Creating high-yielding Hybrid Crops that can be Propagated indefinitely

Unmixed Blessing?

Researchers are Closing in on the long-sought goal of creating high-yielding hybrid crops that can be Propagated Indefinitely 

18 MAY 2023  BYERIK STOKSTAD

Science, Vol 380, Issue 6646.

In early summer, unusual pollinators swoop over rice fields in Texas and Arkansas. Small, nimble helicopters fly low and steady so their rotors blow pollen from one row of plants to another. The flights help RiceTec, a plant breeding company, produce seed for high-yielding, robust varieties of rice grown across the southern United States. It’s an expensive and complicated way to create seed.

But the effort is worthwhile because the seeds sprout into plants with a mysterious robustness and resilience. The phenomenon, called hybrid vigor, comes from crossing two strains of inbred parents. Why hybrids are superior to normal plants is not clear, but one long-standing hypothesis is that favorable versions of genes from one parent dominate poor-performing, recessive genes from the other.

The development of hybrid varieties has boosted the yield of maize, sorghum, and other crops by up to 50% and has resulted in other valuable traits, such as better drought tolerance. But the method is only feasible in some species; there’s no practical way to produce hybrid wheat or soybeans, for example. And when it works, it’s extremely labor intensive.

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In rice, seed companies must first develop a strain of plants that can’t self-pollinate. Then come the helicopters, which sweep in pollen from a second strain. The process has to be repeated for each new batch of seed to avoid the reshuffling of genes and loss of favorable traits that happens during ordinary sexual reproduction. “It’s a very imperfect system,” says José Ré, vice president of research at RiceTec.

Plant breeders have long dreamed of an easier, more powerful way to create hybrid seed. In nature, some plant species reproduce clonally: The eggs inside their flowers become embryos without pollination, part of a process called apomixis—“away from mixing” in Greek. If researchers could genetically engineer crops to reproduce through apomixis, the process of creating the first hybrid generation might still be laborious. But then seed companies could much more easily propagate hybrid offspring.

For decades, scientists had limited success. But recent breakthroughs have brought the concept closer to reality. In 2019, an international team reported that it had successfully engineered a line of rice plants that could reproduce clonally—the first instance of synthetic apomixis in a crop. Groups around the world are working to develop apomictic varieties of sorghum, tomatoes, alfalfa, and other crops. There’s a palpable “sense of excitement” in the field, says Mary Gehring, a molecular biologist at the Whitehead Institute and the Massachusetts Institute of Technology who studies development in apomictic plants.

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The technology won’t be ready to be commercialized for years. “There’s still an awful lot that we don’t understand about how to make it efficient for agriculture,” says Peggy Ozias-Akins, a geneticist at the University of Georgia. But seed companies are paying attention. Apomictic reproduction would simplify how they produce hybrid seeds, quicken the release of new varieties, and reduce costs. The technology could also benefit smallholder farmers in poorer countries who might not have regular access to commercial hybrid seeds, because they could save seeds produced by the previous year’s crop. “It really would be a big game changer,” says Adam Famoso, a rice breeder at Louisiana State University.

Some methods of hybrid rice production employ helicopters to blow pollen from one rice strain to another.RICK SÁ

THE DISCOVERY OF VIRGIN birth in plants is widely credited to John Smith, a 19th century botanist who served as the inaugural curator at London’s Royal Botanic Gardens. For a decade, he had watched three holly plants from Australia bear fruit without having ever produced a male flower or anything that resembled pollen, the vehicle for plant sperm. In 1839, Smith reported to the Linnean Society of London that he could grow new plants from the seeds of the hollies. It was an incendiary claim that was met with “incredulity,” according to Thomas Meehan, a botanist writing decades later

In 1898, however, Swedish botanist Oscar Juel demonstrated, with convincing microscopy, that the egg cells of a plant called alpine catsfoot could develop into embryos in the absence of pollen. Other researchers took a closer look at their own favorite species. As evidence accumulated, more and more botanists began to take the phenomenon seriously. Today, apomictic reproduction has been confirmed in more than 400 plant species but no staple crops.

In the late 1990s, as genetic tools became more readily available, experts were optimistic they could identify the genes behind apomixis and deploy them in crops, creating clones that would bypass the genetic recombination that happens during plant sex, which shuffles away favorable gene combinations. But progress was slow. “People said, ‘OK, we will crack that nut,’” recalls Erik Jongedijk, a plant geneticist at KWS, a major seed company in Europe. And for a long time, “it was never cracked.”

Part of the difficulty stems from the complexity of the reproductive process researchers are trying to modify. During sexual reproduction, gametes—eggs and sperm—are created through meiosis, a process that results in haploid cells, with half the number of chromosomes. To form embryos with a full complement of chromosomes, eggs and sperm need to come together. Many naturally apomictic plants instead create gametes through mitosis, with no change in the chromosome count. The eggs can then turn into an embryo without being fertilized, in a process known as parthenogenesis.

It’s taken decades to identify some of the genes involved and to figure out how to tinker with them. In 2009, a group of scientists led by Raphaël Mercier, a geneticist now at the Max Planck Institute for Plant Breeding Research, showed that if they knocked out three genes involved in meiosis in the model plant Arabidopsis, it would make gametes through mitosis, preserving their full set of chromosomes. They named the trio of mutations MiMe, short for “mitosis instead of meiosis.” In 2016, they replicated the feat in rice, showing that the MiMe mutations would create diploid eggs genetically identical to the mother plant.  .... ' 

Sensors and AI Improve Plant Environments

 Via BBC,  Claim to improved agriculture. 

'We talk to plants - they tell us how happy they are'

Vertical farming - growing plants indoors, on stacked levels, in a highly controlled environment - allows higher yields.

And now, the Gardin company hopes to further improve productivity, using sensors and artificial intelligence to assess individual leaves and suggest changes to each plant's environment.

BBC Click's Laura Goodwin reports.

Wearable for Plants

Completely new to me, but have done some work in agri, seems a good directiion.

ACM TECHNEWS

Wearable Technology for Plants   By American Chemical Society, May 12, 2022

Researchers have developed a wearable sensor for plant leaves that enables remote management of drought stress in gardens and farms.  The goal is to detect water loss early, as visual signs like shriveling or browning leaves emerge when most of the plant's water is gone.

The researchers developed one electrode comprised of nickel, and another made from partially burnt paper coated with a waxy film.   In a test of the electrodes on detached soybean leaves, the researchers found the nickel-based electrodes adhered better to the leaves and generated larger signals as the leaves dried out.

Using the nickel-based electrodes, the researchers then created a wearable device and attached it to a living plant.  They used a machine learning technique to convert the data, which was transmitted wirelessly by the device to a smartphone app and website, to the percent of water content lost.

From American Chemical Society

View Full Article   

Plants Talking

 Am a long-time amateur botanist, and heard of such things long ago, thought little of it, but the science is still evolving.    Here an excerpt of work underway:

Some aspects of plant behavior can be studied in the same terms as animal or human behavior

DENYSE O'LEARY APRIL 9, 2022  in Mindmatters

One genuine surprise in recent decades has been the discovery that plants have nervous systems like animals and use some of the same compounds in communications — for example, TMAO to relieve stress and glutamate to speed transmission.

Venus flytrap at work

Biologist Peter Rogers pointed out recently that the similarities may shed a bit of light on issues around anaesthesia. Surprisingly, it is possible to anesthetize a plant. The shameplant (Mimosa pudica) and the Venus flytrap demonstrated that:

Thirty years after anesthesia debuted in the operating room, Claude Bernard, a French physiologist, demonstrated that the shameplant (Mimosa pudica), which bashfully folds into itself when touched, was unresponsive to touch after exposure to ether, a commonly used anesthetic. The plant also folds into itself at night time, but this movement was not affected by anesthesia. Bernard concluded that anesthesia does not inhibit the ability to move; rather, it inhibits the plant’s ability to sense its environment. That is to say, anesthesia blocks consciousness…

PETER ROGERS, “HOW VENUS FLYTRAPS GIVE SCIENTISTS INSIGHTS ON CONSCIOUSNESS AND ANESTHESIA” AT BIG THINK (MARCH 27, 2022)  ...... '

Portable Device Can Quickly Detect Plant Stress

Powerful idea.   Here wondering how well the measure of stress works for various crops.

Portable Device Can Quickly Detect Plant Stress

MIT News,  January 4, 2021

A device developed by researchers with the Singapore-Massachusetts Institute of Technology (MIT) Alliance for Research and Technology and Singapore's Temasek Life Sciences Laboratory (TLL) can read plant health, enabling sustainable crop yield maximization. The portable Raman leaf-clip sensor can diagnose nitrogen deficiency in plants, which can be connected to premature leaf deterioration and yield loss. MIT's Rajeev Ram said, "Our findings showed that in vivo measurements using the portable leaf-clip Raman sensor under full-light growth conditions were consistent with measurements obtained with a benchtop Raman spectrometer on leaf sections under laboratory conditions." TLL's Nam-Hai Chua said the sensor "was demonstrated on multiple vegetable varieties and supports the effort to produce nutritious, low-cost vegetables as part of the Singapore 30-by-30 initiative."

Identification of Plants and Weeds

Have been testing a plant recognition system for some time.   Effectiveness varies, but continues to improve.

Deere's Farm Version of Facial Recognition Coming to Fields in 2021   By CNBC

Agriculture giant Deere & Co. plans to roll out a system next summer that combines machine vision and machine learning to improve the identification of individual plants and weeds.

Deere's Jahmy Hindman said neural network models could be trained to only spray weeds in crop fields, killing everything except genetically modified plants designed to survive chemical applications.

Said Hindman, "We are interested in being able to manage each plant over the course of its life, minimizing inputs and maximizing productivity."

The technology would take pictures of plants, and a machine cruising the field would make the decision to spray in just seconds.

Jeffries' Stephen Volkmann said, "See-and-spray is one of several advanced farming technologies that seem to be moving closer to an inflection point," but commercialization of full plant recognition technology is still a few years away. ... '

Pollinating by Drone and Bubbles

Fascinating detail.   As a long time part time botanist, of interest. But how well can it effectively being done?  Will the use of drones interfere with natural methods?  Depends on the plants involved and their current pollination mechanisms.  A form of biomimicry.   Also a likely way path for developing smaller drones

Drone With Bubble Machine Can Pollinate Flowers Like a Bee
Pollen-carrying soap bubbles could provide a simple and effective method of artificial pollination  By Evan Ackerman in IEEE Spectrum

Researchers in Japan developed a drone equipped with a bubble maker for autonomous pollination.

The tiny biological machines that farms rely on to pollinate the flowers of fruiting plants have been having a tough time of it lately. While folks around the world are working on different artificial pollination systems, there’s really no replacing the productivity, efficiency, and genius of bees, and protecting them is incredibly important. That said, there’s no reason to also work on alternate methods of pollination, and researchers at the Japan Advanced Institute of Science and Technology (JAIST) have come up with something brilliant: pollen-infused soap bubbles blown out of a bubble maker mounted to a drone. And it apparently works really well.  ... " 

Sensors for Plant Stress

Possible applications for sensing problems with crops.

Nanosensor can alert a smartphone when plants are stressed
Carbon nanotubes embedded in leaves detect chemical signals that are produced when a plant is damaged.

Anne Trafton | MIT News Office

MIT engineers have developed a way to closely track how plants respond to stresses such as injury, infection, and light damage, using sensors made of carbon nanotubes. These sensors can be embedded in plant leaves, where they report on hydrogen peroxide signaling waves.

Plants use hydrogen peroxide to communicate within their leaves, sending out a distress signal that stimulates leaf cells to produce compounds that will help them repair damage or fend off predators such as insects. The new sensors can use these hydrogen peroxide signals to distinguish between different types of stress, as well as between different species of plants.

“Plants have a very sophisticated form of internal communication, which we can now observe for the first time. That means that in real-time, we can see a living plant’s response, communicating the specific type of stress that it’s experiencing,” says Michael Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT.

This kind of sensor could be used to study how plants respond to different types of stress, potentially helping agricultural scientists develop new strategies to improve crop yields. The researchers demonstrated their approach in eight different plant species, including spinach, strawberry plants, and arugula, and they believe it could work in many more.

Strano is the senior author of the study, which appears today in Nature Plants. MIT graduate student Tedrick Thomas Salim Lew is the lead author of the paper.  ... " 

https://www.nature.com/articles/s41477-020-0632-4

Plant Breeding Towards Goals

Goes along my agriculture and botany threads.    Some exiting things happening in this space.  Most recently my interests have been in horticultural innovation, but the applications are broad.

Professor Thomas Bjorkman studies broccoli in a field Software Helps Plant Breeders Bring Out
Their Best

Cornell Chronicle (NY)
By Melanie Lefkowitz

Cornell University researchers have developed a software program based on a statistical method to standardize evaluations of broccoli, to make plant-breeding decisions more consistent and efficient. Breeders can use the open source RateRvaR software to select desired traits and ask multiple people to perform the same evaluation; the program analyzes that data to determine which traits are more or less important in predicting overall quality. The software also can identify traits that do not seem relevant to overall quality, so breeders can collect less data and still get accurate results. Said Cornell researcher Zachary Stansell, "This approach can standardize evaluations and make them faster and more efficient, and it can also reveal individual biases in how a human might respond to a particular variety of a vegetable or plant."  .....

Google Lens Redesigned: Plant Identification

I see that Google Lens for IOS has been redesigned and the App updated.  Before the update did considerable experimentation with it as a plant identifier, especially at multiple stages of plant development,  showed it was not very useful for that.    Looking forward to see what improvements have been made.   Anyone else out there looking at this function, please connect.   Will report back.  (Note I posted a number of speculative blogs on Google Lens usage, see the tag below)

Plants as Sensors and Cyborgs

Have been a long time amateur botanist.    So much like the direction suggested here. Designing alerting and circuits inside plants.   Could a field of corn alert the farmer when it is ready to harvest?  Or was being attacked by weeds?   Trees are being attacked by pests in my backyard, could they alert me to  the need for action?   Bring on the idea, ready to test.

Plants Are Oldest Sensors in the World. Could They Be the Future of Computers? 
Fast Company
By Katharine Schwab

The Massachusetts Institute of Technology's Harpreet Sareen suggests plants as a new building material for computer circuits. Based on previous work using leaves as motion detectors and signal transmitters, Sareen's Phytoactuators project enables computers to send electronic signals back to plants, transforming them into alert systems. "Our vision is to have this layer of digital interaction within the plants themselves so we can not only sense signals through them, but also connect our digital responses with the plant's responses," said Sareen, who envisions such systems as tools for "soft notifications," like the arrival of package deliveries triggering signals, to instruct houseplants to retract their leaves. The more advanced Planta Digitalis project has embedded a conductive wire into a plant stem, linked to a computer and functioning as a sensor, as a first step toward designing circuits inside plants. ... "

The MIT Media Lab work this is referencing:
Cyborg Botany: Augmented plants as sensors, displays, and actuators   By Harpreet Sareen 

Cyber Agriculture

My own strong interest and background in botany makes me consider this closely, consider the implications.  In particular have been experimenting with basil flavors for years.   While the smells of basils can be considerable, they often do not perform as distinctly in dishes.   Can we program in robust flavors?  Following.

MIT’s ‘cyber-agriculture’ optimizes basil flavors   By Devin Coldewey @techcrunch

The days when you could simply grow a basil plant from a seed by placing it on your windowsill and watering it regularly are gone — there’s no point now that machine learning-optimized hydroponic “cyber-agriculture” has produced a superior plant with more robust flavors. The future of pesto is here.

This research didn’t come out of a desire to improve sauces, however. It’s a study from MIT’s Media Lab and the University of Texas at Austin aimed at understanding how to both improve and automate farming.

In the study, published today in PLOS ONE, the question being asked was whether a growing environment could find and execute a growing strategy that resulted in a given goal — in this case, basil with stronger flavors.

Such a task is one with numerous variables to modify — soil type, plant characteristics, watering frequency and volume, lighting and so on — and a measurable outcome: concentration of flavor-producing molecules. That means it’s a natural fit for a machine learning model, which from that variety of inputs can make a prediction as to which will produce the best output.

“We’re really interested in building networked tools that can take a plant’s experience, its phenotype, the set of stresses it encounters, and its genetics, and digitize that to allow us to understand the plant-environment interaction,” explained MIT’s Caleb Harper in a news release. The better you understand those interactions, the better you can design the plant’s lifecycle, perhaps increasing yield, improving flavor or reducing waste.  .... " 

Robotic Houseplant Moves to Light

Kind of obvious, but made me think more generally about the robotics of the problem.   And adding other dimensions like nutrients and water.    Plus the sensors needed to do that effectively, and the dependence on the architecture of the 'field'.  Reminds me too of robot weed pulling and zapping solutions.

MIT researchers create a robot houseplant that moves on its own

By Rachel England, @rachel_england in Engadget

Identifiying Plant Disease

Out of the fall garden and back to the possibilities of pattern recognition.  Back to my alternate botanic tech universe.  Penn State work using deep learning to identifying plant disease.  Great example:

 Phone Powered AI Spots Sock Plants with Remarkable Accuracy,   by Matt Simon, Science

Researchers at Pennsylvania State University (PSU) say they have designed a smartphone-based neural-network program that can automatically identify diseases in the cassava plant with near-flawless accuracy. The network is based on Google's open source TensorFlow machine-learning library, and Google's Pete Warden notes the TensorFlow Mobile app requires only about 25 million parameters, versus the hundreds of millions some networks need. "It only requires about 11 billion floating point operations to actually calculate its result, and some other networks require hundreds of billions of operations to do a similar job," Warden notes. He also says thanks to transfer learning, the network was trained to recognize cassava leaves on much less data. "It really comes down to the data, because garbage in, garbage out," says PSU's Amanda Ramcharan. She believes the growing affordability of smartphones and the continuing simplification of algorithms will combine to make such tools more widely available to farmers. ... " 

Plantoids: Plant Robotics

I am a botanist from way back, so from time to time you will see tech oriented agri and horti cultural notes.   Here from Kickstarter, a still unavailable robotic plant pot that seeks out the best place to live in an environment.  Not very practical, but you might think of ways to have larger scale applications of the idea.  See previous examples of the Tertill plant tending robotic,   more practical I think, but scalability a big problem.

" .. Concept:

Our Plantoids are practical. We actually build plant brained robots (no more abstract models), and approach the educational topics from a mindset of building a model with real hardware and code that results in physical experiments. Your plant-robot cyborg dream can become reality. 

Sensory Input:

The key is using sensors and data to expand and support the survival of the plant specimen on the robot. When you can achieve that, the robot can perform interesting experiments and missions to expand life to new environments--previously devoid of life! 

Using an Arduino-based sensory suite to provide data on the quality of life of its plant center, a Plantoid can autonomously explore its environment in search of the best location for its own prosperity. Modeling the extension of life can lead to literacy that may inspire new solutions to big problems that we face today: send life to other planets, change food production, or model survival and sustainability in harsh environments. 

Currently, the sensors included in the Plantoids Base Kit:

Soil moisture
Air temperature and humidity
Ambient light
Air quality sensors.  .... " 

Identifying Plant Species

Another example of using many images to train via AI.   Also describes the data needs for such a process, done via Deep Learning neural methods.

From the CACM: 
Digitizing plant specimens is opening up a whole new world for researchers looking to mine collections from around the world.

Computer algorithms trained on the images of thousands of preserved plants have learned to automatically identify species that have been pressed, dried and mounted on herbarium sheets, researchers report. ....  " 
Artificial Intelligence Identifies Plant Species for Science  In Nature 
" .... Bonnet's team had already made progress automating plant identification through the Pl@ntNet project. It has accumulated millions of images of fresh plants — typically taken in the field by people using its smartphone app to identify specimens.

Researchers trained similar algorithms on more than 260,000 scans of herbarium sheets, encompassing more than 1,000 species. The computer program eventually identified species with nearly 80% accuracy: the correct answer was within the algorithms’ top 5 picks 90% of the time. That, says Wilf, probably out-performs a human taxonomist by quite a bit. .... " 

Tertill Weeds Gardens

Really like the premise.  From my IdeaConnection affiliation. I have decades of experience managing garden plantings, big and small, so pardon me for having considerable skepticism about the practical application.  Even more so at commercial scale.  But particularly like the potential to do this in a swarming way as well.   But the garden can be a hostile place.  Would love to give it a practical test. Will certainly follow.  Kickstarter.

The Tertill solar powered weeding robot from Franklin Robotics removes weeds without chemicals.

A bit like a Roomba for the yard, the Tertill travels the garden to seek out weeds and cut them down with a small ‘weed-whacker’ thread at its base. The Tertill will treat all small plants as weeds, so intentional plants must first be protected by the provided plant collars. Any plants tall enough to touch the device’s sensor will trigger the Tertill to turn away, and seek weeds elsewhere. .... " 

Indoor Smart Garden

I am a long time gardener, nursery planner and amateur botanist,  and a practitioner of 'smart', so this was intriguing.   Seems impractical for any reasonable and useful volume of results.   Still,  makes me think about what might work.

Indoor Smart Garden uses Artificial Intelligence to Grow Real Plants   By Lulu Chang 

No one will know if you lack a green thumb so long as you have a smart garden. No matter how agriculturally dumb you may be, artificial intelligence is here to help. It comes in the form of AVA Byte from AVA Technologies. Heralded as the first indoor smart garden to combine AI technology, including machine learning, and a straightforward user experience, you can have a farmer’s market right in your own home.

By leveraging “continuously optimized” algorithms, the AVA Byte purports to be able to sustain year-round plant cultivation. Whether you’re interested in growing vegetables, micro-greens, fruits, or even mushrooms (apparently, AVA is among the first indoor gardening device to offer fungus support), you can do it with this garden.

The AVA Byte depends on LED lights that emit a mixture of red, white, and blue light to encourage growth, fruiting, and flowering regardless of your home environment. Its hydroponic irrigation system allows you to water every few weeks instead of every few days, and a companion app will keep you updated on your plants’ progress. .... " 

Flower and Plant Recognition

As a Botanist of sorts, always of interest.   And how it differs from face recognition.

Machine Learning Researchers Team Up With Chinese Botanists on Flower-Recognition Project

Microsoft Research Asia scientists, working with botanists at the Institute of Botany, Chinese Academy of Sciences (IBCAS), have developed the Smart Flower Recognition System, which is designed to quickly identify any flower or plant.

The researchers trained a deep neural network to recognize images using a set of learnable filters. Each filter is initially convolved across the width and height of the input volume, computing the dot product between the entries of the filter and the input. The process produces a two-dimensional activation map of that filter, and the system then learns filters that activate specific types of features at a given spatial position in the input.

After entering millions of pictures into the deep-learning framework, the researchers say they enabled the engine to accurately identify images more than 90% of the time. ... " 

Visualizing Small Species in our Lives

Brought to my attention, somewhat specialized, but links to some of my work and interest in Botany, horticulture and agriculture.   It is also useful to see unexpected linkages between sciences. " ...  Rob Dunn and the scientists, communicators and volunteers in his lab aim to tell the stories of the small species–whether on our bodies, under our beds or in our backyards–humans interact with every day but tend to ignore. The ecology and evolution of these species in our private places has barely begun to be explored ... "