New approaches in the discovery and introgression of disease resistance genes from wild tomato

The conceptual framework of the plant disease pyramid serves to emphasize how pathogen movement and environmental change have contributed to epidemics. The conceptual framework also highlights the challenges of resistance discovery and deployment in response to an unpredictable future. In tomato, modifying the host vertex of the disease pyramid has traditionally been accomplished through screening of wild crop relatives, identification of resistance, and breeding new varieties. This process can take years to decades, an unsatisfying timeline to address rapid change in pathogen populations. Survey data of the Xanthomonas population causing bacterial spot in the Midwestern United States demonstrates both species and race shifts over the last decade. Despite concerns about managing emerging and evolving pathogens driven by globalization and climate change, there are promising strategies for the control of tomato disease. Current technology is revolutionizing how plant breeders approach the identification and deployment of resistance. Tomato has long been a model of introgression from wild relatives, and well-developed genetic and genomic resources are enhancing this tradition. Abundant full genome resequencing and emerging reference quality sequences permit Pan Genome analysis. These genomic resources now support background genome selection, identification of coupling phase recombination to create resistance cassettes, and genomic prediction as an extension of marker-assisted selection to counter emerging species and races of Xanthomonas.