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Award Abstract #0923752

Agroecological Annotation of Gene Function and Computational Analysis of Gene Networks

NSF Org:    IOS Division of Integrative Organismal Systems

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Initial Amendment Date:    June 10, 2010   
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Latest Amendment Date:     August 2, 2013    
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Award Number:    0923752   
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Award Instrument:     Continuing grant   
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Program Manager:    Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences   
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Start Date:     June 15, 2010   
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Expires:    May 31, 2015 (Estimated)   
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Awarded Amount to Date:     $5,652,782.00    
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Investigator(s):    Cynthia Weinig cweinig@uwyo.edu (Principal Investigator)
Julin Maloof (Co-Principal Investigator)
Stephen Welch (Co-Principal Investigator)
Sanjoy Das (Co-Principal Investigator)
C. Robertson McClung (Co-Principal Investigator)

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Sponsor:     University of Wyoming
1000 E. University Avenue
Laramie, WY 82071-2000 (307)766-5320    
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NSF Program(s):    PLANT GENOME RESEARCH PROJECT    
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Program Reference Code(s):     7577, 9109, 9150, 9178, 9179, BIOT, SMET    
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Program Element Code(s):    1329    

ABSTRACT

PI: Cynthia Weinig (University of Wyoming)

CoPIs: Sanjoy Das (Kansas State University), Julin N. Maloof (University of California - Davis), C. Robertson McClung (Dartmouth College), Stephen M. Welch (Kansas State University)

Key Collaborators: Doina Carragea and Gerard Kluitenberg (Kansas State University), and Paula X. Kover [University of Manchester (United Kingdom)

The research will examine plant responses to vegetation density, which are commonly referred to as "shade-avoidance" and which greatly affect yield in crop species. Two plant species, Brassica rapa and Arabidopsis thaliana, are used in this research as models for developing computational approaches that will enable both reconstruction of gene networks that regulate density responses and prediction of different traits (such as flowering time, height, and fruit set) from complex genotypes. Data collection will include 1) quantifying the developmental, morphological, and transcriptional responses of experimental genetic material (such as mutants and segregating progeny) to realistic density treatments and controlled manipulations of light quality indicative of high- and low-density; and 2) recording near-plant environmental conditions in the field, including soil and atmospheric variables, and incident spectra at 15-min intervals. Field studies will provide an agroecologically relevant picture of gene function. In modeling, the project will integrate genetic and environmental data to generate a more complete gene network than is possible from mutant or laboratory studies alone. Finally, because yield and other phenotypes serve as model outputs, the computational approaches will enable the prediction of diverse traits from plant genotypes.

The project will 1) develop evolutionary genetics modules to educate teachers on evolutionary theory and basic molecular genetic approaches and 2) provide seed "kits" to be used in age-appropriate, inquiry-based exercises. Approximately 75 teachers will be hosted annually in Wyoming, and this educational outreach should ultimately reach between 60-70% of all biology teachers in the state. As a further outreach component, the computational technology to be used involves a network of computing volunteers. Via the project website, this network provides another venue to distribute educational materials. Finally, long-term, high-sampling-rate time series of incident irradiance spectra are extremely rare but of interest to communities ranging from plant scientists to solar energy researchers. The National Renewable Energy Laboratory will web-deliver the wide-band spectral measurements made as part of this research. DNA sequence and gene expression information will be deposited in the NCBI (http://www.ncbi.nlm.nih.gov/) SRA and GEO databases.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

C. R. McClung. "The Genetics of Plant Clocks," Advances in Genetics, v.74, 2011, p. 105-139.

Brock, M. T., P. X. Kover, and C. Weinig. "Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana," New Phytologist, v.195, 2012, p. 58-70.

Maloof J.N., K. Nozue, M.R. Mumbach, and C.M. Palmer. "LeafJ: an ImageJ plugin for semi-automated leaf shape measurement," Journal of Visualized Experiments, v.21, 2013, p. 71.

P. Lou, J. Wu, F. Cheng, L.G. Cressman, X. Wang, and C. R. McClung. "Preferential retention of circadian clock genes during
diploidization following whole genome triplication in Brassica rapa," Plant Cell, v.24, 2012, p. 2415-2426.

Brock, M. T., P. X. Kover, and C. Weinig. "Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana.," New Phytologist, v.195, 2012, p. 58.

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