Award Abstract #0218166
Potato Functional Genomics: Aplication to Analysis of Growth, Development, Metabolism and Responses to Biotic and Abiotic Stress

NSF Org:	IOS Division of Integrative Organismal Systems
Initial Amendment Date:	September 20, 2002
Latest Amendment Date:	December 13, 2007
Award Number:	0218166
Award Instrument:	Cooperative Agreement
Program Manager:	Diane Jofuku Okamuro IOS Division of Integrative Organismal Systems BIO Directorate for Biological Sciences
Start Date:	October 1, 2002
Expires:	September 30, 2008 (Estimated)
Awarded Amount to Date:	$8368574
Investigator(s):	Barbara Baker bbaker@berkeley.edu (Principal Investigator)
Sponsor:	University of California-Berkeley Sponsored Projects Office BERKELEY, CA 94704 510/642-8109
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9251, 9184, 9109, 7218, 2886, 1228
Program Element Code(s):	1329

ABSTRACT



Award Abstract

As the fourth most important contributor to human calorie consumption, the potato bears an enormous influence worldwide. Its economic significance is evidenced by the large output percentage of potato by the developing world. Thus, the global influence and impact of potato makes it extremely important and relevant to plant biology and genome research. No other crop system currently being subjected to intensive genomic research possesses such a high degree of real-world applicability juxtaposed with biological uniqueness.

This project is focused on furthering the understanding of important features of potato biology: tuber development, disease resistance, heterozygosity, and polyploidy. As potato is highly related to other important Solanaceae species such as tomato, we will incorporate other Solanaceae species into our studies such that comparative analyses can be performed and that we can leverage our potato-based resources for maximal gain.

This project will provide a comprehensive set of resources for genome and transcriptome profiling of disease resistance responses and key developmental traits and pathways. These comprehensive resources include: targeted genome sequence analysis of potato and other Solanaceae genomic regions where numerous resistance (R) genes and general resistance traits have been identified; an evolutionary resource for resistance traits including models and bioinformatic tools for prediction and functional analysis of durable candidate resistance genes. A transcriptome resource will be generated by microarray analysis of Solanaceae development, and response to abiotic and biotic stress. We will extend the use of these arrays outside the project by soliciting proposals focused on additional physiological conditions from the Solanaceae community. All data will be made public in a rapid fashion to allow the entire Solanaceae community access to the data. This database will provide the first comprehensive resource for gene expression patterns in the Solanaceae family.

We will extend our knowledge of plant genomics to the community through an outreach program that will include a training program for high school and college students and instructors in plant genomics including bioinformatics and data mining for marker development for tracing the origin of Native American potato varieties and for studies on potato evolution and breeding for crop improvement.

Solanacae gardens and associated public educational programs on plant genetic diversity, plant breeding and the impact of plant genome research on society. We will also have

Each of these components, in conjunction with the overarching project objectives, will lead to a comprehensive understanding and working knowledge of potato, one of the most important dicot foods in the world.

Deliverables:

Public Solanaceae dataset of annotated R gene region sequence, R genes and R gene candidates (SOLAR)

Conatcts: Baker, Buell, Brown, Jahn, Jiang, May, Bradeen, Helgeson, Austin-Phillips

Public predictive bioinformatic tools to identify candidate resistance traits for functional testing of resistance genes

Contact: May

Public functional genomic Solanaceae resource, Solanaceae Gene Expression Database, of expression profiles

Contacts: Buell, Baker, Jiang

Gene expression profiling of Solanaceae through external collaborations with the plant community

Contact: Buell

Functional identification of genes operating in pathogen defense pathways using silencing

Contact: Baker

Genomics training program for high school and college students. Community Solanum gardens and public information on Solanum

Contacts: Baker, Brown, Buell

Internet Addresses (Web or Email) for Project Information:

1. NSF Potato Genome Project http://www.bakerlab.usda.gov/NSFPotatoGenome/

2. TIGR: NSF Potato Functional Genomics http://www.tigr.org/tdb/potato/

3. Solanaceae Genome Network http://soldb.cit.cornell.edu/index.html

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