A tomato NBS-LRR gene Mi-9 confers heat-stable resistance to root-knot nematodes

Root-knot nematodes (RKNs) are the most widespread soil-borne obligate endoparasites. They can infect the roots of many crops and cause significant yield losses. The only commercially available RKN-resistant gene in tomatoes, Mi-1.2, fails at soil temperatures above 28°C. We cloned the heat-stable RKN-resistant gene, Mi-9, from a gene cluster composed of seven nucleotide-binding sites and leucine-rich repeat (NBS-LRR) type resistant genes in Solanum arcunum accession LA2157. Screening nematode infections in individual and combinatorial knockouts of five NBS-LRR genes showed that Mi-9 Candidate 4 (MiC-4) alone is sufficient to confer heat-stable RKN resistance. Our study identifies a new source of heat-stable resistance to RKN in tomatoes for challenging environmental conditions. We also showcase a roadmap for rapid characterization of resistance genes by combining comparative genomics and genome editing, with the potential to be utilized in other crops.