Dry beans provide a source of plant-based protein, key micronutrients such as iron, zinc, and folate, and fiber for millions of people around the world. However, dry beans have long and highly variable cooking times that limit their consumer appeal. Long cooking times can be further exacerbated by high temperature and humidity post-harvest storage conditions prevalent in some bean production environments. The goal of this research was to 1) identify quantitative trait loci (QTL), genes, and genetic mechanisms that have been associated with cooking time in dry beans in the literature; 2) quantify gene expression patterns related to genetic variability for cooking time in beans during soaking (a common method used by home cooks to lower dry bean cooking times), identify candidate genes for fast cooking time via joining of RNA-seq and QTL data, and investigate the phenotypic effects of candidate genes via biochemical analyses such as enzyme and substrate (i.e., phytate and total nutrient) assays; 3); understand the effects of high temperature and humidity post-harvest storage on dry beans on a transcriptomic and biochemical level; and 4) validate molecular and phenotypic markers for cooking time in multiple populations. The literature review revealed that a total of 60 unique QTL have been delineated for cooking time, several of which overlap at key regions in the genome. Transcriptomic analysis was conducted on dry bean varieties with contrasting cooking times exposed to different soaking and storage conditions. Patterns in gene expression and candidate genes for cooking time related to cell wall modification (i.e., pectin interconversions, pectin demethylesterfication, and phenolic compound deposition) were identified in both studies, several of which were found within QTL for cooking time. A gene related to cell wall modification, pectin methylesterase, was found to be more active in slow-cooking dry beans, and calcium levels were found to be higher in slow-cooking genotypes across planting locations and years. Kompetitive allele-specific PCR (KASP) markers were designed that target candidate genes and QTL for cooking time. The results of this work elucidated multiple genetic mechanisms for cooking time in dry beans stored in both temperate and hot, humid environments and identified several markers that could be useful for developing faster cooking germplasm.
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