Gene expression profiling of soaked dry beans reveals cell wall modification plays a role in cooking time

Dry beans are a nutritious food, but their lengthy cooking requirements are barriers to consumption for which, pre-soaking can reduce cooking times. While soaking allows hydration to occur prior to cooking, there is evidence that enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. The role of soaking on reducing cooking time is genotype dependent with some genotypes exhibiting larger and faster rates of cooking time reduction than other genotypes. Little is known about gene expression changes that occur during soaking that influence cooking times or gene expression patterns related to genetic variability for cooking time. The goal of this study was to 1) identify gene expression patterns that occur during a soaking time course and 2) compare gene expression in fast-cooking and slow-cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 hrs) and was sequenced via Quant-seq. Differential gene expression and weighted gene co-expression network analysis (WGCNA) was performed with results compared with previously identified QTL for water uptake and cooking time. Coexpression modules correlated with soaking time and cooking time were identified. Genes related to cell wall growth and development, germination, and hypoxic stress were differentially expressed in the fast- and slow-cooking beans during soaking. Several candidate genes for the genetic control of cooking time had elevated expression in the slow-cooking beans, including pectin methylesterase, cell wall modification enzymes and flavonoid biosynthetic pathway genes. The expression of enzymes that strengthen the cell wall in the slow-cooking beans may increase their cooking time by preventing cell separation and water uptake in the cotyledon, as well as improve their ability to resist stress during cultivation.