Toward validation of QTLs associated with pod and seed size in common bean using two nested recombinant inbred line populations

The common bean is an important legume worldwide. The aim of this study was to identify quantitative trait loci (QTLs) associated with seed and pod phenotypes and to evaluate the consistency of these QTLs across different environments and genetic backgrounds. Two nested recombinant inbred populations obtained from the crosses “Xana”/ “Cornell 4924” (XC) and “Xana”/ “BAT93” (XB) were used. The populations were phenotyped with respect to pod and seed size and number of seeds per pod and seed weight over two (XB) or five seasons (XC) using a randomized complete block design. The XC population was re-genotyped, and an updated linkage map, with 732 markers and a total length of 1390 cM, was developed. The XB population was genotyped using genotyping by sequencing (GBS), and the corresponding genetic linkage map consisted of 497 single-nucleotide polymorphisms (SNPs) with a total length of 1547 cM. Altogether, 13 and 18 QTLs for pod traits and 21 and 25 QTLs for seed traits were detected in the XC and XB populations, respectively. In addition, 20 and 27 significant epistatic interactions between QTLs were detected in the XC and XB populations, respectively. The overlap among identified QTLs in the two nested populations was also investigated. Results revealed four overlapping regions for pod traits and eight for seed traits between the XC and XB populations. QTLs for seed or pod phenotypes detected on telomeric genomic regions of chromosomes Pv01, Pv05, Pv06, Pv07, Pv08, and Pv11 overlapped with QTLs associated with pod or seed phenotypes previously reported in other studies. The results showed the complex architecture of the genetic control of the pod and seed phenotype and the use of the bean genome for the integration and validation of QTLs.