1. Genetics and Genomics
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Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

  1. Kathleen Greenham  Is a corresponding author
  2. Ryan C Sartor
  3. Stevan Zorich
  4. Ping Lou
  5. Todd C Mockler
  6. C Robertson McClung  Is a corresponding author
  1. University of Minnesota, United States
  2. North Carolina State University, United States
  3. Dartmouth College, United States
  4. Donald Danforth Plant Science Center, United States
Research Article
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Cite this article as: eLife 2020;9:e58993 doi: 10.7554/eLife.58993

Abstract

An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here, we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three quarters of expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE123654

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Kathleen Greenham

    Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
    For correspondence
    greenham@umn.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7681-5263
  2. Ryan C Sartor

    Crop and Soil Sciences, North Carolina State University, Raleigh, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9621-0824
  3. Stevan Zorich

    Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8717-4211
  4. Ping Lou

    Department of Biological Sciences, Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1084-0671
  5. Todd C Mockler

    Donald Danforth Plant Science Center, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0462-5775
  6. C Robertson McClung

    Biological Sciences, Dartmouth College, Hanover, United States
    For correspondence
    c.robertson.mcclung@dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7875-3614

Funding

National Science Foundation (IOS-1202779)

  • Kathleen Greenham

National Science Foundation (IOS-1711662)

  • Ryan C Sartor

National Science Foundation (IOS-1547796)

  • C Robertson McClung

Rural Development Administration (Next Generation BioGreen 21,grant number SSAC PJ01327306)

  • C Robertson McClung

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Christian S Hardtke, University of Lausanne, Switzerland

Publication history

  1. Received: May 15, 2020
  2. Accepted: September 29, 2020
  3. Accepted Manuscript published: September 30, 2020 (version 1)
  4. Version of Record published: November 10, 2020 (version 2)

Copyright

© 2020, Greenham et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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