Multi-trait selection of common bean lines resistant to Meloidogyne incognita

Meloidogyne incognita (root-knot nematode) is one of the most damaging soilborne pathogens affecting the common bean. Control relies primarily on resistant cultivars, making accurate resistance phenotyping a key component of breeding programs. Here, we developed an integrated phenotyping approach to identify resistant genotypes in a recombinant inbred line (RIL) population. For initial screening, 361 RILs were evaluated with three replications for galling index (GI), number of galls (NG), and egg masses (EM) at 60 days after inoculation (DAI). A subset of 24 segregating RILs was further assessed in a second trial for GI, NG, EM, and reproduction factor (RF), with seven replications at 30 and 60 DAI. A multi-trait factor analytic mixed model was used to derive an overall resistance index (ORI) for genotype classification into moderately resistant (MR), intermediate (I) and susceptible (S) classes. We also assessed the potential of a qPCR-based phenotyping protocol using two contrasting RILs from the segregating subset. High heritability (> 0.8) and strong genotypic correlations among resistance components were observed in the RIL segregants, indicating a robust genetic basis for selection. MR genotypes consistently exhibited reduced GI, NG, EM, and RF, and transgressive segregants were identified within the MR group, confirming that the ORI framework effectively distinguished resistance levels. Moreover, later evaluation improved genotype classification and revealed resistance shifts. qPCR-based phenotyping consistently discriminated MR and S lines in agreement with classical phenotyping, supporting its use as a complementary evaluation tool. Overall, our results validate an integrative multi-trait strategy for more precise resistance phenotyping and genotype selection.