Phenotyping And Quantitative Trait Loci Mapping of the Hard-To-Cook and Yield-Related Traits in Common Bean (Phaseolus vulgaris L.)

Abstract

Common bean (Phaseolus vulgaris L.) is a source of protein, carbohydrates, dietary fiber, and essential minerals to a large population worldwide. However, prolonged cooking time for dry beans is a factor that hinders the production and consumption of common bean seeds in many communities. The study aimed to assess common bean accessions for variation in cooking time of dry grains and identify regions in the genome that control the hard-to-cook (HTC) trait. Plant material used in this study comprised 257 common bean accessions sourced from the National Gene Bank of Kenya, Kenya Agricultural and Livestock Research Organisation (KALRO)-Embu, and from randomly selected local farmers’ fields. F2:6 recombinant inbred lines (RILs) were developed using common bean varieties GLP2, GLPx92, and accession GBK035420. Field experiments were carried out at Jomo Kenyatta University of Agriculture and Technology (JKUAT), Kenya. The experiments were laid down as a randomized complete block design (RCBD) with three replicates for over four seasons. Morphological data recorded included days to flowering, days to maturity, number of pods per plant, pod length, number of seeds for a pod, 100-seed weight, and grain yield. Cooking time was determined for each genotype using freshly harvested seeds and seeds stored at a temperature of 35oC and 50% relative humidity for four months. Beans were soaked for 16 hours in distilled water and cooked at 96oC in a thermostatically controlled water bath. DNA was isolated for each accession and RILs and genotyping were carried out using Single Nucleotide Polymorphism markers (SNPs) markers using Diversity Arrays Technology Sequencing (DArTseq). Data collected from field experiments was subjected to a normality test and analysis of variance (ANOVA). Pearsons phenotypic correlations analysis was conducted for the traits measured. Association analysis was conducted using the genome-wide analysis studies (GWAs) method to identify Quantitative Trait Loci (QTLs) associated with the hard-to-cook trait. Linkage mapping and QTL analysis were used to analyse data collected for RILs. The field experiment study revealed that days to flowering. 100-seed weight and grain yield had high broad-sense heritability and identified 19 common bean accessions that were both early maturing and high-yielding traits. The results revealed significant differences (P≤0.05) among accessions for all the traits evaluated, the seasonal and the interaction between accessions and seasons were also significant. GWAS and QTL study identified QTLs region associated with all the agronomic traits. Agamous-like MADS-box transcripts like Phvul.001G186400.1 locus co-localized with QTLs for days to flowering and maturity. The study revealed significant differences (P≤0.05) within and between fresh and aged bean accessions. Fresh seeds had a lower cooking time with a mean of 40.8 minutes and ranged from 28.1 to 72.2 minutes while aged seeds had a higher average cooking time of 54.1 minutes and ranged from 32.1 to 96.3 minutes. Genome wide association and QTL studies identified a region on chromosome 10 to be significantly associated (P≤0.05) with the cooking time of aged seeds. Consequently, two potential candidate genes Phvul.010G038000 (galacturan 1,4-alpha galacturonidase) and Phvul.010G038100 (polygalacturonase) were revealed. QTL analysis identified polygalacturonase/pectinase, pectin methylesterase, pectinesterase inhibitor, and galacturan 1, 4 alpha-galacturonidase enzymes to co-localize with the detected QTLs for cooking time. The characterized common bean accessions and the identified SNP markers could be utilized in breeding programs to improve common bean for cooking quality. The identified QTLs could be useful in introgressive hybridization of cooking time trait and implementation Markers assisted Selection (MAS) in the common bean.