beans, but this difference was only significant in the slow-cooking genotypes, suggesting that the genotypes responded differently to high heat and high humidity stress. Tropical storage induced the expression of genes related to oxidoreductase activity, plant growth/development, and/or stress tolerance across all four genotypes. A gene that participates in stress-induced cell wall remodeling and calcium signaling, wall associated kinase 5, was upregulated in all four of the genotypes studied after soaking under tropical storage conditions. Slow- and fast-cooking genotypes differed in terms of both physiochemical and gene expression properties, namely the upregulation of genes sensitive to the presence of inorganic substances in the slow-cooking genotypes and impaired germination in the fast-cooking varieties under tropical storage conditions. However, impaired germination was only apparent in dry beans grown under non-irrigated conditions, suggesting that multiple stresses may be required to cause negative trade-offs in fast-cooking germplasm.