Identification of a Candidate Gene in Solanum habrochaites for Resistance to a Race 1 Strain of Pseudomonas syringae pv. tomato

Bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst) is a persistent problem on tomato (Solanum lycopersicum L.). Resistance against race 0 Pst strains is conferred by the Pto protein, which recognizes either of two pathogen effectors: AvrPto or AvrPtoB. However, current tomato varieties do not have resistance to the increasingly common race 1 strains, which lack these effectors. We identified accessions of Solanum habrochaites S. Knapp & D. M. Spooner that are resistant to the race 1 strain T1. Genome sequence comparisons of T1 and two Pst strains that are virulent on these accessions suggested that known microbe‐associated molecular patterns (MAMPs) or effectors are not involved in the resistance. We developed an F2 population from a cross between one T1‐resistant accession, LA2109, and a susceptible tomato cultivar to investigate the genetic basis of this resistance. Linkage analysis using whole‐genome sequence of 58 F2 plants identified quantitative trait loci (QTL), qRph1, in a 5.8‐Mb region on chromosome 2, and qRph2, in a 52.4‐Mb region on chromosome 8, which account for 24 and 26% of the phenotypic variability, respectively. High‐resolution mapping of qRph1 confirmed it contributed to T1 resistance and delimited it to a 1060‐kb region containing 139 genes, including three encoding receptor‐like proteins (RLPs) and 17 encoding receptor‐like protein kinases (RLKs). One RLK gene, Solyc02g072470, is a promising candidate for qRph1, as it is highly expressed in LA2109 and induced on treatment with MAMPs. qRph1 might be useful for enhancing resistance to race 1 strains and its future characterization could provide insights into the plant immune system.