Developing a model to implement marker-assisted selection for root-knot nematode resistance in common bean

Abstract

Common bean (Phaseolus vulgaris L.) is a vital crop for direct human consumption, with essential nutrients and valuable protein that provides food security in developing countries. However, its cultivation faces significant threats from Meloidogyne incognita, a root-knot nematode (RKN), resulting in considerable yield loss. Developing crop resistance remains a key strategy for mitigating nematode infections. To investigate the genetic architecture of common bean responses to RKN (specifically, race 3 of M. incognita), we performed controlled crosses between the genotypes IAC-Tybata and Branquinho with contrasting resistance. The resulting segregating population (F2) of 333 individuals was genotyped using GBS (genotyping-by-sequencing). We used a phenotyping approach, already optimized in the lab, to collect trait data for a subset of 200 F2:3 families. Evaluations of egg mass (EM), root-galling index (GI), and root dry mass (RM) were conducted 30 days after RKN inoculation under greenhouse conditions, in a completely randomized design with ten replicates. Linkage and quantitative trait loci (QTL) mapping were performed, while functional mapping of associated regions facilitated identification of candidate genes. A linkage map encompassing 954 SNPs assigned to 11 linkage groups totaling 1,687 cM formed the basis for Interval Mapping (IM), Composite Interval Mapping (CIM), and Multiple Interval Mapping (MIM), revealing four major QTLs (on Pv03, Pv05, Pv08, and Pv10) and epistasis between QTL on Pv08 and on Pv10 associated with the GI trait. No significant QTL were identified for EM and RM. The model enabled calculation of genotypic values through marker-assisted selection (MAS). The high correlation between observed and predicted values (0.72) underscores the models significance. Candidate genes previously associated with nematode resistance were also identified within the QTL interval on chromosome Pv10. Our results will be valuable for future selection of varieties resistant to this important crop disease.