The Rice Diversity Project (NSF #0606461)
Title: Exploring the genetic basis of transgressive variation in rice

Summary of Scientific Objectives: Evidence to date suggests that the natural subpopulations in rice (Oryza sativa) and its progenitor, O. rufipogon are indicative of general combining ability, similar to the heterotic groups of maize. If true, this hypothesis has immediate implications for applied rice improvement and also offers insight into a fundamental problem in basic biology. We propose to test the hypothesis that sub-population structure in rice is predictive of transgressive variation (the occurrence of progeny displaying phenotypes more extreme than either parent) and to begin to characterize the underlying genetic basis of this phenomenon. To do this, we will:

1. Develop a 10,000 SNP chip for rice and create a haplotype map (ricehapmap) to document the differences in allelic variation within and between the different subpopulations of O. sativa and O. rufipogon
2. Evaluate 26 core agronomic and grain quality traits in replicated field trials to provide the basis for association mapping
3. Develop libraries of chromosome segment substitution lines (CSSLs) along with high-resolution near isogenic lines (NILs) to explore the relationship between diversity and transgressive variation that occurs when sub-populations are crossed
4. Augment the collection of genetic resources for rice and make them available through the Genetic Stocks-Oryza (GSOR) at the Dale Bumpers National Rice Research Center (DBNRRC) in Stuttgart, Arkansas
5. Establish a dataset on rice diversity to help identify and characterize the genes and gene networks underlying a wide range of agriculturally valuable phenotypes in the cereals.

Broader Impacts: 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, we may overlook some of the most promising opportunities to capture superior performance in the world’s inbred crop varieties. The knowledge we gain from this project will help inform our 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 d eveloping inbred and/or hybrid varieties of our most important food staples.

We will work closely with the GRIN and Gramene databases to ensure public availability of data and to enhance its comparative potential for the cereals community. As part of a targeted educational outreach effort, we 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.