PI: Susan r. McCouch (Cornell University-State) CO-PIs: Carlos D. Bustamante (Cornell University), Georgia C. Eizenga (University of Arkansas/ARS), Anna M. McClung (Texas A&M University)

Rice (Oryza sativa) is a complex species consisting of at least five, genetically distinguishable sub-populations that inhabit diverse ecological and geographic zones throughout Asia. Evidence to date suggests that these groups are indicative of general combining ability, similar to the heterotic groups of maize.

This project is designed to test the hypothesis that sub-population structure in rice is predictive of transgressive variation and to begin to characterize the underlying genetic basis of this phenomenon. To do this, the Investigators will 1) document the genome-wide differences in allelic variation within and between the different subpopulations of O. sativa and O. rufipogon using a high resolution SNP assay, 2) undertake association mapping in rice using phenotypic evaluations for 26 core agronomic and grain quality traits, 3) systematically develop genetic materials that will allow us to explore the relationship between diversity and transgressive variation that occurs when subpopulations are crossed and 4) establish a dataset for rice that can be compared with that of the maize diversity project and ultimately with other cereal species. As part of a targeted educational outreach effort, the Investigators will conduct hands-on genomics exercises in local high schools, host high school and undergraduate students as summer interns with an emphasis on broadening participation of underrepresented groups, and will develop a multi-media video presentation exploring the culture of rice in America and in Africa to be shared with K-8th graders.

A better understanding of the genetic basis of transgressive variation in inbred crop species will have an immediate impact on the global research agenda for crop improvement. Presently, there is a great deal of interest in breeding hybrid rice as a mechanism for delivering superior varieties to farmers. But without a sound scientific understanding of the genetic mechanisms that underlie superior performance in naturally inbreeding species, some of the most promising opportunities to capture superior performance in the world's inbred crop varieties may be overlooked. The knowledge to be gained from this project will help inform thinking about how to best characterize and manage Oryza gene pools and about the relative investments that we, as a society, choose to make in developing inbred and/or hybrid varieties of our most important food staples. The genetic stocks produced as part of the project will augment the collection available through the Genetic Stocks-Oryza (GSOR) located at the Dale Bumpers National Rice Research Center (DBNRRC) in Stuttgart, Arkansas and the National Center for Genetic Resources Preservation (NCGRP) facility in Fort Collins, CO. Information on rice diversity will be available over the project web-site, the GRIN database and will be integrated into the Gramene database (www.gramene.org).

Project Report

Asian rice, Oryza sativa, is a cultivated, inbreeding species that feeds over half of the world’s population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving the yield, quality and sustainability of rice grown in the US and around the world. Linking our understanding of how genes control physiological pathways and plant traits will help us translate cutting edge molecular genetics information for use in plant breeding. Over the course of this project we developed new genetic tools and a database of information that are publicly available and can be used as a new research platform for genome wide association studies (GWAS) in rice. This research platform is accelerating the discovery of genes and gene networks underlying complex traits of interest and is facilitating the efficient utilization of diverse sources of natural variation in rice improvement. Among our accomplishments, we 1) developed a set of ~400 diverse varieties of O. sativa collected from 82 countries and made the seeds publicly available through the Genetic Stocks Oryza (GSOR) in Stuttgart, AR and the International Rice Germplasm Center at the International Rice Research Institute (IRRI) in Los Baños, Philippines; 2) evaluated this diversity panel with 44,100 SNP markers across the rice genome to identify genetic variants; 3) characterized the varieties for 37 agronomic, morphological, physiological, and grain quality traits in collaboration with the University of Arkansas in Stuttgart, AR, the Robert Holley Center at Cornell University in Ithaca, NY, and colleagues in the UK and Bangladesh; 4) conducted a genome wide association study (GWAS) and determined that different networks of genes regulate complex traits in each of five known rice subpopulations; 5) developed a set of chromosome segment substitution lines (CSSLs) to systematically explore the breeding value of incorporating genes from wild related species of rice and exotic cultivars into two widely used rice cultivars. Through this project, we have gained a deeper understanding of the breadth and depth of genotypic and phenotypic (trait) variation within the rice gene pool. Evidence to date suggests that there are several deeply diverged subpopulations in rice (O. sativa) and its progenitor, O. rufipogon. Knowledge about the interrelationship of rice varieties from around the world can be used to predict which crosses are likely to generate superior offspring, particularly those that show transgressive variation and will outperform the better parent. The ability to efficiently generate positive transgressive variation is key to making rapid genetic gain in the development of new varieties. This project is empowering the global rice research community to translate knowledge about genotype-phenotype relationships into practical applications for plant improvement, and to more efficiently utilize the enormous wealth of natural diversity available in rice germplasm repositories around the world. Educational outreach activities on the project provided diverse opportunities for interdisciplinary, hands-on learning for K-12, undergraduate, graduate and postdoctoral fellows with emphasis on groups that are currently under-represented in science. In addition to classroom learning, we developed a 3-week Rice: Research to Production field-course in collaboration with IRRI that brings students and researchers together from USA, Asia, Africa and Latin America to learn first hand how rice is produced in the Philippines and how genetic tools will be critical for solving rice production problems around the world.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Jofuku Okamuro
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Cornell Univ - State: Awds Made Prior May 2010
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