Category Archives: Botany

Researchers Are First in the World to Watch Plants ‘Drink’ Water in Real-time (Botany)

Scientists at the University of Nottingham have become the first in the world to find a way to observe how plant roots take in and circulate water at the cellular level, which could help to identify future drought- and flood-resistant crops.

The inability to monitor water uptake inside roots—without damaging the specimen—has been a key stumbling block for researchers seeking to understand the motion of fluids in living plant cells and tissues.

Study lead, Dr. Kevin Webb from the Optics and Photonics Research Group, explains, “To observe water uptake in living plants without damaging them, we have applied a sensitive, laser-based, optical microscopy technique to see water movement inside living roots non-invasively, which has never been done before.

“Fundamentally, the process by which plants are able to thrive and become productive crops is based on how well it can take up water and how well it can manage that process. Water plays an essential role as a solvent for nutrients, minerals and other biomolecules in plant tissues. We’ve developed a way to allow ourselves to watch that process at the level of single cells. We can not only see the water going up inside the root, but also where and how it travels around.

“Feeding the world’s growing population is already a problem. Climate change is causing huge shifts in the pattern and density of waterfall on the planet which leads to problems growing crops in regions hit by floods or droughts. By selecting plants that are better at coping with stress, the goal is to increase global food productivity by understanding and using plant varieties with the best chances of survival that can be most productive in any given environment, no matter how dry or wet.”

How it works

For the study, water transport measurements were performed on the roots of Arabidopsis thaliana, which is a ‘model plant’ for scientists since they can be easily genetically-engineered to interfere with basic processes like water uptake.

The conversion of high-intensity green light into bio-friendly red wavelengths, within the Titanium:Sapphire laser used in the study. Credit: University of Nottingham

Using a gentle laser, the new imaging technique—based on the Nobel Prize-winning Raman scattering technique—allowed researchers to measure water traveling up through the root system of Arabidopsis at the cellular level, and to run a mathematical model to explain and quantify this.

The researchers used ‘heavy’ water (deuterium oxide, or D2O), which contains an extra neutron in the nucleus of each hydrogen atom. By scanning a laser in a line across the root while the plant drank, it was possible to see the ‘heavy’ water moving past via the root tip.

In Arabidopsis that had been genetically-altered to compromise its water uptake, these measurements—combined with the mathematical model—revealed an important water barrier within the root. This confirmed for the first time that water uptake is restricted within the central tissues of the root, inside of which the water vessels are located.

Co-lead, Malcolm Bennett, Professor of Plant Sciences at the University, said, “This innovative technique is a real game-changer in plant science—enabling researchers to visualize water movement at a cell and second scale within living plant tissues for the very first time. This promises to help us address important questions such as—how do plants ‘sense’ water availability? Answers to this question are vital for designing future crops better adapted to the challenges we face with climate change and altered weather patterns.”

The findings of this Leverhulme Trust-funded study, are published in the journal Nature Communications in a paper titled: “Non-invasive hydrodynamic imaging in plant roots at cellular resolution.”

Future applications

While developing the method, the research initially focused on plant cells, which are about 10 times the size of human cells and therefore more easily observed. The research team is currently porting these same methods to human cells to understand exactly the same kinds of processes at an even smaller scale.

Just as with plants, there are tissues in the human body responsible for handling water, which is crucial to function. Transparent tissues of the eye, for example, can suffer from diseases of fluid handling which include ocular lens cataracts; macular degeneration and glaucoma. In future, the new Raman imaging technique could become a valuable healthcare monitoring and detection tool.

Next steps

The researchers are working towards a commercial path for their hydrodynamic Raman imaging technique, and have just applied for funding with four UK and EU agriculture companies to look at tracers that move from plant leaves to roots to understand both directions of water transport. In parallel, the team is working on portable versions of the technology to allow water transport measurements to be taken into the field by farmers and scientists to monitor water handling in crops growing in challenging local environments.

The research team is currently bidding for a European Research Council Synergy Grant with partners in the EU and UK to take the study of water uptake and drought resistance towards being a new tool to help choose and understand how particular crops can be matched to particular local growth conditions.

Featured image: The conversion of high-intensity green light into bio-friendly red wavelengths, within the Titanium:Sapphire laser used in the study. Credit: University of Nottingham

Reference: Flavius C. Pascut et al, Non-invasive hydrodynamic imaging in plant roots at cellular resolution, Nature Communications (2021). DOI: 10.1038/s41467-021-24913-z

Provided by University of Nottingham

Seeds Of This Plant Can Treat COVID-19 (Botany)

Getting back to nature to trial ways to improve critical care outcomes.

A flowering plant native to North Africa and Western Asia could be utilised in the future treatment of COVID-19 infection.

The seeds of the plant, Nigella Sativa, have been used for centuries as a traditional remedy for multiple medical conditions, including inflammation and infections.  Now, an Australian-first research review article has found it could be used to treat COVID-19.

“There is growing evidence from modelling studies that thymoquinone, an active ingredient of Nigella Sativa, more commonly known as the Fennel Flower, can stick to the COVID- 19 virus spike protein and stop the virus from causing a lung infection.

“It may also block the ‘cytokine’ storm that affects seriously ill patients who are hospitalised with COVID-19,” said Professor Kaneez Fatima Shad, lead author of a recently published comprehensive review article in the prestigious journal, Clinical and Experimental Pharmacology and Physiology.

Thymoquinone has been extensively studied in laboratories, including animal studies. These studies have shown that thymoquinone can moderate our immune system in a good way, by preventing pro-inflammation chemicals such as interleukins from been released.

This gives thymoquinone a potential role as a treatment for allergic conditions such as asthma, eczema, arthritis conditions including rheumatoid and osteoarthritis and even possibly multiple sclerosis.

“The review paper provides insight into a natural product that has been used as a traditional remedy for over thousand years and may be finally receiving the recognition it deserves.”

— Associate Professor Dennis Cordato.

The review paper details the mechanisms of action of Nigella Sativa and thymoquinone and how they are a promising future treatment of COVID-19 infection.   There have been many barriers to the development of Nigella Sativa as a therapeutic agent in large part due to its poor natural gastrointestinal absorption.

“Advances in pharmacological development such as nanotechnology have seen the chance to overcome this barrier to enable for its use as an effective oral medication.

“Furthermore, the drug has recently been successfully given to patients as a nasal spray and topical paste,” said Dr Wissam Soubra, co-author.

Nigella Sativa has been shown to be helpful in treating high blood pressure, high cholesterol and diabetes mellitus. As an anti-inflammatory treatment, Nigella Sativa has also been found to help patients with allergic rhinitis and sinusitis, eczema, osteoarthritis and childhood epilepsy.

Nigella Sativa has also been proven to be effective in a laboratory environment in killing bacteria such as staphylococcus aureus that can cause a range of mild to severe infections if they enter the skin, and viruses including influenza.

“The review paper provides insight into a natural product that has been used as a traditional remedy for over thousand years and may be finally receiving the recognition it deserves,” said Associate Professor Dennis Cordato, co-author.

The study, The role of thymoquinone, a major constituent of Nigella sativa, in the treatment of inflammatory and infectious diseaseswas recently published in the journal Clinical and Experimental Pharmacology and Physiology.

Featured image: Seeds from the Nigella Sativa plant, better known as the Fennel Flower.

Reference: Kaneez Fatima Shad et al, The role of thymoquinone, a major constituent of Nigella sativa, in the treatment of inflammatory and infectious diseases, Clinical and Experimental Pharmacology and Physiology (2021). DOI: 10.1111/1440-1681.13553

Provided by UTS

This Plant Derivative Inhibit SARS-CoV-2 Entry (Botany)

Using a bioactivity-guided chromatographic approach, in addition to mass-spectrometry (MS), Guillermo H. Jimenez-Aleman and colleagues identified the antiviral metabolite as Pheophorbide a (PheoA), a porphyrin chlorophyll derivative very similar to animal antiviral metabolite Protoporphyrin IX, in the bryophyte Marchantia polymorpha. Their study recently appeared in BioRxiv.

To confirm the antiviral potential of PheoA, a commercially available PheoA stock solution was serially diluted and mixed with a virus stock to inoculate Vero E6 and Huh7-ACE2 cells (human hepatoma cells expressing ACE2). They found that PheoA has an extraordinary antiviral activity against SARS-CoV-2 preventing infection of cultured monkey and human cells, without noticeable citotoxicity. Additionally, it has been shown that, PheoA prevents coronavirus entry into the cells by directly targeting the viral particle.

Antiviral spectrum of PheoA against different RNA viruses © Guillermo H. Jimenez-Aleman et al.

They also determined the antiviral spectrum of PheoA on different enveloped and non-enveloped viruses. They showed that, besides SARS-CoV-2, PheoA also displayed a broad-spectrum antiviral activity against enveloped (+)strand RNA viral pathogens such as HCV, West Nile, and other coronaviruses, but not against (-)strand RNA viruses, such as VSV.

Finally, they determined whether the addition of PheoA to remdesivir treatment could result in a synergistic effect on viral infection. They showed that increasing concentrations of PheoA (upto 40nM) improved remdesivir efficacy and viceversa.

“Our results indicate that PheoA displays a remarkable potency and a satisfactory therapeutic index, and suggest that it may be considered as a potential candidate for antiviral therapy against SARS-CoV-2.”

— they concluded.

Featured image: Scheme of Pheophobide a preparation from plant material. KG, Silica gel 60. AcOEt, ethyl acetate. MeOH, methanol. © Guillermo H. Jimenez-Aleman et al.

Reference: Guillermo H Jimenez-Aleman, Victoria Castro, Addis Longdaitsbehere, Marta Gutierrez-Rodriguez, Urtzi Garaigorta, Pablo Gastaminza, Roberto Solano, “SARS-CoV-2 fears green: the chlorophyll catabolite Pheophorbide a is a potent antiviral”, bioRxiv 2021.07.31.454592; doi:

Note for editors of other websites: To reuse this article fully or partially kindly give credit either to our author/editor S. Aman or provide a link of our article

In Plant Cells, A Conserved Mechanism For Perceiving Mechanical Force Resides in Unexpected Location (Botany)

Minuscule tunnels through the cell membrane help cells to perceive and respond to mechanical forces, such as pressure or touch. A new study in the journal Science is among the first to directly investigate what one type of these mechanosensitive ion channels is doing in the tip-growing cells in moss and pollen tubes of flowering plants, and how.

Biologists led by Elizabeth Haswell at Washington University in St. Louis discovered that so-called PIEZO channels are not found along the plasma membrane in plant cells as they are in animal cells.

Instead, they observed that PIEZO channels have retreated into the plant cell, an unexpected discovery. PIEZO channels are found deeper within the cell, in the membranes of vacuoles — the large, intracellular organelles that help to maintain cell turgor and fulfill a number of other roles in the plant cell.

Elizabeth Haswell, front left, leads a laboratory focused on a plant mechanobiology. Also pictured are co-authors on the Science paper, clockwise from Haswell: Josh Coomey, Ivan Radin and Ryan Richardson. (Photo: Whitney Curtis/Washington University)

“PIEZO channels in plants play a dramatic and critical role in regulating the shape of the vacuole and how much membrane there is,” said Haswell, professor of biology in Arts & Sciences and a Howard Hughes Medical Institute-Simons Faculty Scholar.

“This is the first example of PIEZO channels involved in regulating organelle morphology,” she said. “The data we present could lead to new lines of investigation for both plant and animal PIEZO homologs.”

As the name suggests, mechanosensitive ion channels are paths, or tunnels, through cell membranes that respond to mechanical forces. Under certain forces a channel opens, allowing the flow of ions across the membrane.

In humans, PIEZO channels are essential for life; without them, cell development halts. They are recognized for their role in perceiving light touch, shear force and compressive force. Dysfunction in PIEZO channels has been linked to multiple human diseases.

PIEZO channels were first identified in plant genomes in 2010. After a decade of research on animal homologs, this new research shines a spotlight on plant cells and explores how they differ from animal cells. Other research teams have recently shown that PIEZO channels are involved in mechanical sensing in plant roots.

The researchers made their initial discoveries using the tip-growing cells of a somewhat atypical model plant, spreading earthmoss (Physcomitrium patens).

Spreading earthmoss (Photo: Ivan Radin)

But the scientists were able to extend their findings beyond moss to cells from other distantly related plants, including in pollen tubes in a classic model, the flowering plant Arabidopsis thaliana.

Ivan Radin © WUSTL

“Mosses are one of the groups that comprise the bryophytes, which are the second largest land plant lineage,” said Ivan Radin, a research scientist in the Haswell laboratory and first author of the new paper.

“When we can show that the same thing happens both in moss and a flowering plant, as we did here, the most likely conclusion is that the process is ancestral — it’s at least as old as the land plants are,” Radin said, noting that land plants colonized Earth about a half a billion years ago.

Radin became the Haswell laboratory’s de facto moss specialist with coaching from co-author Magdalena Bezanilla, a professor of biological sciences at Dartmouth University. Bezanilla previously worked with Washington University’s Ralph Quatrano, emeritus dean and the Spencer T. Olin Professor Emeritus of Biology, who was an early adopter of moss.

“The more time passes, the more we love it,” Radin said. “Moss proved to be an exceptionally good model.”

As a next step in this research, scientists in the Haswell laboratory are now conducting additional experiments to show how external and internal forces directly affect PIEZO channels in moss cells.

“Plant PIEZO channels are likely to be controlled by membrane tension in plants the same way they are in animals,” Haswell said. The scientists are also exploring the evolution of these channels in algae.

Now they know where PIEZO channels are found in the cell, Haswell and her team are poised to find out what these proteins are doing in the vacuoles.

“We are looking at how PIEZO channel activation results in membrane elaboration and how it is regulated,” Haswell said. “We want to know how the localization evolved and what it does in other cell types. We plan to compare and contrast the structure and function with the animal channels and in organisms across the green lineage.”

Reference: Ivan Radin et al., “Plant PIEZO homologs modulate vacuole morphology during tip growth”, Science  30 Jul 2021: Vol. 373, Issue 6554, pp. 586-590. DOI:

Provided by WUSTL

Duckweed and Amazon Shrub Reveal Potential For Bioenergy Production (Botany)

Duckweed and Senna reticulata, common name mata-pasto (“pasture killer”), plants frequently found in Brazil’s North region, have significant potential for use as raw material to produce bioenergy, according to studies by researchers affiliated with the National Institute of Science and Technology (INCT) for Bioethanol, one of the INCTs supported by FAPESP and the National Council for Scientific and Technological Development (CNPq) in the state of São Paulo.

Laboratory tests show that when biomass from duckweed is submitted to saccharification it produces large amounts of simple sugar than sugarcane, the main raw material currently used to produce second-generation ethanol. S. reticulata grows very fast and could be a viable option for bioelectricity production in the Amazon without causing deforestation, the researchers say in reports on their studies published in Bioenergy Research.

S. reticulata and duckweed could be complementary or alternative to sugarcane for the production of bioenergy,” Marcos Silveira Buckeridge, head of INCT-Bioethanol and principal investigator for the projects, told Agência FAPESP.

The researchers analyzed the composition and biomass saccharification potential of both plants for bioenergy production. The results of their analysis of five species of duckweed (Spirodela polyrhizaLandoltia punctataLemna gibbaWolffiella caudata and Wolffia borealis) show that three monosaccharides – glucose, galactose and xylose – account for 51.4% of the cell wall in this plant.

They also show that duckweed biomass displays low resistance to hydrolysis or saccharification. In this process, lignocellulosic biomass is placed in contact with an enzymatic cocktail to convert the complex sugars present in cell walls into simple sugars that can be fermented by yeast to produce second-generation ethanol.

“Duckweed displays low resistance to hydrolysis, probably because it contains very little lignin,” Buckeridge said. Lignin is a macromolecule that enhances plant tissue rigidity, impermeability and resistance to biological and mechanical attack when it is associated with cell wall hemicellulose and cellulose.

The analysis of S. reticulata showed that almost 50% of the plant’s leaf and stem biomass consisted of pectin, hemicellulose and cellulose. Lignin varied considerably in the plant’s organs. The largest proportions were found in the roots (35%), leaves (10%) and stem (7%).

“When we analyzed the whole biomass of the plant, we found that the leaves contained a huge amount of starch – far more than we’ve ever detected in other plants,” Buckeridge said.

The researchers also evaluated the effect of rising levels of carbon dioxide (CO2) in the atmosphere on biomass composition in S. reticulata. They concluded that the increase in CO2 did not significantly alter the proportion of cell wall lignin, but reduced the proportion of lignin in leaves and roots. It also increased the amount of leaf starch by 31% and improved biomass saccharification by 47%.

“The plant develops very well at high temperatures, so it’s a worthwhile option for producing bioelectricity by burning its biomass, especially in the North of Brazil,” Buckeridge said.

Duckweed is found in all parts of the world. Besides being an option for the production of second-generation ethanol, it can also be used for water cleansing thanks to its lower resistance to hydrolysis than sugarcane. “Another advantage of duckweed compared with other plants that have been studied for bioenergy production is that it doesn’t take up any space on land and hence doesn’t compete with food crops,” Buckeridge said.

The article “Senna reticulata: a viable option for bioenergy production in the Amazonian region” (doi: 10.1007/s12155-020-10176-x) by Adriana Grandis, Bruna C. Arenque-Musa, Marina C. M. Martins, Thais Olivar Maciel, Rachael Simister, Leonardo D. Gómez and Marcos S. Buckeridge can be retrieved by subscribers to Bioenergy Research at:

The article “High saccharification, low lignin, and high sustainability potential make duckweeds adequate as bioenergy feedstocks” (doi: 10.1007/s12155-020-10211-x) by Débora Pagliuso, Adriana Grandis, Eric Lam and Marcos S. Buckeridge can be retrieved by subscribers to the same journal at:

Featured image: Two plants frequently found in the North of Brazil could become alternatives to sugarcane as raw materials for the production of second-generation ethanol and bioelectricity, according to studies by Brazilian researchers (Senna reticulata; photo: Dick Culbert/Wikimedia Commons)

Provided by FAPESP

How ERF1 Regulates Flowering? (Botany)

Floral initiation must be strictly regulated to achieve reproductive success. ETHYLENE RESPONSE FACTOR1 (ERF1) functions as an important integrator of several phytohormone signals to regulate both development and stress responses. However, the underlying mechanism for its role in flowering-time regulation remained unclear. 

In a study published in Journal of Integrative Plant Biology, researchers from the Xishuangbanna Tropical Botanical Garden of the Chinese Academy of Sciences demonstrated that ERF1 played an important role in floral initiation by directly modulating the expression of FLOWERING LOCUS T (FT), a major integrator of inductive flowering pathways. 

The researchers first sought to investigate whether ERF1 also participated in flowering-time regulation. By analyzing flowering time in ERF1 knockdown and overexpression lines, they found that regulation of flowering time in Arabidopsis was closely correlated with ERF1 expression. Consistent with expression of ERF1 being induced by 1-aminocyclopropane-1-carboxylic acid, ERF1 contributed to ethylene-induced late flowering. ERF1 participated in flowering-time regulation under both normal and stressed conditions. 

To understand how ERF1 mediated flowering-time control, the researchers next compared the expression patterns of diverse flowering-related genes among ERF1 RNAi, wild type and expression of ERF1 (ERF1ox) plants. 

They revealed that an ethylene-induced delay in flowering may also be achieved through negative regulation of FT expression by ERF1. The ERF1 acted upstream of FT and negatively regulated floral initiation in a largely FT-dependent manner. ERF1 was also involved in modulation of ethylene-induced late flowering.  

“The molecular mechanisms revealed in this study may help us understand the sophisticated flowering-time regulatory networks controlled by ethylene response factors,” said CHEN Ligang, correspondence author of the study. 

Featured image: Loss of ERF1 function accelerates floral initiation. (Image by CHEN Yanli)

Reference: Chen, Y., Zhang, L., Zhang, H., Chen, L. and Yu, D. (2021), ERF1 delays flowering through direct inhibition of FLOWERING LOCUS T expression in Arabidopsis. J Integr Plant Biol. Accepted Author Manuscript.

Provided by Chinese Academy of Sciences

Researchers Identify A Gene That Regulates The Angle Of Root Growth In Corn (Botany)

The discovery of a gene that regulates the angle of root growth in corn is a new tool to enable the breeding of deeper-rooting crops with enhanced ability to take up nitrogen, according to an international team of researchers, led by Penn State.

The gene, called ZmCIPK15—a moniker indicating where it is located in the genome and how it functions—was found to be missing in a naturally occurring mutant corn line that grows roots at steeper angles that make them go deeper into the soil. They identified the gene using a technique called a genome-wide association study, which involves a painstaking statistical analysis of a genome-wide set of genetic variants in different plant lines to see what genes are associated with a trait.

Identifying a gene that controls the angle of root growth in corn—influencing the depth to which roots forage—is important because deeper roots have a greater ability to capture nitrogen, according to research team leader Jonathan Lynch, distinguished professor of plant science in Penn State’s College of Agricultural Sciences. Corn with an enhanced ability to take up nitrogen has implications for the world’s environment, economy and food security, he noted.

“Corn is the most important crop in the world. In rich countries like the U.S., the biggest energy, economic and environmental cost of growing corn is nitrogen fertilizer,” Lynch said. “And more than half of the nitrogen fertilizer applied to corn is never even taken up. It’s just wasted—washed deeper into the soil where it pollutes groundwater, and some of it goes into the atmosphere as the greenhouse gas, nitrous oxide. It’s a massive problem.”

In contrast, in regions like Africa where people are more dependent on corn for food, soils are nitrogen deficient and farmers can’t afford to buy fertilizer, if it even is available, Lynch added. Corn yields in Africa are just a fraction of what they are in the U.S. Deeper-rooting corn would help poor countries harvest more food with the limited amount of nitrogen that they have.

To find the gene regulating the angle of roots, researchers at Penn State screened nearly 500 lines of corn over four years in South Africa. Field experiments at Penn State’s Russell E. Larson Agricultural Research Center and greenhouse experiments at the University Park campus were conducted to confirm the phenotype of the mutant and wild-type plants and to test the functional utility of changes in root angle for nitrogen capture.

Researchers identify a gene that regulates the angle of root growth in corn
Researchers observed a wide variation in crown root angles in corn, ranging from shallow to steep. They reported that a steeper root growth angle markedly improved nitrogen capture. Credit: Hannah Schneider/Penn StatE

Roots of selected plants were excavated and measured, validating the functional importance of the ZmCIPK15 gene. It caused an approximate 10-degree change in root angle, noted Hannah Schneider, former postdoctoral scholar in the Lynch lab, now a faculty member at Wageningen University in the Netherlands, who spearheaded the research.

“Along with enhanced deep nitrogen acquisition, we expected to see that the steeper growth angle of cipk15 mutants’ roots would result in better performance in drought, but in our experiments, it did not translate to improved plant water status,” she said. “However, that only may be because we have difficulty simulating drought conditions in Pennsylvania.”

In findings recently published in Plant, Cell and Environment, the researchers reported that a steeper root growth angle markedly improved nitrogen capture. In field studies under suboptimal nitrogen availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type, after 70 days of growth.

The results of the research are eye-opening, Lynch pointed out, admitting that he was surprised by the outcome. It’s quite unusual, when you knock something out, that the plant gets better, he explained. Because plants are like finely tuned machines.

“You take a gene out of that finely tuned machine, you don’t expect it to work better, but this shows that if you knock out the single gene, you’ll get deeper roots and better nitrogen capture,” he said. “For America, here’s a way to reduce a major cost and environmental impact from corn production. For Africa, this discovery could result in higher corn yields that will reduce food insecurity. And this discovery may support the discovery of genes regulating steeper root angles for other cereal plants, especially those closely related to corn, like sorghum and pearl millet.”

Also involved in this research at Penn State were Kathleen Brown, professor of plant stress biology, Meredith Hanlon, postdoctoral scholar, and Alden Perkins, graduate student. Vai Sa Nee Lor, Shawn Kaeppler, Xia Zhang and Jonas Rodriguez, Department of Agronomy, University of Wisconsin, Madison; Aditi Borkar, Malcolm Bennett and Rahul Bhosale, University of Nottingham; and Alexander Bucksch, Department of Plant Biology, University of Georgia, also are part of the team.

Featured image: These images of root architecture in the field show the cipk15 mutant corn genotype had significantly steeper angles compared to the wildtype genotype. Plants were grown in low nitrogen conditions. The mutant corn line that produced the root on the right lacks a gene that regulates root growth. Credit: Hannah Schneider/Penn State

Reference: Hannah M. Schneider et al, Root angle in maize influences nitrogen capture and is regulated by calcineurin B‐like protein (CBL) ‐interacting serine/threonine‐protein kinase 15 ( ZmCIPK15 ), Plant, Cell & Environment (2021). DOI: 10.1111/pce.14135

Provided by Pennsylvania State University

Juicy Past Of Favorite Okinawan Fruit Revealed (Botany)


  • Citrus fruits from the mandarin family have important commercial value but how their diversity arose has been something of a mystery
  • Researchers analyzed the genomes of the East Asian varieties and found a second center of diversity in the Ryukyu Islands along with the previously known center in the mountains of southern China
  • They discovered a new citrus species native to Okinawa that arose about two million years ago when the Ryukyu archipelago became disconnected from mainland Asia
  • Other citrus from Okinawa and mainland Japan, including shiikuwasha and tachibana, are hybrids of this newly discovered wild species with different mainland Asian varieties
  • This research may have commercial implications and opens the potential to create additional hybrids with favorable traits

Press release

Citrus fruits from the mandarin family are popular throughout the world for their tasty and healthy characteristics. Within Japan, the tiny shiikuwasha and the ornamental tachibana are of special cultural and historical importance. However, the origin of these two varieties, and other East Asian citrus, was always something of a mystery, until now.

Shiikuwasha have an important commercial value in Okinawa and are used to create many different products. Within Okinawa, Ōgimi and Katsuyama are the biggest citrus productive area in Okinawa. Top photo: Products from Katsuyama. Credit: Katsuyama Shiikuwasha Co., Ltd. Bottom photo: Products from Ōgimi. Credit: Hidekazu Sumi

In a new study, published in Nature Communications, scientists from the Okinawa Institute of Science and Technology Graduate University (OIST), and collaborators from other institutes, analyzed 69 genomes from the East Asian mandarin family, alongside their mainland Asian relatives, to reveal a far-ranging story of isolation, long-distance travel, and hybridization.

The story starts in the Hunan Province of southern China, which is the center of wild mandarin diversity and the genetic source of most well-known mandarins. When the scientists re-analyzed previously published genomic data, they unexpectedly found that wild mandarins of this mountainous region are split into two subspecies.   

“We found that one of these mandarin subspecies can produce offspring that are genetically identical to the mother,” said Dr. Guohong Albert Wu, a research collaborator at the Lawrence Berkeley National Laboratory in California. “Like many other plants, wild citrus typically reproduces when the pollen of the father combines with the egg of the mother, mixing the genes from both parents in the seed. But we found a subspecies of wild mandarins from Mangshan, in southern China, where the seed contains an identical copy of the mother’s DNA without any input from a father. So, the seed grows to be a clone of the mother tree.”

Back in Okinawa, the researchers looked more carefully at a strange shiikuwasha-like citrus that produces small, acidic fruit and had been ignored by local farmers since it has little commercial value. To their surprise, they found that this strange citrus represented a previously undescribed species, which they named the Ryukyu mandarin or, more formally, Citrus ryukyuensis. And in contrast to the well-known shiikuwasha, which reproduces clonally (like the subspecies in Mangshan), the new species always reproduces sexually.

Remarkably, the researchers found that all shiikuwasha are hybrids of a very specific type—one parent is from the local Ryukyuan species and the other, from mainland Asia. Surprisingly, all shiikuwasha have the same mainland mandarin parent, meaning that all shiikuwasha are half-siblings. 

A shiikuwasha flower photographed in Ōgimi, Okinawa. The researchers found that this well-known plant is both a hybrid and a clone. Credit: Dr. Chikatoshi Sugimoto.

They concluded that tens of thousands of years ago a mainland Asian mandarin was transported, either by people or by natural methods, to the land that would become the Ryukyu Islands. There it mated with the native Ryukyu citrus. The researchers traced the ancestry of this mainland Asian mandarin back to Mangshan, where it acquired its ability to reproduce asexually. This ability was passed on to its children.

Thus, all the shiikuwasha varieties found in Okinawa’s markets today are descended from this mating, and reproduce asexually, allowing stable varieties like golden shiikuwasha to be propagated from generation to generation.    

And what of tachibana and the other East Asian mandarin variations?

“They’re all hybrids!” explained Dr. Chikatoshi Sugimoto, Postdoctoral Scholar in OIST’s Molecular Genetics Unit. “The tachibana lineage also seems to have descended from the newly described Ryukyu species and another mandarin from China, but its birthplace was probably what is now mainland Japan.”

Once they saw the genetic pattern in shiikuwasha and tachibana, the researchers also recognized another half-sibling family comprising various traditional Ryukyuan types—oto, kabuchii, tarogayo, and other unnamed citrus. This family, which the researchers called ‘yukunibu’ (sour citrus in the native Okinawan language), is much younger than shiikuwasha and tachibana. It arose when the famous kunenbo—also the father of satsuma mandarins—hybridized with the native Ryukyu mandarin. Kunenbo was brought to Okinawa from Indochina around 4-500 years ago by maritime trade. Like the mainland parents of shiikuwasha and tachibana, it was also able to clone itself by seeds, due to its distant Mangshan ancestry, and it passed this trait on to its children.

“It’s fascinating to puzzle out the story of mandarin diversification and its relationship to the biogeography of the region,” concluded Prof. Dan Rokhsar, Principal Investigator of OIST’s Molecular Genetics Unit. “But it also could have commercial value. What other possibly hybrid types are there? Could we create new hybrids that are more resilient to disease or drought, or have other desirable characteristics? By looking into the past, we can create all sorts of possibilities for the future.”

To unravel this diversity, the researchers worked closely with industry and individuals in Okinawa, including Okinawa Prefectural Agricultural Research Center, Nago Branch, Katsuyama Shiikuwasha, and local farmer, Hiroshi Kobashigawa.

Cover photo by Mr. Fumimasa Mitsube from Okinawa Prefecture Agricultural Research Center.

Article information

Title: Diversification of mandarin citrus by hybrid speciation and apomixis
Journal: Nature Communications
DOI: 10.1038/s41467-021-24653-0
Author: Guohong Albert Wu, Chikatoshi Sugimoto, Hideyasu Kinjo, Chika Azama, Fumimasa Mitsube, Manuel Talon, Frederick G. Gmitter Jr., Daniel S. Rokhsar

Provided by OIST

Blushing Plants Reveal When Fungi Are Growing in Their Roots (Botany)

Scientists have created plants whose cells and tissues ‘blush’ with beetroot pigments when they are colonised by fungi that help them take up nutrients from the soil.

We can now follow how the relationship between the fungi and plant root develops, in real-time, from the moment they come into contact.

— Sebastian Schornack

This is the first time this vital, 400 million year old process has been visualised in real time in full root systems of living plants. Understanding the dynamics of plant colonisation by fungi could help to make food production more sustainable in the future.

Almost all crop plants form associations with a particular type of fungi – called arbuscular mycorrhiza fungi – in the soil, which greatly expand their root surface area. This mutually beneficial interaction boosts the plant’s ability to take up nutrients that are vital for growth. 

The more nutrients plants obtain naturally, the less artificial fertilisers are needed. Understanding this natural process, as the first step towards potentially enhancing it, is an ongoing research challenge. Progress is likely to pay huge dividends for agricultural productivity.

In a study published in the journal PLOS Biology, researchers used the bright red pigments of beetroot – called betalains – to visually track soil fungi as they colonised plant roots in a living plant. 

“We can now follow how the relationship between the fungi and plant root develops, in real-time, from the moment they come into contact. We previously had no idea about what happened because there was no way to visualise it in a living plant without the use of elaborate microscopy,” said Dr Sebastian Schornack, a researcher at the University of Cambridge’s Sainsbury Laboratory and joint senior author of the paper. 

To achieve their results, the researchers engineered two model plant species – a legume and a tobacco plant – so that they would produce the highly visible betalain pigments when arbuscular mycorrhiza fungi were present in their roots. This involved combining the control regions of two genes activated by mycorrhizal fungi with genes that synthesise red-coloured betalain pigments.

The plants were then grown in a transparent structure so that the root system was visible, and images of the roots could be taken with a flatbed scanner without disturbing the plants.

Using their technique, the researchers could select red pigmented parts of the root system to observe the fungus more closely as it entered individual plant cells and formed elaborate tree-like structures – called arbuscules – which grow inside the plant’s roots. Arbuscules take up nutrients from the soil that would otherwise be beyond the reach of the plant. 

Other methods exist to visualise this process, but these involve digging up and killing the plant and the use of chemicals or expensive microscopy. This work makes it possible for the first time to watch by eye and with simple imaging how symbiotic fungi start colonising living plant roots, and inhabit parts of the plant root system over time.

“This is an exciting new tool to visualise this, and other, important plant processes. Beetroot pigments are a distinctive colour, so they’re very easy to see. They also have the advantage of being natural plant pigments, so they are well tolerated by plants,” said Dr Sam Brockington, a researcher in the University of Cambridge’s Department of Plant Sciences, and joint senior author of the paper.

Mycorrhiza fungi are attracting growing interest in agriculture. This new technique provides the ability to ‘track and trace’ the presence of symbiotic fungi in soils from different sources and locations. The researchers say this will enable the selection of fungi that colonise plants fastest and provide the biggest benefits in agricultural scenarios.

Understanding and exploiting the dynamics of plant root system colonisation by fungi has potential to enhance future crop production in an environmentally sustainable way. If plants can take up more nutrients naturally, this will reduce the need for artificial fertilisers – saving money and reducing associated water pollution. 

This research was funded by the Biotechnology and Biological Sciences Research Council, Gatsby Charitable Foundation, Royal Society, and Natural Environment Research Council.

Featured image: Cells of roots colonised by fungi turn red © University of Cambridge

Timoneda, A. & Yunusov, T. et al: ‘MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation.’ PLOS Biology, July 2021. DOI: 10.1371/journal.pbio.3001326

Provided by University of Cambridge