The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Abstract

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

Keywords: NLR genes; R-genes; evolutionary dynamics; gene clusters; genomic-driven breeding.

Figure 1

The tomato defense arsenal. (A) The full R-gene repertoire was displayed with respect to the NB-LRR subclasses (TNL in blue; CNL in orange and RNL in green). The total number of CNLs, TNLs, and RNLs was shown in brackets. (B) The NB-LRR paralogs identified by OrthoMCL with default settings were grouped (annular segments) and the amount of members in each group was specified. (C) For each group of paralogs, the well-characterized R-gene homolog was indicated (Table S1), when available.

Figure 2

Genomic-driven breeding workflow for disease resistance. The identification, annotation, and characterization of NB-LRR genes are essential to investigate the extent of variability and compare the defense arsenals typical of each tomato/Solanaceae species. Information on gene–gene interaction provides additional evidence on the role and function of NB-LRRs. The different analytical approaches based on the most cutting-edge technologies must be combined to gain valuable knowledge on R-genes. The expanded knowledgebase is then used to apply the most appropriate genome-driven breeding technique to improve tomato disease resistance.