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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Genomic and Genetic Analysis of the Cereal Circadian System and Crop Production

Location: Plant Gene Expression Center Albany_CA

2010 Annual Report

1a.Objectives (from AD-416)
Objective 1: Define the contribution of the circadian clock to plant osmotic and salt stress responses using Arabidopsis as an initial model system. Objective 2: Characterize the contribution of the circadian clock to transcriptional control networks in cereals, using Oryza sativa as a model. Sub-objective 2.A.: Define the circadian transcriptome of Oryza sativa. Sub-objective 2.B.: Identify cis-regulatory elements upstream of co-expressed circadian genes. Objective 3: Determine the function of maize photoperiodism genes identified as naturally occurring alleles in maize recombinant inbred lines. Objective 4: Assess the feasibility of high-throughput screening of maize seedlings or plants for circadian phenotypes as a prelude to screening large RIL populations for circadian quantitative trait loci (QTL).

1b.Approach (from AD-416)
Maize is an important crop as well as a model organism for other cereals such as sorghum, barley, rice and wheat. Our long term goal is to identify and characterize the activity of maize genes involved in plant production including tolerance to stressful growth conditions and regulation of flowering time. Recent work in model systems demonstrates that the circadian regulation of physiological activities is required for optimal plant growth and for tuning of responses to environmental cues. A comprehensive understanding of the circadian system in cereals is lacking; therefore, this proposal seeks to define the maize circadian system and assess the circadian oscillator’s contribution to important agronomic traits. Known circadian mutants will be tested for their response to salt and osmotic stress. Genes under circadian regulation in cereals will be identified by expression profiling, and this information used to computationally predict regulatory DNA elements that contribute to circadian gene expression. Reverse genetic approaches will evaluate the role of candidate photoperiodism genes in determining the timing of maize flowering. Maize inbreds and recombinant inbred lines will be analyzed for natural variation in overt circadian rhythms. DNA sequences, genes, mutants, and inbred lines identified here provide two types of tools: a better understanding of fundamental processes in environmental responses and targets that can be used to improve crop productivity. Formerly 5335-21000-025-00D (4/08).

3.Progress Report
Objective 1, showed that a protein of unknown function, known as early flowering 3, is a required part of the core machinery that generates circadian rhythms in plants. Established circadian rhythms are necessary for plants to respond to high environmental temperatures. We published these results in PNAS. Under Objective 2, determined the maize genes with expression regulated by the circadian clock. Also, demonstrated circadian clock control of gene expression is integral to maize photosynthesis, carbohydrate metabolism, cell wall synthesis, and phytohormone production. We published these results in BMC Plant Biology. Under Objective 3, identified genes likely to control flowering time in the newly solved genome of the model grass Brachypodium distachyon. These findings were included in a paper by ARS and university scientists published in Nature. Under Objectives 3 and 4, ongoing CRADA delivered five novel maize lines with mutations that may disrupt normal circadian rhythms and, therefore, circadian clock-dependent processes.

1. The plant circadian clock is important for normal plant responses to elevated temperatures. High temperature effects on plant growth were evaluated in circadian clock mutants. Plants adjust their growth in response to light and temperature signals. How plants sense a warmer environment is unknown. Study of mutants without normal circadian rhythms showed these plants could not distinguish between moderate and warm temperatures. These mutants are being used by ARS scientists at Albany, CA to examine the regulatory systems governing growth control in response to temperature signals. This research provides a basic understanding of how plants respond to warmer environments.

Review Publications
Thines, B., Harmon, F.G. 2010. Ambient temperature response establishes ELF3 as a required component of the Arabidopsis core circadian clock. Proceedings of the National Academy of Sciences. 107(7):3257-3262.

Vogel, J.P., Garvin, D.F., Gu, Y.Q., Lazo, G.R., Anderson, O.D., Bragg, J.N., Chingcuanco, D.L., Weng, Y., Belknap, W.R., Thomson, J.G., Dardick, C.D., Baxter, I.R. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.

Khan, S., Rowe, S.C., Harmon, F.G. 2010. Coordination of the maize transcriptome by a conserved circadian clock. Biomed Central (BMC) Plant Biology. 10:126.

Last Modified: 4/17/2014
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