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Abstract The pattern‐triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe‐derived molecules known as microbe‐ or pathogen‐associated molecular patterns or molecules derived from compromised host cells called damage‐associated molecular patterns. Membrane‐localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced. This review describes what is known about this variation. We discuss how variation in the PTI response can be measured and how this knowledge might be utilized in the control of plant disease and in developing plant varieties with enhanced disease resistance. 

SUMMARY Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, includingSolanum lycopersicoides, have been crossed toS. lycopersicumfor the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome‐scale genome assembly forS. lycopersicoidesLA2951, which contains 37 938 predicted protein‐coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of theS. lycopersicoidesintrogressions in a set ofS. lycopersicumcv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity‐associated function of the clusteredPtogene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of theAuberginelocus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild speciesS. lycopersicoides, which we use to shed light on theAuberginelocus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β‐cyclase whose function we demonstrate.