Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations

Bean (Phaseolus vulgaris L.) production is challenged by many limitations with drought being among the top causes of crop failure worldwide. In this study, we constructed three small‐red‐seeded bean recombinant inbred line (RIL) mapping populations (S48M, S94M, and S95M) with a common parent (‘Merlot’) and performed joint interval mapping analysis as a small nested association mapping (NAM) population for agronomic traits and performance under rainfed conditions in Michigan. The objective was to identify novel sources of improved performance and genomic regions associated with desirable traits under rainfed and water‐sufficient conditions in small‐red bean breeding materials adapted to temperate zones. A composite linkage map was constructed using single‐nucleotide polymorphism (SNP) markers from the three populations and resulted in an improved version of the individual linkage maps shown by a greater genome span covered in the composite map (909 cM). A number of quantitative trait loci (QTL) of different size effects were identified for seed yield (R2 = 15.4–30.7%), seed size (R2 = 16.4–20.2%), days to flowering (R2 = 12.4–36.1%), days to maturity (R2 = 16.2%), lodging score (R2 = 10.3–12.9%), and canopy height (R2 = 17%). Our study confirmed previously reported QTL on five chromosomes and identified a new QTL for canopy height on chromosome Pv10. The use of a composite map and QTL analysis under a NAM population structure increased our ability to detect small‐effect QTL that were segregating in at least two of the populations but would not have been detected using individual linkage maps.