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Cited by 140Circadian rhythm and melatoninPlant Molecular Biology ResearchLight effects on plants

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Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

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Kerwin, Rachel E., Jimenez-Gomez, Jose M., Fulop, Daniel, Harmer, Stacey L., Maloof, Julin N., Kliebenstein, Daniel J.·2011·The Plant Cell
DOI 10.1105/tpc.110.082065PMC PMC3077772
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Abstract

Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. We developed a genomic quantitative genetic approach to overcome this problem, allowing us to examine the function(s) of the plant circadian clock in different populations derived from natural accessions. Using existing microarray data, we defined 24 circadian time phase groups (i.e., groups of genes with peak phases of expression at particular times of day). These groups were used to examine natural variation in circadian clock function using existing single time point microarray experiments from a recombinant inbred line population. We identified naturally variable loci that altered circadian clock outputs and linked these circadian quantitative trait loci to preexisting metabolomics quantitative trait loci, thereby identifying possible links between clock function and metabolism. Using single-gene isogenic lines, we found that circadian clock output was altered by natural variation in Arabidopsis thaliana secondary metabolism. Specifically, genetic manipulation of a secondary metabolic enzyme led to altered free-running rhythms. This represents a unique and valuable approach to the study of complex networks using quantitative genetics.

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Metadata

Authors
Kerwin, R. E., Jimenez-Gomez, J. M., Fulop, D., Harmer, S. L., Maloof, J. N., & Kliebenstein, D. J.
Affiliations
  • University of California, Davis (US)
  • Department of Plant Biology, University of California, Davis, California 95616
ORCID
Venue
The Plant Cell
Publisher
Oxford University Press (OUP)
Published
2011-02-01
Volume
23
Issue
2
Pages
471-485
ISSN
  • 1040-4651 (ISSN-L)
  • 1532-298X
DOI
10.1105/tpc.110.082065
PMC
PMC3077772
OpenAlex
W2161545623
Cited by
140
References
1
Citations by year
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FWCI
6.96
Type
journal article
Language
en
Open access
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Locations
  • The Plant Cell (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • HAL (submittedVersion)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Max Planck Digital Library (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • National Science Foundation
  • National Institutes of Health
  • National Institute of General Medical Sciences (R01 GM06418, R01GM069418)
Topics
  • Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
Keywords
circadian clock, quantitative trait loci, Arabidopsis thaliana, secondary metabolism, natural genetic variation, recombinant inbred lines, free-running rhythm, isogenic lines
MeSH terms
Chromosome Mapping, Epistasis, Genetic, Glucosinolates, Arabidopsis, Gene Expression Regulation, Plant, Oligonucleotide Array Sequence Analysis, Quantitative Trait Loci, Metabolome, Circadian Clocks

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