In-silico analysis of Rcr3 polymorphism in Solanaceous species and its influenceon tomato Cf-2 mediated recognition of the Fulvia fulvum Avr2 effector

Understanding how pathogen recognition has evolved in plants is essential for uncovering the mechanisms of host resistance and enhancing crop resilience. In this study, we examined how polymorphisms influence the evolutionary dynamics of Avr2 effector recognition from Fulvia fulvum across selected Rcr3 proteins in Solanaceae species. Rcr3, a co-receptor protein central to pathogen recognition, displays notable sequence variation that may affect its interaction with Avr2. Amino acid sequences of Rcr3 from ten Solanaceous plant species were obtained from public databases and categorized into compatible or incompatible groups according to their hypersensitive response. Structural modeling and comparative analyses revealed significant polymorphism in the Rcr3 binding sites, with 73 amino acid substitutions in the compatible group and 33 in the incompatible group, relative to the reference species Solanum lycopersicum. Structural assessments indicated that amino acids within the binding grooves of Rcr3 variants exhibit considerable diversity, particularly within incompatible species, where tighter binding interactions (less than 2Å) were observed. In contrast, compatible species displayed more variable, longer-range interactions (up to 6Å), suggesting a correlation between binding site polymorphism and recognition capability. These findings provide critical insights into the molecular basis of pathogen resistance in Solanaceae, highlighting the evolutionary pressures shaping Rcr3 diversity and its functional implications for plant immunity.