Rice, vital for global food security, faces production challenges during the heading-flowering stage. Traditional phenotyping struggles for large-scale analysis, prompting a shift to advanced computer vision and deep learning. While methods like SIFT and neural networks enhance rice panicle analysis, capturing dynamic growth necessitates merging field cameras with deep learning for precise, real-time monitoring.
Another fantastic year of discovery is over – read on for our 2016 plant science top picks!
January
A Zostera marina meadow in the Archipelago Sea, southwest Finland. Image credit: Christoffer Boström (Olsen et al., 2016. Nature).
The year began with the publication of the fascinating eelgrass (Zostera marina) genome by an international team of researchers. This marine monocot descended from land-dwelling ancestors, but went through a dramatic adaptation to life in the ocean, in what the lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial… species can undergo”.
One of the most interesting revelations was that eelgrass cannot make stomatal pores because it has completely lost the genes responsible for regulating their development. It also ditched genes involved in perceiving UV light, which does not penetrate well through its deep water habitat.
Plants are known to form new organs throughout their lifecycle, but it was not previously clear how they organized their cell development to form the right shapes. In February, researchers in Germany used an exciting new type of high-resolution fluorescence microscope to observe every individual cell in a developing lateral root, following the complex arrangement of their cell division over time.
Using this new four-dimensional cell lineage map of lateral root development in combination with computer modelling, the team revealed that, while the contribution of each cell is not pre-determined, the cells self-organize to regulate the overall development of the root in a predictable manner.
Watch the mesmerizing cell division in lateral root development in the video below, which accompanied the paper:
In March, a Spanish team of researchers revealed how the anti-wilting molecular machinery involved in preserving cell turgor assembles in response to drought. They found that a family of small proteins, the CARs, act in clusters to guide proteins to the cell membrane, in what author Dr. Pedro Luis Rodriguez described as “a kind of landing strip, acting as molecular antennas that call out to other proteins as and when necessary to orchestrate the required cellular response”.
This plant root is infected with arbuscular mycorrhizal fungi. Image credit: University of Zurich.
In April, we received an amazing insight into the ‘decision-making ability’ of plants when a Swiss team discovered that plants can punish mutualist fungi that try to cheat them. In a clever experiment, the researchers provided a plant with two mutualistic partners; a ‘generous’ fungus that provides the plant with a lot of phosphates in return for carbohydrates, and a ‘meaner’ fungus that attempts to reduce the amount of phosphate it ‘pays’. They revealed that the plants can starve the meaner fungus, providing fewer carbohydrates until it pays its phosphate bill.
Author Professor Andres Wiemskenexplains: “The plant exploits the competitive situation of the two fungi in a targeted manner, triggering what is essentially a market-based process determined by cost and performance”.
The transition of ancient plants from water onto land was one of the most important events in our planet’s evolution, but required a massive change in plant biology. Suddenly plants risked drying out, so had to develop new ways to survive drought.
In May, an international team discovered a key gene in moss (Physcomitrella patens) that allows it to tolerate dehydration. This gene, ANR, was an ancient adaptation of an algal gene that allowed the early plants to respond to the drought-signaling hormone ABA. Its evolution is still a mystery, though, as author Dr. Sean Stevensonexplains: “What’s interesting is that aquatic algae can’t respond to ABA: the next challenge is to discover how this hormone signaling process arose.”
Sometimes revisiting old ideas can pay off, as a US team revealed in June. In 1930, Ernst Münch hypothesized that transport through the phloem sieve tubes in the plant vascular tissue is driven by pressure gradients, but no-one really knew how this would account for the massive pressure required to move nutrients through something as large as a tree.
Professor Michael Knoblauch and colleagues spent decades devising new methods to investigate pressures and flow within phloem without disrupting the system. He eventually developed a suite of techniques, including a picogauge with the help of his son, Jan, to measure tiny pressure differences in the plants. They found that plants can alter the shape of their phloem vessels to change the pressure within them, allowing them to transport sugars over varying distances, which provided strong support for Münch flow.
BLOG: We featured similar work (including an amazing video of the wound response in sieve tubes) by Knoblauch’s collaborator, Dr. Winfried Peters, on the blog – read it here!
July
Preserved remains of rope, seeds, reeds and pellets (left), and a desiccated barley grain (right) found at Yoram Cave in the Judean Desert. Credit: Uri Davidovich and Ehud Weiss.
In July, an international and highly multidisciplinary team published the genome of 6,000-year-old barley grains excavated from a cave in Israel, the oldest plant genome reconstructed to date. The grains were visually and genetically very similar to modern barley, showing that this crop was domesticated very early on in our agricultural history. With more analysis ongoing, author Dr. Verena Schünemannpredicts that “DNA-analysis of archaeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants”.
BLOG: We interviewed Dr. Nils Stein about this fascinating work on the blog – click here to read more!
August
Another exciting cereal paper was published in August, when an Australian team revealed that C4 photosynthesis occurs in wheat seeds. Like many important crops, wheat leaves perform C3 photosynthesis, which is a less efficient process, so many researchers are attempting to engineer the complex C4 photosynthesis pathway into C3 crops.
This discovery was completely unexpected, as throughout its evolution wheat has been a C3 plant. Author Professor Robert Henrysuggested: “One theory is that as [atmospheric] carbon dioxide began to decline, [wheat’s] seeds evolved a C4 pathway to capture more sunlight to convert to energy.”
Professor Stefan Jansson cooks up “Tagliatelle with CRISPRy fried vegetables”. Image credit: Stefan Jansson.
September marked an historic event. Professor Stefan Jansson cooked up the world’s first CRISPR meal, tagliatelle with CRISPRy fried vegetables (genome-edited cabbage). Jansson has paved the way for CRISPR in Europe; while the EU is yet to make a decision about how CRISPR-edited plants will be regulated, Jansson successfully convinced the Swedish Board of Agriculture to rule that plants edited in a manner that could have been achieved by traditional breeding (i.e. the deletion or minor mutation of a gene, but not the insertion of a gene from another species) cannot be treated as a GMO.
Phytochromes help plants detect day length by sensing differences in red and far-red light, but a UK-Germany research collaboration revealed that these receptors switch roles at night to become thermometers, helping plants to respond to seasonal changes in temperature.
Dr Philip Wiggeexplains: “Just as mercury rises in a thermometer, the rate at which phytochromes revert to their inactive state during the night is a direct measure of temperature. The lower the temperature, the slower phytochromes revert to inactivity, so the molecules spend more time in their active, growth-suppressing state. This is why plants are slower to grow in winter”.
A fossil ginkgo (Ginkgo biloba) leaf with its modern counterpart. Image credit: Gigascience.
In November, a Chinese team published the genome of Ginkgo biloba¸ the oldest extant tree species. Its large (10.6 Gb) genome has previously impeded our understanding of this living fossil, but researchers will now be able to investigate its ~42,000 genes to understand its interesting characteristics, such as resistance to stress and dioecious reproduction, and how it remained almost unchanged in the 270 million years it has existed.
Author Professor Yunpeng Zhaosaid, “Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions [such as the] phylogenetic relationships of gymnosperm lineages, [and the] evolution of genome and genes in land plants”.
The year ended with another fascinating discovery from a Danish team, who used fluorescent tags and microscopy to confirm the existence of metabolons, clusters of metabolic enzymes that have never been detected in cells before. These metabolons can assemble rapidly in response to a stimulus, working as a metabolic production line to efficiently produce the required compounds. Scientists have been looking for metabolons for 40 years, and this discovery could be crucial for improving our ability to harness the production power of plants.
Attending SPPS 2015 was a fantastic opportunity to hear about progress across a really broad spectrum of plant biology research. The program included sessions on development, epigenetics and gene regulations, high-throughput biology, photobiology, abiotic stress, education and outreach, and biotic interactions. There really was something for everyone! Additionally, the organizers had made a notable effort to include a good mix of both established and early career researchers, further adding to the diversity of talks on offer.
I was struck by the contributions from the various Society awards so will focus on these.
Beautiful Stockholm where the meeting was held
SPPS awards
Gunnar Öquist (Umeå University, Sweden) was given the SPPS Award in recognition of his outstanding merited contribution to the science of plant biology. His talk entitled “My view of how to foster more transformative research” provided a reminder that the dual aims of research, both to solve problems and to seek new knowledge, are very important if global challenges are to be met.
The SPPS early career award recognizes a highly talented scientist who has made a significant contribution to Scandinavian plant biology. This year two early career awards were given. The first recipient, Ari-Pekka Mähönen (University of Helsinki, Finland), received the award for his work on growth dynamics in Arabidopsis thaliana, and showed some amazing sections to follow cambium development. Nathaniel Street (Umeå University, Sweden) also received an award for his work “Applying next generation sequencing to genomic studies of Aspen species and Norway Spruce”. Both gave great talks including strong research in these areas; it was great to see upcoming researchers take the spotlight and give us a glimpse to the future of plant biology.
Torgny Näsholm (SLU, Umeå Sweden) was awarded the Physiologia Plantarum award. This award is given to a scientist that has made significant contribution to the areas of plant science covered by the journal Physiologia Plantarum. Torgny uses microdialysis, a technique currently used by neuroscientists, to investigate the availability of soil nitrogen to plants. Data generated using this technique are now bringing into question our current view of nitrogen availability measured using traditional methods.
Additional activities included a tour of the Bergius Botanic Garden
The Popularisation prize, awarded to Stefan Jansson (Umeå University, Sweden), recognizes significant contributions to science communication and public engagement. Stefan’s work in public engagement has been wide-ranging. He has been involved with The Autumn Experiment, a citizen science project engaging schools in observation, data collection and real research. Recently Stefan published a book in Sweden, called ‘GMO’, which tackles the response of societies to genetically modified organisms.
At the congress, Stefan took over as the new President of the SPPS. This could lead to further emphasis and resources being placed on communicating science as the society moves forward.
Poster prizes
Prizes for the best posters are also awarded at the meeting. Five judges, including myself, assessed the posters, and the competition was fierce. It was impossible to split the top prize, so joint 1st prizes were awarded to Veli Vural Uslu (Heidelberg University, Germany) on “Elucidating early steps of sulfate sensing mechanisms by biosensors” and to Timo Engelsdorf (Norwegian University of Science and Technology, Norway) for “Plant cell wall integrity is maintained through cooperation of different sensing mechanisms”. Joint second prizes went to Zsofia Stangl (Umeå University, Sweden) on “Nutrient requirement of growth in different thermal environments” and to Annika Karusion (University of Tartu, Estonia) for “Circadian patterns of hydraulic and xylem sap properties: in situ study on hybrid aspen.”
Additional activities
Like any meeting, SPPS wasn’t all work and no play! Lisbeth Jonsson (Stockholm University, Sweden) and her team organized an excellent program. I feel very fortunate, on this short trip, to have had the opportunity to view Stockholm’s fine City Hall where Nobel laureates have dined, as well as the incredibly preserved Vasa ship, which sank in Stockholm bay on its maiden voyage in 1628.
I very much look forward to seeing how the society progresses in the future, and nurturing new friendships and collaborations I made at the congress.
The Drinks reception at the City Hall, walking in the footsteps of Nobel Laureates