The promise of a fast-cooked healthy meal: common genomic regions for cooking time and iron and zinc content in beans revealed by meta-analysis

Abstract

Short cooking time (CT) is a highly desired trait in common beans, and several quantitative trait loci (QTL) were identified for bean grain quality traits (GQT), including CT. However, although several correlations were reported among these traits, these genomic regions were limitedly integrated and characterized. In this study, we collected 245 QTL for bean GQT from 12 mapping studies, of which 55 were for CT. A consensus map of the QTL was built based on the Phaseolus vulgaris G19833 genome v2.0, using QTL flanking positions when only these are available or physical positions corrected with study-reported linkage disequilibrium (LD) extent or a standard LD of 300 kbp to define QTL end and start positions. Then, the genes with the genomic regions concerning CT were prioritized through a series of in-silico analyses, such as keyword searches and protein-protein interaction networks. We resolved the map to 106 genomic regions, of which 27 were associated with multiple traits. Seventeen multi-trait (MTGR) and 17 single-trait genomic regions (STGR) involved QTL for CT. Nine CT-related MTGRs involved either or both Fe and Zn content, indicating a possibility of combining these traits in new varieties. These results generally agree with a previous meta-analysis conducted for Fe and Zinc QTL. We prioritized 566 that showed a significant PPI at the default confidence level of 0.4 (PPI enrichment p-value<1.0e-16), of which 122 were coexpressed, 138 experimentally determined, 298 based on database annotation, and 480 based on text-mining.