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

Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article numbere58993
Pages (from-to)1-68
Number of pages68
StatePublished - Sep 2020

Bibliographical note

Funding Information:
Arabidopsis-like TF ortholog was supported by the presence of conserved noncoding sequences

Funding Information:
We thank three anonymous reviewers for their helpful suggestions. This work was supported by

Funding Information:
National Science Foundation grants IOS-1202779 to KG, IOS-1711662 to RCS, IOS-1547796 to


  • Circadian clock
  • Diversification
  • Gene regulatory network
  • Polyploidy
  • Transcriptome

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

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