Sales of quinoa (Chenopodium quinoa) have exploded in the last decade, with prices more than tripling between 2008 and 2014. The popularity of this pseudocereal comes from its highly nutritious seeds, which resemble grains and contain a good balance of protein, vitamins, and minerals. The nourishing nature of quinoa meant it was prized by the Incas, who called it the “Mother grain”.
Quinoa is a popular ‘grain’, but it is more closely related to spinach and beetroot than cereals like wheat or barley. Image credit: Flickr user. Used under license: CC BY 2.0.
Quinoa is native to the Andes of South America, where it thrives in a range of conditions from coastal regions to alpine regions of up to 4000 m above sea level. Its resilience and nutritious seeds means that quinoa has been identified as a key crop for enhancing food security, but there are currently very few breeding programs targeting this species.
The challenge of improving the efficiency and sustainability of quinoa production has so far been restricted by the lack of a reference genome. This week, a team of researchers led by Professor Mark Tester (King Abdullah University of Science & Technology; KAUST) addressed this issue, publishing a high-quality genome sequence for quinoa in Nature. They compared the genome with that of related species to characterize the evolution and domestication of the crop, and investigated the genetic diversity of economically important traits.
The evolution of quinoa
Tester and colleagues used an array of genomics techniques to assemble 1.39 Gb of the estimated 1.45-1.50 Gb full length of quinoa’s genome. Quinoa is a tetraploid, meaning it has four copies of each chromosome. The researchers shed light on the evolutionary history of this crop by sequencing descendants of the two diploid species (each containing two sets of chromosomes) that hybridized to generate quinoa; kañiwa (Chenopodium pallidicaule) and Swedish goosefoot (Chenopodium suecicum). Comparing these sequences to quinoa and other relatives, the team showed that the hybridization event likely occurred between 3.3 and 6.3 million years ago. A comparison with other closely related Chenopodium species also suggested that, contrary to previous predictions, quinoa may have been domesticated twice, both in highland and coastal environments.
Quinoa seeds are coated with soap-like chemicals called saponins, which have a bitter taste that deters herbivores. Saponins can disrupt the cell membranes of red blood cells, so they have to be removed before human consumption, but this process is costly, so quinoa breeders are always looking for varieties that produce lower levels of saponins.
Sweet (low-saponin) quinoa strains do occur naturally, but the genes that regulate this phenotype were previously unknown. Tester and colleagues investigated sweet and bitter quinoa strains and discovered that a single gene (TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR-LIKE 1 [TSARL1]) controls the amount of saponins produced in the seeds. The low-saponin quinoa strains contained mutations in TSARL1 that prevented it from functioning properly. This is a key target for the improvement of quinoa in the future, although farmers will have to find new ways to protect their crops from birds and other seed predators!
The high-quality reference genome for quinoa generated by Tester and colleagues is likely to be vital for allowing many exciting improvements in the future. Breeders hoping to improve the yield, ease of harvest, stress tolerance, and saponin content of quinoa can develop genetic markers to speed up breeding for these key traits, improving the productivity of quinoa varieties and enhancing future food security.
Read the paper in Nature: Jarvis et al., 2017. The genome of Chenopodium quinoa. Nature. DOI: 10.1038/nature21370
Thank you to Professor Mark Tester (KAUST) for providing information used in this post!
Another fantastic year of discovery is over – read on for our 2016 plant science top picks!
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”.
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!
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!
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.