Milestone achievements in crop research now enable difficult challenges to be addressed rapidly and effectively using innovative approaches. These achievements include DNA sequences and measurements of traits relevant to productivity and quality for large numbers of varieties within individual crop species, powerful computational approaches and data management tools, increasingly detailed molecular understanding of plant biology including responses to the environment, and new methods to precisely test the function of particular DNA sequences. Building on these resources and tools, this project will address the longstanding challenge of identifying DNA sequences responsible for traits that vary in a quantitative way, called "quantitative trait loci" (QTL), and making them amenable for crop improvement. While QTL are key determinants of crop productivity, they have been exceedingly difficult to study, and very little is known about them. This project focuses on QTL for disease resistance, disease susceptibility, and tolerance to acid soils in the globally important crop species, rice. The project will isolate DNA sequences associated with high levels of these traits and test whether those sequences are responsible by moving them into rice varieties that show low trait levels and measuring the result. The project will improve understanding of crop resistance to stresses caused by pests and poor soil conditions and lead to improved crop productivity. More broadly, the project will establish effective ways to connect variation across individuals with the DNA sequences that cause that variation, which will be useful not only for plant research, but other life sciences, including medicine. The project will further benefit society by integrating its research objectives with educational activities and materials that will engage and inform the public and increase participation by members of underrepresented groups. These include a combined classroom and research experience program for small-college undergraduates, training workshops for plant biologists, multi-media educational resources to engage middle and high school students, and a project web site (www.ricediversity.org) for public access to project-related materials, publications, and data. Moreover, the project will foster the development of diverse junior personnel into independent scientists
Compilations of genomic and other genotypic as well as phenotypic and associated metadata for large numbers of rice, powerful informatics approaches and data management tools, the unprecedented ability to precisely edit plant genomes to probe gene function, and increasingly detailed molecular understanding of rice responses to biotic and abiotic stresses, together provide a foundation for this project. This project applies large-scale statistical genetics and genome editing technology to examine distinct QTL for disease resistance, disease susceptibility, and acid soil tolerance. Building on genomic and phenotypic data, computational methods, and infrastructure generated under previous NSF awards and elsewhere, including the recently released genome sequences of 3,000 rice accessions, the project will connect genotype to phenotype for each trait, using genome editing to functionally evaluate isolated genetic polymorphism in new genetic backgrounds. Co-variation will also be examined for each trait to test for genetic background effects on allele viability, and in the case of disease susceptibility and resistance, allelic variation in pathogen-targeted genes will be queried for evidence of purifying or positive selection. Findings will be used to expand the tools and the collection of genotypic and phenotypic data associated with the project, and tailor these resources for the community, while improving understanding of and the ability to enhance plant resistance to biotic and abiotic stresses. Under the outreach objectives of the project, the combined classroom and research experience program for small-college undergraduates will integrate computational and molecular biology aspects of the proposed research and include summer internships in the research laboratories at Cornell. The training workshops will focus specifically on genome editing for plant biologists, especially those from underserved and underrepresented groups; the multimedia educational resources will include stories, podcasts, and interactive web modules and will be distributed through major media outlets; the project web site (www.ricediversity.org) for scientists, the general public, and educators will provide access to project-related materials, protocols, publications, and data (data will be released on or before publication of analytical results). Finally, the development of diverse junior personnel into capable, creative, and collaborative independent scientists will be fostered by a multi-institutional, cross-disciplinary research environment.
