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.
- Kathleen Greenham
- Ryan C Sartor
- C Robertson McClung
- C Robertson McClung
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Christian S Hardtke, University of Lausanne, Switzerland
- Received: May 15, 2020
- Accepted: September 29, 2020
- Accepted Manuscript published: September 30, 2020 (version 1)
© 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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