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

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, 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 root-knot nematode (specifically, race 3 of M. incognita), we performed controlled crosses between the genotypes "IAC-Tybatã" and "Branquinho" with contrasting resistance. The resulting segregating population (F2) of 333 individuals was genotyped using 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, root-galling index, and root dry mass (RM) were conducted 30 d after root-knot nematode inoculation under greenhouse conditions, in a completely randomized design with 10 replicates. Linkage and quantitative trait loci 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, Composite Interval Mapping, and Multiple Interval Mapping, revealing four major quantitative trait locis (on Pv03, Pv05, Pv08, and Pv10) and epistasis between quantitative trait loci on Pv08 and on Pv10 associated with the root-galling index trait. No significant quantitative trait loci were identified for egg mass and RM. The model enabled calculation of genotypic values through marker-assisted selection. The high correlation between observed and predicted values (0.72) underscores the model's significance. Candidate genes previously associated with nematode resistance were also identified within the quantitative trait loci interval on chromosome Pv10. Our results will be valuable for future selection of varieties resistant to this important crop disease.