Agricultural genomics and subterranean plant-plant communications

Agricultural genomics has the potential to dramatically enrich the availability and quality of food supplies worldwide. However, because thousands of different plant species are grown for food, the application of genomics to crop improvement faces issues distinct from those in medical research. The challenge to agricultural plant scientists is to exploit the databases being generated for rice, maize, and Arabidopsis toward the genetic improvement of non-model crop species. The work in our lab illustrates one example of how genomic approaches can be applied to a non-model plant. Our overall goal is to understand how roots of different plants interact and use this information to improve the subterranean performance of crops in relation to weeds. The most obvious manifestation of root-root interactions is haustoria development. Haustoria are parasitic plant-specific organs that invade host plants and rob them of water and nutrients. Parasitic members of the Scrophulariaceae develop haustoria in vitro when exposed to molecules released by host roots. This is a useful phenotype for investigating plant-plant interactions because it is rapid, highly synchronous, and strictly dependent on exogenous haustoria-inducing factors (HIFs). Using a PCR-based subtractive hybridization, we cloned several hundred cDNAs representing transcripts one to two orders of magnitude more abundant in the roots of a parasitic plant after HIF exposure. Putative functions for about 90% of these transcripts could be assigned by searching the public databases. These have been arrayed on nylon filters and interrogated with a variety of probes from different parasitic and nonparasitic plants. Results from these experiments allowed us to identify likely candidate genes for the perception and processing of root signals by neighboring plants.