Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

Authors: JEFFERY, HANNAH - Michigan State University; MUDUKUTI, NYASHA - University Of Notre Dame; BUELL, C ROBIN - University Of Georgia; CHILDS, KEVIN - Michigan State University; Cichy, Karen

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2023
Publication Date: 7/6/2023
Citation: Jeffery, H.R., Mudukuti, N., Buell, C., Childs, K.L., Cichy, K.A. 2023. Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time. The Plant Genome. 16(3). Article e20364. https://doi.org/10.1002/tpg2.20364.
DOI: https://doi.org/10.1002/tpg2.20364

Interpretive Summary: Dry beans are a nutritious food that often have long and highly variable cooking times. Pre-soaking is one of the major methods used by consumers to reduce cooking times. In this study gene expression analysis was used to understand molecular changes that occur in dry beans during soaking. After 12 hrs. of soaking, the fast-cooking bean genotypes (TZ-37 and Ervilha) took 18-19 minutes to completely cook whereas the slow cooking beans (TZ-27 and PI527538) took 23.5-30 mins. The cooking times of all four bean genotypes decreased drastically from 0-12 hours of soaking and remained stable after 12 hours. Nine gene co-expression pathways were significantly associated with changes in both soaking time and cooking time in the beans. Thirty-nine genes within these co-expression modules were also within genomic regions previous associated with water uptake and/or cooking time, differentially expressed in fast- and slow-cooking beans, and differentially expressed in response to water uptake. The functions of the candidate genes were related to hormone-mediated cell wall modification and response to hypoxia. The slow-cooking beans expressed more genes that increase stress tolerance than the fast-cooking beans did. Candidate genes for cooking time differed in brown and yellow beans. Genes that affect cell wall expansion and increase calcium levels in cotyledon cells were upregulated in the slow-cooking brown bean TZ-27 relative to TZ-37. By contrast, genes that form calcium-pectin crosslinks and synthesize condensed tannin precursors were upregulated in PI527538 relative to Ervilha. Differentially expressed genes between the fast- and slow-cooking genotypes may impact the stability of the cell wall in dry bean which could lead to shorter cooking times in dry bean and less resistance to abiotic stress.

Technical Abstract: Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Pre-soaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to 1) identify gene expression patterns that are altered by soaking 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 expression abundances were detected using Quant-seq. Differential gene expression analysis and weighted gene co-expression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed in the fast- and slow-cooking beans due to soaking. Candidate genes identified in the slow-cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall strengthening enzymes in the slow-cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.