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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
Initial Amendment Date: June 10, 2010
Latest Amendment Date: August 2, 2013
Award Number: 0923752
Award Instrument: Continuing grant
Program Manager: Diane Jofuku Okamuro IOS Division Of Integrative Organismal Systems BIO Direct For Biological Sciences
Start Date: June 15, 2010
End Date: May 31, 2016 (Estimated)
Awarded Amount to Date: $5,652,782.00
Investigator(s): Cynthia Weinig cweinig@uwyo.edu (Principal Investigator) C. Robertson McClung (Co-Principal Investigator)Stephen Welch (Co-Principal Investigator)Sanjoy Das (Co-Principal Investigator)Julin Maloof (Co-Principal Investigator)
Sponsor: University of Wyoming 1000 E. University Avenue Laramie, WY 82071-2000 (307)766-5320
NSF Program(s): PLANT GENOME RESEARCH PROJECT
Program Reference Code(s): 9109, 9150, BIOT, SMET, 7577, 9178, 9179
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

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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 duringdiploidization 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. 58-70.  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.  C. R. McClung. "The Genetics of Plant Clocks," Advances in Genetics, v.74, 2011, p. 105-139.  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.  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.  McClung, CR. "Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock," F1000Prime Rep, v.6, 2014, p. 2.  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. 
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. 

Dechaine, J. M., M. T. Brock, and C. Weinig. "QTL architecture of reproductive fitness in Brassica rapa," BMC Plant Biology, v.14, 2014, p. 66. 

Dechaine, J.M., M.T. Brock, and C. Weinig. "Maternal environmental effects of competition influence evolutionary potential in rapeseed (Brassica rapa)," Evolutionary Ecology, v.29, 2015, p. 77.

Gehan, M.A., K. Greenham, T.C. Mockler & C.R. McClung. "Transcriptional networks ? crops, clocks, and abiotic stress," Current Opinion in Plant Biology, v.24, 2015, p. 39. 

Greenham, K., P. Lou, H. Farid, S.E. Remsen & C.R. McClung. "TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation," Plant Methods, v.11, 2015, p. 33. 

Kazunari Nozue, An V Tat, Upendra Kumar Devisetty, Matthew Robinson, Maxwell R Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, Julin N Maloof. "Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling," PLoS Genetics, v.11, 2015, p. e1004953. 

Kerwin, R., J. Feusier, J. Corwin, M. Rubin, C. Lin, A. Muok, B. Larson, B. Li, B. Joseph, M. Francisco, D. Copeland, C. Weinig, and D. J. Kliebenstein. "Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness," eLife, 2015. 

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

Montaigu, A., A. Giakountis, M.J. Rubin, R. Toth, F. Crémer, A. Porri, M. Reymond, C. Weinig and G. Coupland. "Natural diversity in the Diurnal Waveform of GIGANTEA expression impacts on Arabidopsis growth," PNAS, v.NA, 2014, p. NA.

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

Upendra Kumar Devisetty, Michael F Covington, An V Tat, Saradadevi Lekkala, Julin N Maloof. "Polymorphism identification and improved genome annotation of Brassica rapa through deep RNA Sequencing," G3: Genes| Genomes| Genetics, v.4, 2015, p. 2065. 

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. 

Xie, Q., P. Lou, V. Hermand, R. Aman, H.J. Park, D.-J Yun, W.Y. Kim, M.J. Salmela, B.E. Ewers, C. Weinig, S.L. Khan*, D.L.P. Schaible*, & C.R. McClung. "Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa," Proceedings of the National Academy of Sciences USA, v.112, 2015, p. 3829. 

Xie, Q., P. Wang, X. Liu, L. Yuan, L. Wang, Y. Li, H. Xing, L. Zhi, Z. Yue, C. Zhao, C.R. McClung & X. Xu. "LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator," Plant Cell, v.26, 2014, p. 2843. 
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