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From The Current State of The World’s Plants To How Plants Conquered The Land

May 2016 was an especially rich month for fascinating reports about plant research.

So, let’s get on with it….

  • What is the current state of plants…on a global scale?

    A major report regarding this question was published by the Royal Botanic Garden, Kew.

    Kew report makes new tally for number of world’s plants.

  • Roses are red, violets are blue. Everybody knows that, but what makes them so? Although plant breeders were aware of some of the genes involved, there was as yet no quantitative study of how pigment turns a flower red, blue or yellow. Casper van der Kooi conducted just such a study, combining biology and physics.

    The anatomy of flower color.

  • Stem cells are typically thought to have the intrinsic ability to generate or replace specialized cells. However, a team of biologists at NYU showed that regenerating plants can naturally reconstitute their stem cells from more mature cells by replaying embryogenesis.

    Biologists Find How Plants Reconstitute Stem Cells.

  • Mathematical biologists love sunflowers. The giant flowers are one of the most obvious—as well as the prettiest—demonstrations of a hidden mathematical rule shaping the patterns of life: the Fibonacci sequence, a set in which each number is the sum of the previous two (1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, …), found in everything from pineapples to pine cones.

    Sunflowers show complex Fibonacci sequences.

  • An almost entirely accidental discovery by University of Guelph researchers could transform food and biofuel production and increase carbon capture on farmland.
    By tweaking a plant’s genetic profile, the researchers doubled the plant’s growth and increased seed production by more than 400 per cent.

    Chance Finding Could Transform Plant Production.

  • Research at the University of Leeds has identified a key gene that assisted the transition of plants from water to the land around 500 million years ago.

    How plants conquered the land.

    Next Up: Plant news from June 2016….

    HowPlantsWork © 2008-2017 All Rights Reserved.

  • From Cancer-Fighting Plants To Cadmium-Sniffing Moss

    Sadly, those who teach classes about plant physiology often feel the need to justify why plants are important.

    That’s how I usually began the first lecture in my Botany and Plant Physiology courses back in the day when I was boring undergraduate students.

    Most of these students could appreciate that plants were often the basis for many medicines, but few of them had heard about the idea of using plants as bio-indicators of heavy-metal air pollution.

    The April 2016 plant research news had stories about both of these plant uses…and more.

  • Can the plants that have been used for thousands of years as traditional Chinese remedies be used as the basis for effective modern medicines? A crucial step toward answering this question is to determine the metabolic pathways in plants that lead to the biosynthesis of beneficial compounds.

    For example, “The Chinese skullcap, Scutellaria baicalensis – otherwise known in Chinese medicine as Huang-Qin – is traditionally used as a treatment for fever, liver and lung complaints.
    New research led by Professor Cathie Martin of the John Innes Centre has revealed how a plant used in traditional Chinese medicine produces compounds which may help to treat cancer and liver diseases.

    Scientists discover how Chinese medicinal plant makes anti-cancer compound.

  • Plasmodesmata are complex “…communication channels in plants that bridge individual cells with their neighboring cells for distribution and exchange of nutrients, minerals and cellular signals….

    How the flow of materials through these channels is regulated is not well understood.

    Researchers identify two enzymes that regulate communication channels in plants.

  • Is the Earth getting greener? A recent NASA study says yes.

    One of the most important questions currently puzzling plant ecologists and physiologists is how the increasing levels of atmospheric CO2 will affect plants.

    From a quarter to half of Earth’s vegetated lands has shown significant greening over the last 35 years largely due to rising levels of atmospheric carbon dioxide, according to a new study published in the journal Nature Climate Change on April 25.

    Carbon Dioxide Fertilization Greening Earth, Study Finds

  • Many plants, especially legumes, benefit from symbiotic soil bacteria that can chemically modify atmospheric nitrogen to make it plant-usable.

    Scientists at the University of California, Riverside have discovered that a strain of beneficial nitrogen-fixing bacteria has spread across California, demonstrating that beneficial bacteria can share some of the same features that are characteristic of pathogens.

    Bacteria Beneficial to Plants Have Spread Across California

  • Moss have been used as bioindicators—living organisms that can help monitor environmental health—by the Forest Service and other agencies for decades. Because moss lack roots, they absorb all of their water and nutrients from the atmosphere, inadvertently taking up and storing whatever compounds happen to be in the air.

    Research published last April from the U.S. Forest Service Pacific Northwest Research Station indicates that moss may be a sensitive indicator for airborne cadmium.

    Moss is useful bioindicator of cadmium air pollution, new study finds.

    To Be Continued….

    HowPlantsWork © 2008-2017 All Rights Reserved.

  • From Blocking Pollen To Blocking Disease

    If there was a recurring theme in the March 2016 plant news it may have been plant defense.

    Defense against foreign genes, defense against herbivores, and defense against disease all made an appearance.

  • “Contamination of organic corn by genetically modified pollen is a major concern for growers, who stand to lose a large price premium paid for organic corn if their grain is found to be contaminated.”

    “Research at North Carolina State University has identified “pollen blockers” in corn that can prevent organic corn from being pollinated by genetically modified (GM) plants.”

    Block that pollen.

  • Thorns, poisons, and partnerships with biting insects are just a few of the ways that plants avoid getting eaten. Now, researchers have added one more to the list: armor made of sand.

    Plants defend themselves with armor made of sand.

  • “C4 crops, such as maize and sugarcane, are the most photosynthetically efficient crops in the world.” One of the major reasons for this is something called “Kranz Anatomy”.

    And “…dissecting the networks responsible for the development of Kranz Anatomy in C4 species could potentially be translated into C3 crops that are less efficient in hot and dry environments in an effort to increase yield in a sustainable way.

    Understanding Kranz Anatomy to help boost photosynthetic efficiency in plants.

  • Do plants have an immune system? As explored in a previous post, it depends on how you define “immune system”. A new finding, reported last March, supports the idea that plant and animal immune systems may share an important common feature.

    “A protein that signals tissue damage to the human immune system has a counterpart that plays a similar role in plants, report researchers at the Boyce Thompson Institute (BTI).”

    Discovery shows parallels between plant and human immune systems.

    More “Greatest Hits” of 2016 Plant News to Come….

    HowPlantsWork © 2008-2017 All Rights Reserved.

  • From Glowing Plants to “Talking” Plants

    As usual, the plant news of February 2016, ranged from the molecular level to ecosystem level, from single plant cells to whole plants.

    And since I can’t discern any common themes, I’ll go with the stories that I “tweeted” during February of last year that were “re-tweeted+favorited” the most.

  • “Synthetically engineered biosensors, which can be designed to detect and signal the presence of specific small-molecule compounds, have already unlocked potential applications, such as fuel, plastics, and pharmaceuticals. Until now, however, scientists have been challenged to leverage biosensors for use in eukaryotic cells, which comprise yeast, plants, and animals.

    A team of researchers at Harvard’s Wyss Institute and Harvard Medical School (HMS) has engineered plants that can emit fluorescence when they detect a molecule of interest, such as the human hormone progesterone or the drug digoxin.

    Plants with biosensors may light the way.

  • Last February, biologists at the University of Illinois reported the following: “The types of beneficial fungi that associate with tree roots can alter the fate of a patch of tropical forest, boosting plant diversity or, conversely, giving one tree species a distinct advantage over many others,…

    Fungi are at the root of tropical forest diversity – or lack thereof.

  • Plant health and interaction with microbes is maintained by intricate antennas – plant immune receptors. A certain class of receptors is turning out to be highly informative about plant disease resistance.

    Researchers in the UK “…have surveyed immune genes across flowering plants to uncover the molecular ‘traps’ that plants use to detect pathogens.”

    Immunity gene fusions uncovered in plants.

  • It has been known for some time that plant roots can communicate with plant shoots. Now, a new paper from Oxford researchers (working in collaboration with researchers from the Chinese Academy of Sciences in Beijing) tells us how.

    Shooting the breeze: how parts of a plant can ‘talk’ to one another for the benefit of the whole.

    And for those looking for a bit longer read….

    Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

    This is a review article published in the 19 February 2016 issue of Science magazine. In it, the authors “…have highlighted recent advances in plant priming, memory, and epigenetics. These findings serve to demonstrate the capacity to confer acclimation and adaptive benefits within the life of a plant or future generations.

    Next Up: We “March” on….

    HowPlantsWork © 2008-2017 All Rights Reserved.

  • Happy New Year!

    Since 2012, here at the “How Plants Work” blog, I’ve ended the year by taking a look back at the plant-research news from my HPW Twitter feed over the past twelve months, and then sharing a few of the “tastier” tidbits, month-by-month.

    So, welcome to the fifth-annual review of plant research news for 2016.

    Let’s get the ball rolling with news from January 2016…

    From Orchid BO to Dandelion Latex

  • “Orchids are masters of deception. To lure potential pollinators, some resemble nectar-laden flowers, yet offer no sweet reward. Others smell like rotting meat. Still others look and smell like female insects. Now, sensory biologists have discovered orchids that emit an odor just like the human body. Their target: tiger mosquitoes.

    One of the most re-tweeted plant news items from January 2016 was:

    Orchids give off human ‘body odor’ to attract mosquitoes.

  • Agricultural grafting dates back nearly 3,000 years. By trial and error, people from ancient China to ancient Greece realized that joining a cut branch from one plant onto the stalk of another could improve the quality of crops.
    Now, researchers at the Salk Institute and Cambridge University have used this ancient practice, combined with modern genetic research, to show that grafted plants can share epigenetic traits,…

    Grafting a part of one plant onto another plant for crop improvement has been around for a long time. Scientists have recently discovered that small bits of genetic material can move across the graft.

    Grafted plants’ genomes can communicate with each other.

  • No plant is an island. By this I mean that no plant in nature lives in isolation from other organisms, especially microorganisms. And many plants may rely on some bacteria and fungi for their survival. Thus, research in the field of plant-microbe interactions is quite lively.

    Two examples of such research were published last January:

    Scientists have wondered for years how legumes such as soybeans, whose roots host nitrogen-fixing bacteria that produce essential plant nutrients out of thin air, are able to recognize these bacteria as both friendly and distinct from their own cells, and how the host plant’s specialized proteins find the bacteria and use the nutritional windfall.” Researchers at Mass Amherst have recently published findings that show, at the molecular level: how plants interact with beneficial microbes in the soil.

    Most land plants get a large portion of their mineral nutrients through a symbiotic relationship with soil fungi called arbuscular mycorrhizal (AM) symbiosis. But, despite decades of research, many of the genes required to form this relationship remain elusive.” Recently at the Boyce Thompson Institute
    researchers have uncovered a core set of genes for plant-fungal symbiosis.

  • Dandelions are troublesome weeds that are detested by most gardeners. Yet dandelions also have many insect enemies in nature. However, they are able to protect themselves with their latex, a milky, bitter-tasting sap.

    Recently, scientists in Germany and Switzerland collaborated to discover a single chemical compound that may be responsible for how a dandelion uses latex to protect its roots against insect feeding.

    Next Up: Plant research news highlights from February 2016…

    HowPlantsWork © 2008-2017 All Rights Reserved.

  • numb (adjective): “devoid of sensation; insensible”

    Pain in the Ash?

    In the previous post, I posed the question whether or not plants experienced something analogous to pain when physically wounded.

    I concluded that they did….depending on how one defines “pain”.

    At the present time, when even academic biologists are expanding the meanings of “know”, “feel”, “smell”, “think”, “talk”, “hear”, “see”, “remember”, etc., to include plants (e.g., see Refs. 1-5 below), I think it’s fair to also broaden the concept of “pain” to include plants.

    But before I proffer my definition of “plant pain”, let’s take a look at the classic definitions, specifically as it’s related to physical injury.

    What Is Pain?

    According to the online dictionary.com, the two leading definitions are 1. “physical suffering or distress, as due to injury, illness, etc.” and 2. “a distressing sensation in a particular part of the body“.

    A medical definition, provided by International Association for the Study of Pain: “Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.”

    More interesting definitions, however, and perhaps more germane to the discussion at hand, have to do with the biological functions of pain.

    Here are a few examples found on the internet that I think most people would agree with:

  • “Pain is a universal experience that serves the vital function of triggering avoidance.
  • Pain motivates the individual to withdraw from damaging situations, to protect a damaged body part while it heals, and to avoid similar experiences in the future.
  • Pain is a vital function of the nervous system in providing the body with a warning of potential or actual injury.

    And the definition of “pain” gets even more interesting when one delves into biological mechanisms of pain.

    Although it’s difficult to succinctly describe the complex neurobiology of pain, the beginning of pain is the perception of injury, which starts with nociceptors.

    “Nociceptors are the specialised sensory receptors responsible for the detection of noxious (unpleasant) stimuli, transforming the stimuli into electrical signals, which are then conducted to the central nervous system.” (from Ref. 5 below)

    Also, as Dr. Chamovitz points out, “…“touch and pain are biologically not the same phenomena. Pain does not simply result from an increase in the signals emanating from touch receptors. Our skin features distinct receptor neurons for different types of touch, but it also has unique receptor neurons for different types of pain. Pain receptors (called nociceptors) require a much stronger stimulus before they send action potentials to the brain.” (From Ref. 2 below)

    As I mentioned in the previous post, how plants perceive and respond to mechanical stimulation (e.g., wind, touch, etc.) is also different and distinct from how plants perceive and respond to physical wounding (i.e, cellular damage).

    There are several well-known “wound signals” produced by physical damage to plant tissue that can travel from the wound site all throughout the plant, which are called “systemic” wound signals. And some of these figure prominently in what I’ll refer to as “plant pain”.

    Plant “Pain” = Waves of Systemic Wound Signals?

    I should first mention that this and the previous post were prompted, in part, by a couple of reviews by Dr. Simon Gilroy and colleagues regarding rapid systemic signaling in plants (see Refs. 7 & 8 below).

    Briefly, when plants are exposed to abiotic (physical) stress, most of the scientific evidence supports the idea that waves of hydraulic, chemical, and/or electrical long-distance signals may propagate – within minutes – throughout the plant to initiate systemic stress responses.

    Therefore, I think it’s not too much of stretch to say that there is a plant analog to what we commonly call “pain” and that this analog is this wave of systemic wound signals.

    Though this plant “pain”, and the plant’s responses to it, occur much more slowly compared to animals, we should remember that plants function within a different time framework than animals, what I call “plant time”.

    Bottom Line: Plants are not “comfortably numb” when it comes to physical wounding, because waves of systemic wound signals – what I call “plant pain” – alert the plant that it has been physically damaged (or what others have referred to as “damaged-self recognition”).

    References

    1. Pollan, M. (2013) “The intelligent plant.” The New Yorker, December 23 & 30, 2013 issue. (Full Text)

    2. Chamovitz, D. (2012) What A Plant Knows.

    3. Ananthaswamy, A. (2014) “Smarty Plants: They think. They react. They remember. It’s time we rethought intelligence.” New Scientist, 6 December 2014 issue, pp. 34-37. (Full Text PDF)

    4. Leopold, A. C. (2014) “Smart plants: Memory and communication without brains.” Plant Signaling & Behavior, Vol. 9, e972268. DOI: dx.doi.org/10.4161/15592316.2014.972268 (Full Text)

    5. Popova, M. “The Secret Life of Trees: The Astonishing Science of What Trees Feel and How They Communicate.” Brain Pickings, 9/26/2016. (Full Text)

    6. Reddi, D. “An introduction to pain pathways and mechanisms.” (Full Text PDF)

    7. Gilroy, S., et al. (2016) “ROS, Calcium, and Electric Signals: Key Mediators of Rapid Systemic Signaling in Plants.” Plant Physiology, Vol. 171, pp. 1606-1615. (Full Text)

    8. Choi, W.-G, R. Hilleary, S. J. Swanson, S.-H. Kim, and S. Gilroy (2016) “Rapid, Long-Distance Electrical and Calcium Signaling in Plants.” Annual Review of Plant Biology, Vol. 67, pp. 287-307. (Abstract)

    HowPlantsWork © 2008-2016 All Rights Reserved.

    David Gilmour & David Bowie – Comfortably Numb

  • Feelin’ No Pain?

    An amazing short story, entitled “The Sound Machine”, by the British writer Roald Dahl was first published in the September 17, 1949 issue of the New Yorker. In this story, “A man named Klausner invents a machine that can hear sound the human ear cannot hear. It reproduces the sounds on a lower pitch so that human beings can hear it. With this machine he hears roses scream as his neighbor cuts them. The next morning he hears a tree scream when he cuts into it with an axe.” (from The New Yorker)

    Note: If you can’t access a copy of the story, you can view a video dramatization of it on YouTube.

    Here’s a brief excerpt from “The Sound Machine”:
    He put the earphones on his head and switched on the machine. He listened for a moment to the faint familiar humming sound; then he picked up the axe, took a stance with his legs wide apart and swung the axe as hard as he could at the base of the tree trunk. The blade cut deep into the wood and stuck there, and at the instant of impact he heard a most extraordinary noise in the earphones. It was a new noise, unlike any he had heard before-a harsh, noteless, enormous noise, a growling, low-pitched, screaming sound, not quick and short like the noise of the roses, but drawn out like a sob, lasting for fully a minute, loudest at the moment when the axe struck, fading gradually fainter and fainter until it was gone.

    That plants could experience pain (let alone scream) in response to wounding is a silly notion, right? Since plants don’t have a nervous system or a brain, like animals, how could a plant feel pain?

    Mr. Klausner posits: “You might say,” he went on, “that a rosebush has no nervous system to feel with, no throat to cry with. You’d be right. It hasn’t. Not like ours, anyway. But how do you know, Mrs. Saunders, – and here he leaned far over the fence and spoke in a fierce whisper – “how do you know that a rosebush doesn’t feel as much pain when someone cuts its stem in two as you would feel if someone cut your wrist off with a garden shears? How do you know that? It’s alive isn’t it?

    But how would a plant scientist likely respond to Mr. Klausner?

    No Pain, No Gain?

    A likely response from most plant physiologists can be found in the popular book “What a Plant Knows” by Dr. Daniel Chamovitz: “While plants feel touch, they don’t feel pain.

    This statement is from Chapter Three of this book, entitled “What a Plant Feels”. In this chapter, Dr. Chamovitz compares and contrasts the perceptions of, and responses to, varying degrees of mechanical stimulation in plants versus people.

    He introduces the notion that plants can sense physical disturbances with: “It’s probably a bit surprising, and maybe even a bit disconcerting, to discover that plants know when they’re being touched. Not only do they know when they’re being touched, but plants can differentiate between hot and cold, and know when their branches are swaying in the wind. Plants feel direct contact: some plants, like vines, immediately start rapid growth upon contact with an object like a fence they can wrap themselves around, and the Venus flytrap purposely snaps its jaws shut when an insect lands on its leaves. And plants seemingly don’t like to be touched too much, as simply touching or shaking a plant can lead to growth arrest.

    OK, but I’d say that plants do not “know” or “feel” anything, with respect to the common usage of these words. For example, would you say that an iPhone or iPad “feels” the touch of fingertips on the touch-screen? I think not. But I get that anthropomorphizing plants sells more books, and I’ve already had my rant on this subject, so I’ll drop it for now.

    Anyway, it’s generally accepted that plant cells can indeed detect or sense mechanical disturbances (in nature, mostly caused by wind). This is amply supported by cellular and molecular evidence. (For example, please see Ref. 1 below)

    And we also know that, when physically wounded with cellular damage – by cutting or by herbivory, for instance – parts of the plant far removed from the wound site may begin to produce defensive chemicals. (Please see Ref. 2 below, for example.)

    In other words, most experimental evidence supports the idea that plants respond systematically to physical wounding (cellular damage), sometimes within minutes, and that such “wound responses” are different than how plants respond to mechanical stimulation (without cellular damage) such as wind or touch.

    Interestingly, this is somewhat analogous to the difference between “touch” and “pain” receptors in our nervous system.

    Given that there appears to be systemic wound signals in plants that may travel from the wound site throughout the whole plant within minutes, the question remains: Do plants experience something akin to what we call physical “pain”?

    I’d say that the evidence supports the idea that plants do indeed experience “pain” when physically wounded, which, in turn, triggers wound responses.

    This very much depends, however, on how one defines “pain”.

    To Be Continued….

    References

    1. Monshausen, G. B. and E. S. Haswell (2013) “A force of nature: molecular mechanisms of mechanoperception in plants.” Journal of Experimental Botany, Vol. 64, pp. 4663-4680. doi: 10.1093/jxb/ert204 (Full Text)

    2. León, J, E. Rojo and J. J. Sánchez‐Serrano (2000) “Wound signalling in plants.” Journal of Experimental Botany, Vol. 52, pp. 1-9. doi: 10.1093/jexbot/52.354.1 (Full Text)

    HowPlantsWork © 2008-2016 All Rights Reserved.

    Public Domain

    Public Domain

    Double helix in the sky tonight
    Throw out the hardware
    Let’s do it right
    ” – Steely Dan

    Here A CRISPR, There A CRISPR, Everywhere A CRISPR, CRISPR….

    Yikes! You can hardly go through a week these days without reading some headline with “CRISPR” in the title. (Even in Time magazine!)

    Yes, “CRISPR” currently is (and has been for about the past year or so) a pretty big deal in the popular press. (In mainstream scientific journals, such as Nature and Science, it’s been a big deal since about 2013.)

    Why?

    Well, because CRISPR, or more precisely the CRISPR/Cas9 system, is a powerful new way to edit DNA.

    If you’re unfamiliar with CRISPR, here’s a nice YouTube video (from my old home town, btw) that I think does a pretty good job explaining it.

    Nota bene: This is an excellent example of how a basic research project can lead to a major technological advance and of why it’s so critically important to support basic research (a.k.a., fundamental or pure research), in addition to “applied” research.

    OK, so molecular biologists now have a new “toolkit” for tinkering with the genomes of biological organisms.

    But why do many plant scientists say that CRISPR may “change everything” when it comes to the realm of plant genetic engineering and, ultimately, the fundamental nature of plant “GMO’s”?

    Please allow me to explain….

    Using a “Scalpel” Instead of a “Shotgun”

    Up until recently, most plant GMOs have pretty much been the result of a “shotgun” approach to plant genetic engineering.

    That is, using Agrobacterium or a “gene gun” to deliver foreign genes into plant cells, these genes were randomly inserted into the plant genome, sometimes multiple times, in several different locations within the genome.

    “In addition, and due to the random transfer process, insertion may disrupt a resident gene and, accordingly, bring on unwanted phenotypic side-effects.”

    “From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology.”

    “…zinc-finger and TALEN nucleases, were based on specific polypeptide-to-DNA binding which is tedious to optimize; CRISPR-Cas9 is based on DNA-RNA hybridization which is well mastered. CRISPR-Cas9 nowadays appears as the most efficient system to achieve site-specific genome editing–easiest, more reliable and cheapest as well.” (From: Quetier below)

    With CRISPR/Cas9, plant genetic engineers now have the ability to relatively easily and precisely “edit” the plant genome, that is, with a molecular “scalpel” instead of a “shotgun”.

    Are CRISPR-modified plants GMOs?

    What’s especially important to the whole anti-GMO debate is that researchers have recently devised a way to use CRISPR to precisely modify a plant’s genome without introducing any foreign DNA. (See Cyranoski below)

    This whole issue has been nicely summarized by Dr. Johannes Fütterer, a Senior researcher at the Institute of Agricultural Sciences, ETH Zurich, in an article entitled The future of plant breeding”:
    “The special feature of CRISPR/Cas is that the modifications produced in the genome do not differ from naturally occurring mutations in plants and animals caused by environmental influences on the genome, such as natural radioactive radiation, reactive metabolites or even by defects in DNA replication and inheritance. Random mutagenesis by chemical treatment or irradiation has been used in mutation breeding for many years and contributed to major yield gains in our crops in the 20th century. Worldwide this type of mutation breeding led to currently more than 3088 varieties from 190 species.
    As plants modified with CRISPR/Cas cannot be distinguished from those modified with conventional breeding techniques, the question arises: if a new breeding method triggers a targeted modification in the genome of the given species that can also be achieved through conventional breeding – admittedly with significantly greater effort – or accidental mutation, should the resulting product be regarded as a GMO (genetically modified organism) or not? The current debate focuses accordingly on whether a regulation should be process- or product-related.

    And what’s amazing is that some have suggested that this new “toolkit” for precise gene editing in plants is compatible with organic farming, since it will facilitate the “rewilding” of crop plants. (See Andersen et al below)

    I’m skeptical that organic farmers would accept crop plants genetically modified using these “new breeding techniques”. But these are early days for CRISPR/Cas 9, and it’s possible that this new technology may eventually overcome zealotry.

    Online Resources

  • On the usefulness of CRISPR for exploring how genomes work: CRISPR: gene editing is just the beginning
  • Are CRISPR-modified plants GMOs? :

    “GREEN LIGHT IN THE TUNNEL”! SWEDISH BOARD OF AGRICULTURE: A CRISPR-CAS9-MUTANT BUT NOT A GMO (13 May 2016)

    Are plants engineered with CRISPR technology genetically modified organisms? (14 June 2016)

    Brave New Crops: Gene Editing Comes to Agriculture (17 June 2016)

    Recent CRISPR News: 9/22/2016 – Titanic Clash Over CRISPR Patents Turns Ugly

    References

    Andersen, M. M., et al. (2015) “Feasibility of new breeding techniques for organic farming.” Trends in Plant Science, Vol. 20, pp. 426–434. DOI: 10.1016/j.tplants.2015.04.011 (Abstract)

    Belhaj, K., A. Chaparro-Garcia, S. Kamoun and V. Nekrasov (2013) “Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system.” Plant Methods, 20139:39, DOI: 10.1186/1746-4811-9-39. (Full Text)

    Cyranoski, D. (2015) “CRISPR tweak may help gene-edited crops bypass biosafety regulation.” Nature, DOI:10.1038/nature.2015.18590. (Full text)

    Khatodia, S., et al. (2016) “The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops.” Frontiers in Plant Science, Vol 7, pp. 506. DOI: 10.3389/fpls.2016.00506 (Full Text)

    Quetier, F. (2016) “The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.” Plant Science, Vol. 242, pp. 65–76. DOI: 10.1016/j.plantsci.2015.09.003 (Abstract)

    HowPlantsWork © 2008-2016 All Rights Reserved.

  • Firstly, What Is A Roundup Ready® Crop?

    Well, let’s start out with: What’s Roundup®?

    Briefly, Roundup® is the commercial name for the herbicide glyphosate, first made and sold by Monsanto in the 1970’s.

    You can read more about Roundup® HERE.

    “Roundup Ready®” is Monsanto’s trade name for crops (soybean, maize, cotton & alfalfa, e.g.) that have been genetically engineered to tolerate glyphosate.

    Simply put, a bacterial gene (or genes) coding for an enzyme that promotes the breakdown of glyphosate has been transferred to these plants. (You can see how HERE.)

    Thus, farmers can spray Roundup® on Roundup Ready® crops, and they don’t die, because they can detoxify the herbicide.

    Glyphosate-resistant soybean was the first crop launched and marketed under the Roundup Ready brand in the USA in 1996.” (from Ref. 1 below)

    Secondly, What Is A “Superweed”?

    To answer this question, I wanted to know what professional weed scientists thought. Here’s the official answer from the Weed Science Society of America (WSSA):

    Use of superweed has snowballed in recent years, along with considerable misinformation that isn’t supported by scientific facts.  Most online dictionaries, for example, associate superweeds with herbicide resistance caused by the suspected transfer of resistance genes from crops to weeds.  To date, there is no scientific evidence to indicate that crop to weed gene transfer is contributing to the herbicide resistance issues faced by farmers.

    And the official definition, from the WSSA:

    Superweed:  Slang used to describe a weed that has evolved characteristics that make it more difficult to manage due to repeated use of the same management tactic. Over-dependence on a single tactic as opposed to using diverse approaches can lead to such adaptations.”
    “The most common use of the slang refers to a weed that has become resistant to one or more herbicide mechanisms of action (www.weedscience.org) due to their repeated use in the absence of more diverse control measures.”

    OK, I’ll go with this definition.

    But the WSSA is careful to point out that so-called “superweeds” can arise not only from the overuse of a herbicide, but also ““Dependence on a single mechanical, biological, or cultural management tactic….

    So, if a single herbicide is used, year-after-year, to kill “weeds”, then this selection pressure promotes the proliferation of individual “weeds” that resist, even tolerate, the herbicide, eventually leading to populations of so-called “superweeds”.

    But why are Roundup Ready® crops often blamed for a rise in “superweeds” in recent years?

    Cause: Predominance of Roundup Ready® Crops

    The estimated annual agricultural use of glyphosate in the USA for 2014 equaled over 250 million pounds, over 10 times more than in 1994.

    Why this massive increase?

    I think the graph below provides pretty good clues for answering the question. (“HT” = “herbicide-tolerant” & “Bt” = Bacillus thuringiensis. By the way, the “HT” crops are mostly Roundup Ready® crops.)

    ImageGen ashx

    Effect: Relatively Rapid Appearance Glyphosate-Tolerant “Superweeds”

    It seems to me that the evidence that the excess and wide-spread use of Roundup®, due primarily to the huge increase in the adoption of Roundup Ready® crops in the past twenty years (see above graph), have led to the current problems with “superweeds”. But I’m no weed science expert.

    What do the experts say?

    “…herbicides exert a high selection pressure on weed populations, and density and diversity of weed communities change over time in response to herbicides and other control practices imposed on them. Repeated and intensive use of herbicides with the same mechanisms of action (MOA; the mechanism in the plant that the herbicide detrimentally affects so that the plant succumbs to the herbicide; e.g., inhibition of an enzyme that is vital to plant growth or the inability of a plant to metabolize the herbicide before it has done damage) can rapidly select for shifts to tolerant, difficult-to-control weeds and the evolution of herbicide-resistant weeds, especially in the absence of the concurrent use of herbicides with different mechanisms of action or the use of mechanical or cultural practices or both.” (from Ref. 2 below)

    And from the USDA plant physiologist Dr. Stephen O. Duke: “Just as with overuse of certain antibiotics in medicine, overuse of a superior technology has been a recipe for accelerated evolution of resistance. Nature abhors a vacuum, and even though evolution of resistance to glyphosate was thought to be unlikely, or at the most, to occur very slowly and only to low levels, the massive selection pressure caused by the world’s most-used herbicide, has resulted in weeds evolving often novel and unpredicted mechanisms of resistance that can impart resistance to glyphosate doses far above those that are recommended.” (from Ref. 3 below)

    OK, now what are farmers to do?

    The Road To Nowhere?

    In response to increasing number of agronomically-significant glyphosate-tolerant “superweeds”, the chemical companies have developed GMO crops with tolerance to multiple herbicides.

    Though this may be a really bad idea, these GMO crops have recently been approved (e.g., see here and here) and are currently being propagated in the fields, already with some unintended consequences.

    Will this approach be the ultimate solution to weed control?

    Likely not. (Please see here, for example.)

    Recent News: Monsanto Seeds Unleash Unintended Consequences Across U.S. Farms.

    Online Resources:

    1. What Do We Really Know About Roundup Weed Killer? by Elizabeth Grossman, National Geographic

    2. History of Roundup Ready Crops

    3. Selection Pressure, Shifting Populations, and Herbicide Resistance and Tolerance by University of California, Riverside

    4. Why Roundup Ready Crops Have Lost their Allure, by Jordon Wilkerson, Harvard University

    References

    1. Dill, G. M. (2005) “Glyphosate-resistant crops: history, status and future.” Pest Management Science, Vol. 61, pp. 219–224. (Full Text PDF)

    2. Vencill, W. K., et al. (2012) “Herbicide Resistance: Toward an Understanding of Resistance Development and the Impact of Herbicide-Resistant Crops.” Weed Science, Vol. 60, pp. 2-30. (Full Text)

    3. Duke, S. O. (2015) “Perspectives on transgenic, herbicide-resistant crops in the United States almost 20 years after introduction.” Pest Management Science, Vol. 71, pp. 652–657. Abstract

    4. Keim, B. (2015) “Monsanto’s Newest GM Crops May Create More Problems Than They Solve.” Wired, (Full Text)

    Talking Heads – “Road to Nowhere”

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    From Decaf Coffee Plants To Non-Browning Apples

    Have you ever had a really good cup of decaf coffee?

    Me neither.

    This is likely because most decaf coffee results from chemical processing of normal coffee beans.

    But why would anyone want coffee without caffeine? And why do plants make caffeine in the first place?

    These questions have been addressed in a previous post, but suffice it to say here that there certainly is a very large potential market for coffee beans that naturally have very low or no caffeine.

    Indeed, coffee plant breeders have been trying to develop such varieties for decades, with very little success.

    In 2003, a more efficient gene-silencing technology was used in order to shut off caffeine production in coffee plants. (See Ref. 1 below.)

    This approach is called RNA interference (RNAi).

    The Benitec Biopharma website has provided a nice summary of this biological process:
    RNA interference (RNAi) is a natural process that cells use to ‘turn off’ or silence unwanted or harmful genes. The initial discovery of this phenomenon was in 1991, by scientists trying to deepen the colour of petunias. Surprisingly, by introducing a gene for colour, they found that they had turned off the gene.
    Several years after the petunia experiments, the mechanism of RNA interference was revealed: it is triggered by double-stranded RNA (dsRNA), not usually found in healthy cells, but needed to turn genes off, if the cell is threatened or damaged by invading viruses.

    To learn more about how this technology may impact plant breeding, please see Ref. 2 below.

    Back to decaf coffee plants….Unfortunately, it’s been difficult to produce coffee plants that don’t make caffeine because its biosynthesis involves a complex metabolic pathway. Thus, to develop “decaf” coffee plants has been especially challenging for plant genetic engineers, but they’re still trying. (e.g., see Ref. 3 below.)

    There are, however, plant products produced using RNAi gene-silencing that you will likely soon encounter.

    Arctic® Apples and Innate® Potatoes

    According to the official Arctic® apples website: “Arctic® apples aren’t slow browning. They aren’t low browning. They’re nonbrowning! By silencing the enzyme that causes apples to brown when bitten, sliced or bruised popular apple varieties like Golden Delicious and Granny Smith can be enhanced with the Arctic Advantage™. Our goal? To help consumers eat more apples by making them more convenient, and reducing food waste while we’re at it!

    What is the “Arctic Advantage™”?

    Briefly, these apple plants were genetically modified using RNA interference to silence genes coding for the enzyme polyphenol oxidase, which is primarily responsible for the browning of apples and other fruits and vegetables.

    These apple trees were approved for commercial planting by the USDA in 2015.

    A year earlier, another crop plant with specific genes silenced by RNAi was USDA-approved, namely, the Innate® potato.

    According to the official Innate® potato website:
    “Innate® potatoes are less prone to bruising and black spots, which means consumers waste less and fewer potatoes end up in landfills. Innate potatoes also contain less asparagine. By producing less asparagine, Innate potatoes provide the potential for the formation of acrylamide to be reduced by 58-72% when potatoes are baked, fried or roasted at high temperatures.”

    As I understand it, in the first generation of Innate® potatoes, RNAi gene-silencing was used to block the production of two enzymes, namely, polyphenol oxidase (see Arctic® apples, above) and asparagine synthetase.

    The second generation of Innate® potatoes blocked the biosynthesis of these two enzymes, plus two more – starch-associated R1 and phosphorylase-L. These two enzymes are involved in converting starch into reducing sugars, such as glucose and fructose. By blocking the production of these two enzymes, this results in a decrease in reducing sugars in stored potatoes, which also contributes to the lowering of acrylamide in French fries, for example.

    Online Resources: More thorough considerations of Innate® potatoes can be found at:

  • A look at the Innate Potato
  • Q&A with Haven Baker on Simplot’s Innate™ Potatoes
  • Recent News: Genetic improvement of tomato by targeted control of fruit softening

    References

    1. Ogita, S., et al. (2003) “Producing decaffeinated coffee plants.” Nature, Vol. 243, p. 823. (Full Text)

    2. Younis, A., et al. (2014) “RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding.” International Journal of Biological Sciences, Vol. 10, pp. 1150–1158. (Full Text)

    3. Borrell, B. (2012) “Plant biotechnology: Make it a decaf.” Nature, Vol. 483, pp. 264–266. (Full Text + Extras)

    *Please Note: The subject of RNAi mediated gene-silencing has also popped up on this blog in a previous post, entitled “Spray and Pray? – Will Spraying RNA on Plants Revolutionize Agriculture?”.

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