For decades, plant scientists have made impressive progress in understanding how fruits like tomatoes and cucumbers get their shapes, but far less is known about how storage organs — tubers and fleshy roots — develop their morphology. Radish offers a uniquely valuable model: unlike potato tubers or beet roots, the radish taproot develops from both the hypocotyl and root tissues, expanding through secondary growth and massive xylem parenchyma proliferation. This distinctive developmental pathway has made radish an ideal system for studying storage organ formation. Yet the genetic architecture underlying its remarkable shape diversity has remained poorly understood. Based on these challenges, there is a pressing need for in-depth investigation into the regulatory mechanisms that govern taproot morphogenesis in root crops.
A team of researchers from the Beijing Academy of Agriculture and Forestry Sciences, China Agricultural University, Guangxi University, and Hebei Normal University of Science and Technology reports (DOI: 10.1093/hr/uhag127) these findings on April 7, 2026, in Horticulture Research. Using a structural variant-based genome-wide association study across 144 radish accessions, the team identified RsOFP2.3 as the major determinant of taproot shape — and uncovered a transposable element insertion that represses its expression.
The study combined population genetics, molecular biology, and functional experiments to dissect the root-shape regulatory network. The researchers found that RsOFP2.3 is highly expressed in cambial tissues — the root's growth engine — and its expression levels strongly correlate with root morphology: higher expression means rounder, wider roots; lower expression means longer, thinner ones. A 312-base-pair transposable element insertion in the promoter region was identified as the key switch that represses RsOFP2.3 expression. When the team overexpressed RsOFP2.3 in transgenic radish plants, the roots became significantly thicker and shorter — the result of enhanced cambial cell division and increased xylem parenchyma proliferation. Conversely, silencing the gene produced the opposite effect: longer, thinner roots. At the protein level, RsOFP2.3 physically interacts with RsTRM4 (a TONNEAU1-recruiting motif protein), pulling it from the microtubule cytoskeleton into the cytoplasm — a relocation that appears to reorient growth from longitudinal to radial expansion. Overexpressing RsTRM4 in Arabidopsis partially reversed the organ-shape defects caused by RsOFP2.3 overexpression, revealing an antagonistic relationship that finely balances lateral and longitudinal growth.
The authors said: “What excites us most is that we've uncovered two coordinated layers of regulation — one at the DNA level, where a transposable element insertion acts as a genetic dimmer switch, and another at the protein level, where RsOFP2.3 and RsTRM4 engage in a tug-of-war that fine-tunes root architecture. This dual mechanism gives us a remarkably clear picture of how nature sculpts root shape, and it opens the door to precise breeding strategies that could transform how we cultivate root vegetables.”
The findings carry significant implications for agriculture and food production. Root shape directly affects harvest efficiency, postharvest handling, processing costs, and consumer appeal. By identifying the TE-mediated regulatory switch and the OFP-TRM protein interaction module, this research provides molecular targets for precision breeding of radish and other storage root crops. Breeders could potentially use gene-editing tools to fine-tune RsOFP2.3 expression, creating varieties with optimized root shapes for different markets — round roots for fresh consumption and processing, longer roots for mechanical harvesting and storage. Moreover, because the OFP-TRM module appears to be conserved across diverse plant species, similar mechanisms may operate in other root crops such as carrot, beet, and sweet potato, offering a broader roadmap for improving storage organ morphology in the world’s most important staple and vegetable crops.
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References
DOI
https://doi.org/10.1093/hr/uhag127
Original Source URL
https://doi.org/10.1093/hr/uhag127
Funding information
Collaborative Innovation Program of the Beijing Vegetable Research Center (XTCX202302); Construction Program of Science and Technology Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences (KJCX202416, KJCX20230126); Beijing Natural Science Foundation (6222015).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.