Shan Shengchen, Pisias Michael T, Mavrodiev Evgeny V, Spoelhof Jonathan P, Hauser Bernard A, Barbazuk W Brad, Soltis Pamela S, Soltis Douglas E, Yang Bing
Florida Museum of Natural History, University of Florida, Gainesville, FL, United States.
Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.
Front Genome Ed. 2025 Aug 29;7:1645542. doi: 10.3389/fgeed.2025.1645542. eCollection 2025.
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. (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 . Using the and genes as examples, we successfully knocked out the targeted homeolog in (4) 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 and , respectively. Biallelic modification of the targeted homeolog occurred in the T generation. These results demonstrate the robustness of homeolog-specific editing in polyploid , laying the foundation for future studies of genome evolution following WGD in nature.
多倍体，即全基因组复制（WGD），是一种重要的进化驱动力。异源多倍体形成后，重复的基因拷贝（同源基因）具有不同的进化轨迹：一些基因优先以重复形式保留，而另一些则倾向于恢复为单拷贝状态。研究同源基因丢失（即基因剂量变化）对相关表型的影响，对于阐明多倍体基因组进化的遗传机制至关重要。然而，仅在少数作物物种中证明了同源基因特异性编辑，并且在农业应用之外仍未得到探索。菊科（Asteraceae）包含一个用于研究自然界中多倍体直接后果的进化模型系统。在本研究中，我们在异源四倍体中开发了一种CRISPR介导的同源基因特异性编辑平台。以 和 基因为例，我们成功地在 （4）中敲除了靶向同源基因，而未编辑另一个同源基因（即无脱靶事件）。靶向同源基因的编辑效率，定义为至少一个靶向同源基因等位基因被修饰的植物百分比，对于 和 分别为35.7%和45.5%。靶向同源基因的双等位基因修饰发生在T代。这些结果证明了多倍体 中同源基因特异性编辑的稳健性，为未来研究自然界中WGD后的基因组进化奠定了基础。
