Award Abstract #0110140
Functional Analysis of the Sorghum Transcriptome

NSF Org:	IOS Division of Integrative Organismal Systems
Initial Amendment Date:	September 13, 2001
Latest Amendment Date:	April 24, 2006
Award Number:	0110140
Award Instrument:	Continuing grant
Program Manager:	Diane Jofuku Okamuro IOS Division of Integrative Organismal Systems BIO Directorate for Biological Sciences
Start Date:	September 1, 2001
Expires:	November 30, 2006 (Estimated)
Awarded Amount to Date:	$3677642
Investigator(s):	Lee Pratt lpratt@plantbio.uga.edu (Principal Investigator) John Mullet (Co-Principal Investigator) Robert Klein (Co-Principal Investigator) Patricia Klein (Co-Principal Investigator) Marie-Michele Cordonnier-Pratt (Co-Principal Investigator) Alan Gingle (Former Co-Principal Investigator)
Sponsor:	University of Georgia Research Foundation Inc 621-630 GRADUATE STUDIES ATHENS, GA 30602 706/542-5939
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9251, 9109, 1228
Program Element Code(s):	1329

ABSTRACT



Initial NSF PGRP funding has permitted the development of a public sorghum unigene resource that will approach 14,000 members during the coming year. This renewal proposal is designed to augment the size, and thus value, of this resource while simultaneously using it to explore the genomic/genetic/biochemical basis of sorghum's special adaptation to adverse environments. The results of this research effort will reveal potential strategies for improvement of the productivity of not only this, but other, cereals that do not have sorghum's ability to withstand environmental extremes such as drought. Fusion of the differing strengths of two research groups will lead to a synergistic outcome. The University of Georgia (UGA) group has developed substantial expertise in construction of a comprehensive unigene resource and in development and mining of a secure and versatile Oracle-based relational database management system (RDBMS). The Texas A & M University and USDA/ARS group has extensive experience with the experimental system (sorghum), its physiology, genetics, and genome characteristics, and has recently developed a powerful new tool for identifying on a combined physical/genetic sorghum map the location of many of the ESTs that already have been, and will continue to be, developed at UGA.

We propose to increase the sorghum unigene set to ~20,000 members by selective sequencing of 50,000 cDNAs from ~20 new libraries. Libraries will be enriched in full-length cDNAs through a no-cost collaboration with Dr. Sumio Sugano. The UGA RDBMS will be enhanced so that we can mine 5' and 3' UTRs to explore their participation in regulation of genome expression in this monocot. The RDBMS has already been modified to incorporate all returned BLAST data in readily mined tables. We will use this information to investigate as well the potential role of alternative splicing in regulation of genome expression. The unigene set will be maintained and distributed as a public resource, and the UGA web site will be enhanced to make this information available to the scientific community. Data will also be made available to the developing Gramene database resource.

Sorghum genome function will be explored by coordinated microarray experiments designed to permit the construction of a compendium of gene expression profiles. While conducting assays that will answer specific biological questions, we will simultaneously design experimental protocols with this objective in mind. Specific immediate objectives include examination of well-characterized genotypes to explore relationships between genome expression, light perception and flowering time and to characterize pre- and post-flowering responses (drought tolerance) in contrasting genotypes. The UGA RDBMS will be expanded to include all relevant information, not only array data, but also experimental parameters, phenotype, and so on. Microarray experiments will be designed around a common core set of parameters such that variations in abiotic factors within a single genotype or between different genotypes and a standard reference genotype can inasmuch as possible be related always to this core. Such experimental design will permit the development of a true compendium that will be available for extensive mining beginning during this project period, but also extending well beyond it.

Deliverables

1. sorghum ESTs

ESTs are available from GenBank (dbEST) and from http://fungen.botany.uga.edu/Projects/Sorghum/Sorghum.htm

ESTs have been mapped to the rice genome at http://www.gramene.org

2. sorghum unigene set

information about sorghum unigenes is available at http://fungen.botany.uga.edu/Projects/Sorghum/Sorghum.htm

unigenes have been mapped to the rice genome at http://www.gramene.org

3. sorghum cDNA clones

clones are available by directing email to Dr. Marie-Michele Cordonnier-Pratt at mmpratt@uga.edu (full instructions are at http://fungen.botany.uga.edu/Projects/Sorghum/Sorghum.htm

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