QTL analysis uncovers the genetic architecture of resistance to chocolate spot disease caused by four Botrytis species on faba bean

Background Chocolate spot (CS), caused by Botrytis species, is a major disease constraining faba bean production worldwide. In this study, we investigated the genetic basis of resistance to four Botrytis species ( B. fabae, B. cinerea , B. pseudocinerea , and B. fabiopsis ) using a recombinant inbred line (RIL) population derived from the cross Mélodie/2 × ILB 938/2, screened using a detached-leaflet assay. Results Significant variation in disease severity was observed among parental lines and RILs for all four Botrytis species. The detached-leaf assay was highly correlated with a whole-plant assay conducted with a different B. fabae isolate, validating the use of the screening tool. QTL analysis identified six loci associated with Botrytis infection across Chr1, Chr4, and Chr6, explaining 9–25% of the total phenotypic variance. The overlapping QTLs on Chr1 conferred resistance to all four Botrytis species, while QTLs on Chr4 and Chr6 were specific to B. fabae . None of the other three species showed a unique QTL. Candidate gene analysis within QTL intervals revealed several defense-related gene families, including F-box protein, WRKY, MYB, and AP2/ERF transcription factors, and peroxidases involved in oxidative stress regulation. Conclusion The consistency of response across species and the lack of unique responses from the non- fabae species indicate that selection for resistance to B. fabae should select adequately for the other species. This study provides new insights into the shared and species-specific genetic architecture of Botrytis resistance in faba bean.