Marker analysis for detection of the Mi-1.2 resistance gene in tomato hybrid rootstocks and cultivars

In tomato, the REX-1 marker is typically used to detect the root-knot nematode resistance gene Mi-1.2 in Solanum lycopersicum cultivars with introgression from S. peruvianum (Sp). However, using this marker, false positives have been reported in hybrid tomato rootstocks with introgressions from other Solanum species. We evaluated the reliability of available PCR-based markers Mi23, PMi and PM3 for detection of root-knot nematode resistance in a set of tomato hybrid rootstocks, cultivars and in several accessions of different Solanum species. Results showed that none of the tested markers was able to identify unequivocally lines with resistant phenotype. The Mi23 marker amplified from the susceptible tomato cvs Ailsa Craig and Chatham was Sp-like, while the PMi marker was highly polymorphic in several accessions of Solanum species and did not distinguish between a susceptible accession of S. peruvianum (LA1336) and two resistant accessions/clones (PI270435-2R2 and PI270435-3MH). In addition, the PM3 marker generated amplification products from the susceptible tomato cv. Tyrmes and susceptible accessions of S. chilense (LA1969 and LA2746) that were also Sp-like. Fingerprinting Mi-1.2 gene homologues (MiGHs) using primers flanking intron-1 in the tomato hybrid rootstocks and nematode-resistant and susceptible cvs indicated a great variation in the number and nature of the MiGHs. In silico analysis with the existing Mi-1.2 gene-specific primers C1/2, IMO-F1/R1 and VIGS-F indicated that they were not specific for the Mi-1.2 gene as they could amplify a fragment with a similar size from MiGHs from S. lycopersicum as well as other MiGHs from S. peruvianum. A newly designed Mi-1.2 gene-specific primer, Pau-do, used with an existing primer, C2S4, amplified an identical fragment of 1494 bp from cDNA of nematode-resistant tomato cv. Motelle and rootstocks Beaufort and Maxifort. Overall, this paper provides information to breeders, scientists and growers on the limited reliability of the available molecular tools to characterise root-knot nematode resistance in hybrid tomato rootstocks. The results show that, as most of the current markers are not universal and can lead to the appearance of false positives for root-knot nematode resistance, the resistance response of hybrid tomato rootstocks will still need to be evaluated through infection tests.