AN INTEGRATED APPROACH TO THE DEVELOPMENT OF RESISTANCE TO COMMON BACTERIAL BLIGHT IN COMMON BEAN (PHASEOLUS VULGARIS)

Common bean (Phaseolus vulgaris L.) is a globally important legume, providing proteins, fibres and micronutrients to hundreds of millions of people. This legume plays a central role in food and nutrition security, but yields are threatened by biotic stresses, such as common bacterial blight (CBB) disease. CBB, caused by Xanthomonas phaseoli pv. phaseoli (Xpp) and Xanthomonas citri pv. fuscans, can reduce yields by up to 45 %. Breeding for resistance is the most sustainable control strategy, yet resistance is quantitative and influenced by pathogen diversity. Most known quantitative trait loci (QTLs) derive from Mesoamerican germplasm, leaving Andean market classes such as cranberry bean understudied. This thesis uses a multi‑scale approach, combining QTL mapping, transcriptomics and CBB pathogens comparative genomics, to clarify the genetic basis of CBB resistance and to provide practical tools for breeding. In Chapter 1, two mapping populations in the cranberry bean market class (a recombinant inbred line population and an F₂ population) were analysed using QTL mapping and QTL-seq approaches. Three resistance loci were detected. Major QTLs on chromosomes Pv06 and Pv08 explained most of the phenotypic variance, while a minor QTL on Pv11 was identified only in the RIL population. The Pv08 QTL corresponds to the known SU91 region, whereas the Pv06 QTL does not coincide with the classical BC420 locus, suggesting a novel resistance source. QTL interaction was assessed and confirmed strong epistatic behaviour between the two major loci, expanding our understanding of the CBB resistance genetics in the cranberry market class. Chapter 2 examines host responses to isolates with different virulence features. Four Italian isolates causing CBB were screened on 2 common bean genotypes (one resistant and one susceptible). The screening underlined virulence differences in the susceptible genotype infection, but most importantly two Xpp isolates with contrasting behaviour on the intermediate cultivar Vaillant were identified. USB771 induced resistance response while DEF699 caused a significant infection in Vaillant. RNA‑seq of Vaillant leaves at 48 h post‑inoculation showed that the resistant interaction elicited extensive transcriptional regulation. 1,256 genes were differentially expressed and defence‑related pathways such as plant-pathogen interaction, MAPK signalling and secondary metabolism were enriched. By contrast, the susceptible interaction induced only 269 differentially expressed genes and lacked enrichment in plant-defence related pathways. However, the DEF699 interaction caused upregulation of a Lateral Organ Boundaries (LOB) domain gene, known to be linked to Xanthomonas susceptibility in citrus canker disease. This study provides for the first time a transcriptomic analysis focused on isolate-driven responses within a common genetic background. The chapter 2 analysis highlights: (i) activation of defence mechanism in the resistant interaction; (ii) the repression of the defence response and the concomitant activation of putative susceptibility genes in the susceptible interaction. In Chapter 3, the pathogen perspective is addressed by sequencing two Italian Xpp strains using Nanopore long‑read technology. Comparative analysis based on genome similarity show that USB771 clusters with Canadian strains, while DEF699 groups with a strain isolated in the USA. A key finding is the variation in transcription activator‑like (TAL) effector presence: USB771 contains a single chromosomal tal gene (tal19B) and lacks plasmid‑borne TALs, whereas DEF699 carries chromosomal (tal18A) and plasmid‑encoded tal (tal20B) genes. Because TAL effectors bind host promoters and activate susceptibility genes, such variation might contribute to the observed differences in host responses. Overall, this thesis provided new insights into the genetic and molecular basis of CBB resistance. Identification of novel QTLs provides breeders with additional markers for pyramiding resistance. Transcriptomic analyses reveal that effective resistance involves robust activation of immune signalling and secondary metabolism pathways, whereas the isolate overcoming resistance represses host-defence responses, while exploiting host susceptibility genes. Comparative genomics extends knowledge of pathogen diversity and TAL effectors repertoires and underscores the value of long‑read sequencing for complete genome assembly. By integrating quantitative genetics, gene expression and pathogen genomics, this research advances knowledge for developing durable, broad‑spectrum resistance to common bacterial blight in common bean and illustrates the benefits of cross‑disciplinary approaches for crop protection and food security.