Rice has become a model for grasses and cereal because of its small genome size, available genome sequence, and ease of transformation. The structural and functional analysis of rice genes has broad practical implications for the other economically important cereals such as corn and wheat. One approach, microarray analysis, permits biologists to measure the expression levels of thousands of genes in single experiment. Biologically significant information can be extracted from these data computationally, and then used to assign functions to genes, and to identify genetic regulatory networks.
In this project, our lab is in charge of computationally designing 40,000 70-mer oligoarrays using annotated rice gene sequences provided by TIGR. Subsequent manufacturing, testing and distribution of the arrays will be conducted at collaborating labs at ISU and UC Davis. TIGR will also host the project website for public access to the project information.
Public-sector access to microarrays is critical to ensure that the large public investment in rice structural genomics is converted into public scientific and economic benefits. We will deliver a publicly available oligonucleotide microarray that will be useful for analysis of virtually any trait in rice, a repository for rice microarray expression data, and enhanced functional annotation of the rice genome.
In years one and two, 15,000-element arrays will be distributed. In year three, 40,000-element arrays will be distributed. Information about the arrays and where to order them will be available on the project web site, as well as more information on the NSF Rice Oligonucleotide Array Project.
This project is supported by NSF grant 0313887 to lead PI Dr. Pamela Ronald at UC Davis, with a subaward to ISU Co-PIs Drs. Patrick Schnable and Hui-Hsien Chou.