Genome-wide association study of variation in cooking time among common bean (Phaseolus vulgaris L.) accessions using Diversity Arrays Technology markers

Stored grains of common bean (Phaseolus vulgaris L.) develop the hard-to-cook trait (HTC), which is manifested in a prolonged cooking time, thereby imposing time and energy constraints. The objective of this study was to determine variation in cooking time among common bean genotypes and to identify single nucleotide polymorphism (SNP) markers associated with cooking time.

Seeds of 222 common bean accessions sourced from Kenyan institutions were multiplied in the Jomo Kenyatta University of Agriculture and Technology (JKUAT) field in 2019. The freshly harvested seeds and those stored at 35°C and 50% red haricot (RH) for 4 months for accelerated aging were soaked in distilled water for 16 h and evaluated for cooking time using the finger-pressing method. The accessions were also genotyped to determine variation in SNP markers using Diversity Arrays Technology Sequencing (DArTseq). Genome-wide association study (GWAS) analysis was conducted to identify SNPs significantly associated with cooking time.

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 min and ranged from 28.1 to 72.2 min, whereas aged seeds had a higher average cooking time of 54.1 min and ranged from 32.1 to 96.3 min. GWAS identified a region in Chromosome 10 to be significantly (p ≤ 0.05) associated with the cooking time of aged seeds. Consequently, two potential candidate genes Phvul.010G038000 and Phvul.010G038100 were revealed. The characterized common bean accessions and the identified SNP markers can be utilized in breeding programs to improve the cooking quality of the common bean.