Root-knot nematodes (Meloidogyne spp.) are among the most devastating plant parasites in global food production. For example, M. incognita control is important in tomato production, yet depends on a few resistance (R-)genes. Hence, the rise of resistance breaking (virulent) M. incognita populations is an ever increasing concern, incentivizing the search for novel natural variation for virulence control. Here, we investigated susceptibility to M. incognita in tomato accessions without R-genes. Initially, 179 tomato accessions were screened for M. incognita susceptibility by challenging at least 10 plants per accession with 100 infective juveniles. We found large, accession-dependent, variation in susceptibility. To uncover underlying mechanisms, a high-resolution time-series RNAseq experiment on 10 accessions differing in susceptibility was performed. By isolating galls and corresponding tissue in mock-infected plants at 1, 2, 3, 4, 7, and 10 days post-inoculation, feeding-site establishment was followed. We found >700 genes differential expressed related to feeding-site establishment and >100 genes correlating with accession susceptibility (Bonferroni-corrected p < 0.05). In conclusion, we found R-gene independent variation in susceptibility to M. incognita in tomato. This can help to identify genes associated with feeding site formation and loss-of-susceptibility. Furthermore, it opens the possibility to study the role of natural variation on feeding-site establishment.
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