Genomics-assisted Improvement of Resistance to Insect Pests, Diseases and Nematodes in Tomato: A Critical Appraisal of Discovery, Durability and Deployment

Abstract

Tomato (Solanum lycopersicum L.) is the most produced vegetable crop worldwide and sustains losses from an unusually broad spectrum of viruses, fungi, oomycetes, bacteria, root-knot nematodes, and phloem-feeding and leaf-mining insects. Two decades of genomic investment have transformed the discovery phase of resistance breeding, yet the traits deployed in commercial cultivars remain dominated by a small number of major loci introgressed from wild relatives, several of which have been compromised by pathogen adaptation. This critical narrative review examines whether, and where, genomic technologies have altered breeding outcomes rather than merely accelerating gene discovery. Literature was identified through publicly accessible scholarly indexes and appraised for design adequacy, replication, ecological realism, and the strength of the link between genotype and field performance. The evidence is organised around four themes: the shift from a single reference assembly to graph-based and telomere-to-telomere pangenomes; the mechanistic heterogeneity of characterised resistance loci and its consequences for durability; the persistent gap between quantitative trait locus detection and cultivar release; and the distinct evidentiary status of insect and nematode resistance, where causal genetic architecture is less resolved than for viral resistance. The available evidence indicates that genomic resources have substantially improved the resolution of resistance discovery and the precision of marker-assisted introgression, but have not yet demonstrably improved durability. Resistance erosion is documented for begomovirus, tobamovirus and orthotospovirus resistance, and for the single nematode resistance locus in general use. Editing of susceptibility genes offers a mechanistically distinct route, although fitness costs and regulatory heterogeneity constrain translation. Insect resistance depends largely on trichome-borne specialised metabolites whose genetic control is polygenic and environmentally labile, and validated field evidence remains sparse. Priorities include multi-environment durability trials with explicit pathogen population monitoring, systematic quantification of fitness penalties associated with edited susceptibility alleles, and integration of vector and virus resistance within single genetic backgrounds. Confidence in present conclusions is limited by the geographical concentration of studies and by short evaluation horizons.