Award Abstract #0313887
A Rice Oligonucleotide Array

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	September 3, 2003
Latest Amendment Date:	July 30, 2008
Award Number:	0313887
Award Instrument:	Cooperative Agreement
Program Manager:	Diane Jofuku Okamuro DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	October 1, 2003
Expires:	September 30, 2008 (Estimated)
Awarded Amount to Date:	$4489779
Investigator(s):	Pamela Ronald pcronald@ucdavis.edu (Principal Investigator) David Rocke (Co-Principal Investigator)
Sponsor:	University of California-Davis OR/Sponsored Programs Davis, CA 95618 530/747-3838
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT,9109,7462,1074
Program Element Code(s):	1329

ABSTRACT

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, we will:

1) Design 40,000 70-mer oligomers and construct microarrays for project use and public distribution.

2) Construct a data analysis system, database and user interface for project data. Develop web-based tools for data mining the rice transcriptome.

3) Train the user community in the use of arrays.

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.

Deliverables

In years one and two, 15000-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 at http://www.tigr.org.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

(Showing: 1 - 4 of 4).

1. Jung KH, An G and Ronald P..  "Towards a better bowl of rice: Assigning function to thousands of rice genes.,"  Nature Genetics Review. 2008,  v.9,  2008, 

Chou,HH, AP Hsia, D Mooney, PS Schnable.  "PICKY: an oligo microarray design tool for large genomes,"  Bioinformatics,  v.20,  2004,  p. 2893.

Rocke, DM.  "Design and Analysis of Experiments with High Throughput Biological Assay Data,"  Seminars in Cell and Developmental Biology,  v.15,  2004,  p. 708.

Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik.  "Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PX099A,"  BMC Genomics,  v.9,  2008,  p. 204.


(Showing: 1 - 4 of 4).

Please report errors in award information by writing to: awardsearch@nsf.gov.