TRTech-PGR: Establishment of a community resource for analysis of gene phenotype in a tractable rice variety

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This project will result in a community resource for analysis of gene function in rice, a staple food crop. The fully sequence-indexed mutant collection will provide researchers an 80% probability of identifying a obtaining a rice line with a mutation in their gene of interest. The mutant and associated data will be made publicly accessible via KitBase and public repositories. Public availability and distribution of these tools will enable researchers to advance characterization of genes controlling diverse biological processes rapidly. The proposed genetic resource is expected to facilitate research significantly in rice as well as in other cereal crops and will set the stage for functional genomics analysis of diverse traits in other staple food crops. Graduate students, postdoctoral fellows, visiting scholars, and faculty will receive online tutorials in sequence data analysis, rice growth and genetic techniques, and assays to identify the mutation corresponding to the gene of interest. Sequence-indexed plant mutant collections have significantly facilitated plant and animal biology research, especially in model organisms, e.g., Arabidopsis thaliana. Such a collection is particularly important for rice, which is a globally important staple food crop, and which also serves as a model for other monocotyledonous species. The Ronald laboratory and collaborators created a publicly available, fully sequenced mutant collection in the model, genetically tractable, Japonica rice variety KitaakeX. KitaakeX has a short life cycle (9-10 weeks), approaching that of Arabidopsis. This proposal takes advantage of an established, fast-neutron-mutagenized mutant population generated KitaakeX. Compared to insertional mutagenesis that requires thousands of transformations, fast-neutron irradiation-induced mutagenesis does not require transformation and regeneration, saving labor and time. The aim of the proposed project is to further characterize and distribute the KitaakeX mutant population, providing researchers rice lines with mutations in their genes of interest. In collaboration with the Joint Genome Institute (JGI), the Ronald laboratory has sequenced 3200 mutant lines. In-depth characterization of the first set of 1504 mutant lines reveals a total of 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes, with mutations evenly distributed across the genome. The proposed project will characterize the genetic mutations in 3200 mutant lines and make key data via an optimized database, KitBase. The seeds will be made available upon request.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.