Discovery of novel small compounds that delay flowering in plants
Researchers from Japan investigate chemicals that can control the timing of flowering, aiming to enhance crop yield and resilience
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Arabidopsis seedlings express a reporter of the flowering repressor, FLOWERING LOCUS C (FLC). FLC, seen in blue here, is strongly expressed in vascular tissues
view moreCredit: Makoto Shirakawa
Ikoma, Japan—In an era where climate change threatens food security, scientists worldwide are searching for reliable ways to improve crop production. Extreme weather and shifting seasonal patterns can disrupt traditional agricultural cycles, making technologies that regulate the timing of plant growth invaluable for farmers worldwide.
Plant growth and development are dependent on many factors such as the environment, photoperiod, and genetics. Flowering is an important event in a plant’s life cycle, and in many species, a period of cold exposure (or vernalization) is required before flowering in the spring. Once flowering begins, plants redirect nutrients from their leaves to seed production, reducing the nutritional value of leafy crops. While scientists understand many aspects of this process, mechanisms that can naturally pause or reverse this phase of preparation for flowering (devernalization) remain largely unexplored.
Against this backdrop, a research team led by Assistant Professor Makoto Shirakawa of Nara Institute of Science and Technology (NAIST), Japan, has been investigating the molecular basis of devernalization. They identified a new class of small molecules called devernalizers (DVRs), capable of inducing devernalization without the requirement of heat treatment in the model organism Arabidopsis thaliana. Their findings were published in Volume 8 of Communications Biology on January 22, 2025. This work was co-authored by Nana Otsuka, Ryoya Yamaguchi, Hikaru Sawa, Nobutoshi Yamaguchi, and Toshiro Ito from NAIST; Naoya Kadofusa, Nanako Kato, and Ayato Sato from Nagoya University; and Yasuyuki Nomura and Atsushi J. Nagano from Ryukoku University.
The researchers screened over 16,000 chemical compounds and discovered five DVRs that reactivated the expression of the FLOWERING LOCUS C gene, a key suppressor of flowering. By minimizing specific dynamic modifications to the plant’s genes, these DVRs could delay flowering even after induced vernalization. Notably, three of these DVRs shared two critical structural features—a hydantoin-like region and a spiro-like carbon—which were found to be essential for the devernalizing effect.
Furthermore, the team identified a sixth DVR compound—named DVR06—which was structurally simpler yet retained the above-mentioned key features. Experimental results showed that plants treated with DVR06 exhibited delayed flowering without adverse side effects. A genome-wide analysis revealed that DVR06 affected a more specific set of genes compared to heat-induced devernalization, highlighting its potential for flowering regulation. “It was well known that applying heat treatment to plants in the field is both labor-intensive and costly. So, I was really excited when we found out that DVR06 had a more specific effect than heat treatment. This was the moment when all the time we had spent on screening finally paid off!” shares Shirakawa.
The discovery of DVR06 and its mechanisms could pave the way for new agricultural technologies that allow farmers to effectively regulate flowering times. By delaying flowering, leafy crops may maintain their nutritional quality for longer periods, increasing yields and reducing wastage. The research team aims to improve the efficacy of DVRs, as Ito remarks: “We will conduct further research to change the structure of DVRs to develop compounds with greater activity and specificity. We expect the results of these studies to lead to the development of new technologies for stable food production under a fluctuating global environment.”
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Resource
Title: Small molecules and heat treatments reverse vernalization via epigenetic modification in Arabidopsis
Authors: Nana Otsuka, Ryoya Yamaguchi, Hikaru Sawa, Naoya Kadofusa, Nanako Kato, Yasuyuki Nomura, Nobutoshi Yamaguchi, Atsushi J. Nagano, Ayato Sato, Makoto Shirakawa, and Toshiro Ito
Journal : Communications Biology
DOI: 10.1038/s42003-025-07553-7
Information about the Plant Stem Cell Regulation and Floral Patterning Laboratory can be found at the following website: https://bsw3.naist.jp/ito/
About Nara Institute of Science and Technology (NAIST)
Established in 1991, Nara Institute of Science and Technology (NAIST) is a national university located in Kansai Science City, Japan. In 2018, NAIST underwent an organizational transformation to promote and continue interdisciplinary research in the fields of biological sciences, materials science, and information science. Known as one of the most prestigious research institutions in Japan, NAIST lays a strong emphasis on integrated research and collaborative co-creation with diverse stakeholders. NAIST envisions conducting cutting-edge research in frontier areas and training students to become tomorrow's leaders in science and technology.
Journal
Communications Biology
Method of Research
Experimental study
Article Title
Small molecules and heat treatments reverse vernalization via epigenetic modification in Arabidopsis
Genetic defense breakthrough: plants repurpose stomatal genes to fend off herbivores
Researchers uncovered the evolutionary process behind cruciferous plants’ pungent defense mechanism
Nara Institute of Science and Technology
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WASABI MAKER is strongly expressed at nuclei of idioblast myosin cells in leaf inner tissues (green). Cell walls are stained by SR2200 (magenta).
view moreCredit: Makoto Shirakawa
Ikoma, Japan—Throughout evolution, plants have continuously adapted to survive in changing environments. Apart from complex structural changes, plants have also developed various defense strategies against herbivores, including tougher protective layers, thorns, and chemical deterrents. Delving deeper into the evolution of defense mechanisms, a research team led by Assistant Professor Makoto Shirakawa from Nara Institute of Science and Technology (NAIST), identified a surprising genetic adaptation in the Brassicales plant order. In these cruciferous plants—including cabbage, mustard, and wasabi—genes originally used for gas exchange have been repurposed for defense.
The researchers uncovered the unique mechanism behind this evolutionary adaptation. Their findings were published online on February 24, 2025 and published in Volume 11 of the journal Nature Plants on March 01, 2025. The research team included Tomoki Oguro, Nobutoshi Yamaguchi, and Toshiro Ito from NAIST; Shigeo S. Sugano from National Institute of Advanced Industrial Science and Technology; Shohei Yamaoka and Takayuki Kohchi from Kyoto University; Yasunori Ichihashi from RIKEN Institute; Atsushi Takemiya from Yamaguchi University; and Takamasa Suzuki from Chubu University.
According to the study, FAMA, a protein primarily responsible for regulating gene expression for gas exchange, serves a dual role for the cruciferous plants. Beyond controlling stomatal (tiny pores for gas exchange) guard cells, FAMA also helps to produce myrosin cells—the specialized structures that store mustard oil compounds. So, when a plant is damaged, these compounds create a sharp, pungent taste that repels herbivores.
“We identified a specific gene called WASABI MAKER (WSB), which is directly activated by FAMA and is the key trigger for the development of myrosin cells,” shares Dr. Shirakawa. “When we studied the plants without WSB, we found that these defense cells failed to form, confirming its essential role in myrosin cell production.”
Additionally, the researchers identified another gene called STOMATAL CARPENTER 1 (SCAP1), which is also a target for FAMA. This gene collaborates with WSB in regulating guard cell development, but its role in myrosin cell formation appears to be secondary.
Evolutionary analysis suggests that these genetic pathways originally helped regulate stomatal development but were later repurposed for defense in Brassicales. “This discovery is particularly interesting because it highlights how gene repurposing allows plants to develop new survival strategies without evolving entirely new genes,” adds co-author Toshiro Ito.
This remarkable discovery offers promising avenues for improving crop yield. Modifying key genetic regulators like FAMA could help enhance the chemical defense in crops and vegetables, avoiding pest damage. Additionally, since FAMA also controls gas exchange, it can be optimized for efficient uptake of carbon dioxide in plants.
Moving forward, the researchers aim to uncover the mechanism of how plants have evolved to produce such a diverse range of specialized cells. Highlighting the significance of their research, Dr. Shirakawa concludes, “Beyond offering new insights for crop improvement strategies, we believe our future work will help answer one of biology’s most fundamental questions: How have plants achieved such remarkable diversity with a limited number of genes?”
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Resource
Title: Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales
Authors: Makoto Shirakawa, Tomoki Oguro, Shigeo S. Sugano, Shohei Yamaoka, Mayu Sagara, Mai Tanida, Kyoko Sunuma, Takuya Iwami, Tatsuyoshi Nakanishi, Keita Horiuchi, Kie Kumaishi, Soma Yoshida, Mutsumi Watanabe, Takayuki Tohge, Takamasa Suzuki, Yasunori Ichihashi, Atsushi Takemiya, Nobutoshi Yamaguchi, Takayuki Kohchi, and Toshiro Ito
Journal: Nature plants
DOI: 10.1038/s41477-025-01921-1
Information about the Plant Stem Cell Regulation and Floral Patterning Laboratory can be found at the following website: https://bsw3.naist.jp/ito/
About Professor Makoto Shirakawa from Nara Institute of Science and Technology, Japan
Dr. Makoto Shirakawa is an Assistant Professor at Nara Institute of Science and Technology (NAIST) in Ikoma, Japan. He earned his PhD from Kyoto University, Japan, and specializes in plant biology, molecular biology, cell biology, genome editing, and botany. His key research includes CRISPR/Cas9 applications in Marchantia polymorpha, studies on Arabidopsis thaliana, and plant development. For his remarkable contributions, he is recognized among Japan's top scientists in plant cell and developmental biology.
About Nara Institute of Science and Technology (NAIST)
Established in 1991, Nara Institute of Science and Technology (NAIST) is a national university located in Kansai Science City, Japan. In 2018, NAIST underwent an organizational transformation to promote and continue interdisciplinary research in the fields of biological sciences, materials science, and information science. Known as one of the most prestigious research institutions in Japan, NAIST lays a strong emphasis on integrated research and collaborative co-creation with diverse stakeholders. NAIST envisions conducting cutting-edge research in frontier areas and training students to become tomorrow's leaders in science and technology.
Website: https://www.naist.jp/en/
Journal
Nature Plants
Method of Research
Experimental study
Article Title
Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales
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