• About this Project
• Project Summary
• Significance and Impacts

Significance and Impacts

This project makes use of the wealth of rice genome sequence information to connect genotype and phenotype. We will develop an association mapping platform that will provide new insights into the relationship between genetic and phenotypic diversity, leading to the more efficient utilization of natural variation for crop improvement. By developing a custom, high-resolution rice genotyping array (SNP chip) and using it to genotype a panel of diverse O. sativa and O. rufipogon accessions, we aim to better understand how allelic variation is distributed in cultivated and wild rice. By phenotyping the panel of accessions for morphological, developmental and biochemical variation using controlled vocabularies, we will be able to compare the phenotypic variation in rice with that observed in other plant species.  Such comparisons will facilitate identification of candidate genes and functional polymorphisms associated with these phenotypes.

The project also takes advantage of the unique evolutionary history of the Oryza genus to explore the genetic architecture and combining ability of a series of ancient and highly self-fertile sub-populations that have no parallel in other cultivated grasses. We will construct new genetic resources to provide a set of tools for systematically disrupting these naturally occurring gene complexes, allowing us to explore the genetic basis of transgressive variation that is observed when divergent accessions are crossed. In this context, we will address the following questions:

1. Can we predict the occurrence of transgressive phenotypes based on the particular subpopulations that are mated?
2. Can we identify specific regions of the genome and specific alleles/haplotypes that, when combined, are likely to confer transgressive variation?
3. Can we make predictions about how a specific gene or allele will interact with a given genetic background within the context of a gene network?

Presently, there is a great deal of interest in breeding hybrid rice as a mechanism for delivering superior varieties to farmers. However, without a sound scientific understanding of the genetic mechanisms that underlie heterosis and transgressive variation in naturally inbreeding species like rice, we may overlook some of the most promising opportunities to capture superior performance in the world’s inbred crop plants. 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, make in developing inbred and hybrid varieties of our most important food staples.

To ensure public availability of the data and to enhance its comparative potential for the cereals community, 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 develop multi-media media curricula materials exploring the history and biology of rice in America and in Africa to be shared with middle school students.