Genomic Analysis of a Nematode-plant Interaction: A Tool to Study Plant Biology

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Plant-parasitic nematodes reduce annual US agricultural production by more than $5 billion. The most important group are the root-knot nematodes (RKN: Meloidogyne spp.), which are devastating pathogens of food and fiber crops. With the loss of chemical control agents for health and environmental reasons, the economic importance of RKN is increasing world-wide. A prerequisite to developing any new, environmentally-safe and affordable control strategy is a thorough understanding of the biology of the plant-nematode interaction. Recent advances in genomic techniques make this previously intractable host-parasite system amenable to study. Because of the intimate nature of the interaction, and the obvious developmental and physiological perturbations to the host induced by the nematode, understanding the biology of this association will shed new light on basic plant processes. The very broad host range of RKN (excess of 2,000 plant species) implies that this parasite is able to modulate some very fundamental and widely conserved aspect of host biology.RKN hatch in the soil as developmentally-arrested larvae prior to invading a root, where the parasite establishes an intimate relationship with its host. An elaborate permanent feeding site, characterized by the formation in the host of "giant cells" within a gall, is induced by the nematode. Giant cells serve as the obligate nutritive source for the developing nematode, which becomes sedentary. Functional genomic approaches will be applied to analyze this interaction. This approach is feasible because well developed models of the host and parasite (Arabidopsis and C. elegans respectively) have been established, including complete genomic sequences.Suites of nematode and plant genes that define pathways for establishment of the parasitic interaction will be identified, and their expression quantified. Host responses during feeding-site formation, and the biological transitions in the nematode that are coupled to the host (e.g., exit from developmental-arrest at the onset of feeding) are especially interesting. The histology suggests that phyto-hormone levels are altered in infected roots, and expression of Arabidopsis gene sets, with an emphasis on hormone-responsive genes (new members of this class are anticipated to be identified) will be quantified, as well as genes previously identified as being specifically nematode-responsive. This project addresses three general and inter-related scientific questions: 1) how is the host recognized, and how does the parasite couple its biology and development to host cues, 2) what are the parasite-induced changes in the host, and in particular what is the source and role of phyto-hormones, 3) how has parasitism evolved, what has been the role of horizontal gene transfer, and is this reflected in the organization of parasitism genes?A large body of mostly descriptive information exists for RKN and an important goal will be to couple the genomic findings with this biological data. Many features of the RKN-plant interaction (e.g., gall formation) appear canonical for a broad range of host-parasite associations involving diverse organism (including insects), and also represents a tractable model to study aspects of normal plant development, including phyto-hormone biosynthesis/regulation. Better understanding the host-parasite interaction will reveal the linch-pins from which novel nematode-management strategies can be derived. Furthermore, because this research will be performed within a framework of graduate and undergraduate education, it will provide students with significant opportunities for professional development.