US NSF - National Science Foundation

Page Content   Awards Links   Site Navigation Bar   Advanced Search Form

Award Abstract #0923752

Agroecological Annotation of Gene Function and Computational Analysis of Gene Networks

NSF Org: IOS Division Of Integrative Organismal Sys

divider line
Initial Amendment Date: June 10, 2010
divider line
Latest Amendment Date: August 2, 2013
divider line
Award Number: 0923752
divider line
Award Instrument: Continuing grant
divider line
Program Manager: Diane Jofuku Okamuro
IOS Division Of Integrative Organismal Sys
BIO Direct For Biological Sciences
divider line
Start Date: June 15, 2010
divider line
End Date: May 31, 2016 (Estimated)
divider line
Awarded Amount to Date: $5,652,782.00
divider line
Investigator(s): Cynthia Weinig (Principal Investigator)
C. Robertson McClung (Co-Principal Investigator)
Stephen Welch (Co-Principal Investigator)
Sanjoy Das (Co-Principal Investigator)
Julin Maloof (Co-Principal Investigator)

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


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 ( SRA and GEO databases.


Note:  When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

(Showing: 1 - 10 of 11)
(Showing: 1 - 11 of 11)
Show All

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.

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. doiID

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. doiID

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. doiID

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

C. R. McClung. "Beyond Arabidopsis: The circadian clock in non-model plant species.," Seminars in Cell and Developmental Biology, v.24, 2013, p. 111-222.

Dechaine, J. M., M. T. Brock, L. Iniguez-Luy, and C. Weinig. "Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa," New Phytologist, v.NA, 2013, p. NA. doiID

Dechaine, J.M., M.T. Brock, and C. Weinig. "QTL architecture of reproductive fitness in Brassica rapa," BMC Plant Biology, v.NA, 2014, p. NA. doiID

McClung, CR. "Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock," F1000Prime Rep, v.6, 2014, p. 2. doiID

Rosas, U., Mei, Y., Xie, Q., Banta, J., Zhou, R.W., Seufferheld, G., Gerard-Martinez, S., Chou, L., Bhambhra, N., Flowers, J., McClung, C.R., Hanzawa, Y., Purugganan, M.D.. "Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS," Nature Communications, v.5, 2014, p. 3561. doiID

Weinig, C., B.E. Ewers, and S.M. Welch. "Ecological genomics and process modeling of local adaptation to climate," Current Opinion in Plant Biology, 2014. doiID
(Showing: 1 - 10 of 11)
(Showing: 1 - 11 of 11)
Show All

Please report errors in award information by writing to:

Back to Top of page

FUNDING   AWARDS   DISCOVERIES   NEWS   PUBLICATIONS   STATISTICS   ABOUT NSF   FASTLANE  |  |  National Science Board  |  Recovery Act  |  Budget and Performance  |  Annual Financial Report

Web Policies and Important Links  |  Privacy  |  FOIA  |  NO FEAR Act  |  Inspector General  |  Webmaster Contact  |  Site Map

National Science Foundation Logo

The National Science Foundation, 4201 Wilson Boulevard, Arlington, Virginia 22230, USA
Tel: (703) 292-5111, FIRS: (800) 877-8339 | TDD: (800) 281-8749

Text Only Version


Awards Links

Assistive Options

Top of page

Assistive Options

Open the original version of this page.

Usablenet Assistive is a Usablenet product. Usablenet Assistive Main Page.