BRIEF RESEARCH REPORT article
Front. Genome Ed.
Sec. Genome Editing in Plants
Volume 7 - 2025 | doi: 10.3389/fgeed.2025.1645542
Development of a homeolog-specific gene editing system in an evolutionary model for the study of polyploidy in nature
Provisionally accepted
Shengchen Shan1*
Michael T. Pisias2
Evgeny V. Mavrodiev1
Jonathan P. Spoelhof1
Bernard A. Hauser3
William Brad Barbazuk3
Pamela S. Soltis1,4,5
Douglas E. Soltis1,3,4,5
Bing Yang2,6- 1Florida Museum of Natural History, Gainesville, United States
- 2University of Missouri, Columbia, United States
- 3University of Florida Department of Biology, Gainesville, United States
- 4University of Florida Biodiversity Institute, Gainesville, United States
- 5University of Florida Genetics Institute, Gainesville, United States
- 6Donald Danforth Plant Science Center, St. Louis, United States
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Polyploidy, or whole-genome duplication (WGD), is a significant evolutionary force. Following allopolyploidy, duplicate gene copies (homeologs) have divergent evolutionary trajectories: some genes are preferentially retained in duplicate, while others tend to revert to single-copy status. Examining the effect of homeolog loss (i.e., changes in gene dosage) on associated phenotypes is essential for unraveling the genetic mechanisms underlying polyploid genome evolution. However, homeolog-specific editing has been demonstrated in only a few crop species and remains unexplored beyond agricultural applications. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy in nature. In this study, we developed a CRISPR-mediated homeolog-specific editing platform in allotetraploid T. mirus. Using the MYB10 and DFR genes as examples, we successfully knocked out the targeted homeolog in T. mirus (4x) without editing the other homeolog (i.e., no off-target events). The editing efficiencies, defined as the percentage of plants with at least one allele of the targeted homeolog modified, were 35.7% and 45.5% for MYB10 and DFR, respectively. Biallelic modification of the targeted homeolog occurred in the T0 generation. These results demonstrate the robustness of homeolog-specific editing in polyploid Tragopogon, laying the foundation for future studies of genome evolution following WGD in nature.
Keywords: CRISPR, evolutionary model, genome evolution, homeolog-specific editing, Polyploidy, Tragopogon
Received: 11 Jun 2025; Accepted: 04 Aug 2025.
Copyright: © 2025 Shan, Pisias, Mavrodiev, Spoelhof, Hauser, Barbazuk, Soltis, Soltis and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Shengchen Shan, Florida Museum of Natural History, Gainesville, United States
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