The main utility of ToRuGs will be to construct microarrays to profile transcriptional events defining the root-knot nematode: host interaction. RNA will be harvested from tomato root tissue grown and inoculated in growth pouches (Fig. 5). In a typical experiment, two pools of RNA will be compared using double-dye hybridizations; we are developing non-parametric methods to analyze our array data (Box 1).

Potential experiments will compare:

• healthy vs. infected roots
• infection time course
• M. incognita vs. M. hapla vs. M. javanica, vs. M. arenaria vs. H. glycines etc.
• resistant vs. compatible host

We anticipate identifying new tomato genes involved in nematode parasitism. We hope to place these, and the 197 already identified, into increasingly interconnected regulatory and effector pathways.