Combining two high-density QTL maps with a reference genome to identify candidate genes for morphology, yield, and...

Faba bean (Vicia faba L.) is a key legume crop for sustainable agriculture, but its improvement is constrained by yield instability and susceptibility to major biotic stresses. In this study, we developed high-density linkage maps for two recombinant inbred line (RIL) populations, 29H x Vf136 (P1) and Histal x L8 (P2), phenotyped across multiple environments and years, to identify stable QTLs associated with morphology, yield components and resistance to Ascochyta fabae and the parasitic weed Orobanche spp. Using the Vfaba_v2 Axiom SNP array, the maps comprised 2,043 and 3,903 SNPs for P1 and P2, respectively and were anchored to the reference genome to refine QTL intervals and prioritize candidate genes. Most traits exhibited high heritability and coherent phenotypic correlations, providing strong statistical power for QTL detection. A total of 59 QTLs were identified, with P1 QTLs primarily associated with biotic resistance and P2 QTLs encompassing morphological, yield and resistance to A. fabae. These high-density maps substantially improve resolution compared with previous studies, enabling refined QTL mapping, colocalization analyses and identification of biologically relevant candidate genes. Integration of these QTLs with previously reported QTL and GWAS data and projection onto the physical reference genome revealed 16 overlapping genomic regions (0.003 to 341.10 Mbp) containing 2 to 596 genes. The approach provided cross-validation and suggested the presence of stable loci consistently associated with these traits across diverse genetic backgrounds and environments. These overlapping regions were enriched in genes controlling development, productivity and biotic stress resistance and prioritized candidate genes included transcription factors (MADS-box, GATA, PLATZ, SAGA, CCCH zinc finger, WRKY, MYB-like), signalling proteins (protein kinases, LRR receptor-like proteins, Nudix hydrolases, calcineurin B-like, WD40), and growth and yield related enzymes (cytochrome P450s, glutathione S-transferases, glycosyltransferases, helicases, PPR, PUPs, PAPs, E3 ubiquitin ligases, RING finger, heparanase-like proteins). Several QTLs displayed potential pleiotropy, linking yield components with disease resistance traits. These findings provide a robust genomic framework for functional validation and marker-assisted breeding in faba bean, highlighting candidate genes and stable loci underlying complex agronomic traits.