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If you’ve ever dined on the tropical island of Okinawa, Japan, your plate may have been graced by a remarkable pile of seaweed, each strand adorned with tiny green bubbles. Known as umi-budo or sea grapes, the salty snack pairs well with rice, sashimi and a tall glass of beer. But umi-budo is more than an iconic side dish; it’s a staple crop for Okinawan farmers. Researchers at the Okinawa Institute of Science and Technology Graduate University (OIST) recently decoded the sea grape genome to learn about the plant’s unique morphology and assist farmers in proper cultivation of the succulent seaweed.

“Many farmers face problems with sea grapes growing poorly. Today, they don’t know why such problems occur,” said Dr. Asuka Arimoto, first author of the study and a postdoctoral scholar in the OIST Marine Genomics Unit, led by Prof. Noriyuki Satoh. “Our genomic data can show them which genes are causing such trouble.” With a catalog of all the genes controlling sea grape growth, said Arimoto, the researchers may be able to help farmers diagnose deficient plants when they crop up. The research could also help curb the spread of closely-related green seaweeds, which harm the environment by pushing out local plant varieties in the Mediterranean Sea and Pan-Pacific.

The study, in DNA Research, utilized sample sea grapes from the Onna Village Fishery Cooperative, whose greenhouses are located just around the corner from OIST campus. The scientists deciphered the full sea grape genome and compared it to 15 published plant genomes, collected from unicellular algae, a type of moss, rice and thale cress. The research revealed key genes that allow sea grapes, a unicellular organism, to don its complex shape, and demonstrated the utility of using the algae to explore evolutionary processes in green plants.

“Recently, other countries have started cultivating this and related species of green seaweed,” said Arimoto. “I think this genomic information could help their future development, as well as Okinawa prefecture.”

Collection of Genes Creates “Puchi Puchi”

Tiny green balls branch off the central stem of the umi-budo plant, and when chewed, these teeny orbs burst in a pop of salty goodness. In Japanese, this sensational texture is known as “puchi puchi,” an onomatopoeia mimicking the sound of puny pops. The Marine Genomics Unit was curious as to how a plant made up of just one cell could grow into such a fantastical shape, thus granting sea grapes their singular texture.

“When we started the project, there were no [decoded] green seaweed genomes,” said Arimoto. “It was completely unknown how many genes are present in green seaweed, and which plant hormones are present to drive development.” The researchers succeeded in deciphering a high-quality genome from an umi-budo plant and compared it to known plant genomes to see whether certain genes appeared in different quantities between them.

The results suggest that the sea grapes contain an expanded set of genes thought to be descended from a core gene set found in a common ancestor of green plants. Among these genes are those that code for nuclear transport regulators—proteins that help control how information moves between the nuclei and the cytosol, the liquid in which a cell’s organelles float. In multicellular organisms, transport regulators tune whole cells to only receive certain signals, like a dial on a radio. In umi-budo, a unicellular organism, the proteins do the same for individual nuclei in the cell.

The mechanism allows single cells to take on complex shapes despite lacking cell membranes to separate one region from the next. Without nuclear transport regulators, sea grapes couldn’t grow in their signature clusters.

Compared to other green algae, sea grapes also have extra genes to code for homeobox proteins, which help to regulate the physical development of plants. Homeobox proteins flip switches on critical genes to turn them “on” or “off,” said Arimoto, which triggers cellular processes and shapes an organism’s anatomical structure down the line.

Helping Sea Grape Farmers in Okinawa and Beyond

In the future, the Marine Genomics Unit hopes to analyze gene expression as it occurs throughout the sea grape life cycle. For instance, evidence suggests that specific homeobox genes are highly expressed in the pollens and eggs of land plants. They may hold similar importance in the early life stages of umi-budo. As sea grape cultivation takes root beyond Okinawa and across the Pacific, this genomic data could help farmers establish more effective growing strategies.

While OIST researchers work with umi-budo in the lab, food-lovers can continue to order the delectable seaweed in restaurants across Japan, likely topped with a light dressing of vinegar, mirin and soy sauce. Oishi!

Read the paper: DNA Research

Article source: Okinawa Institute of Science and Technology Graduate University (OIST)

Image: Ken Maeda (OIST)

Duckweeds – for many aquatic animals like ducks and snails, a treat, but for pond owners, sometimes a thorn in the side. The tiny and fast-growing plants are of great interest to researchers, and not at least because of their industrial applications – for example, to purify wastewater or generate energy. An international research team from Münster, Jena (both Germany), Zurich (Switzerland) and Kerala (India) have recently studied the genomics of the giant duckweed. They discovered that genetic diversity, i.e. the total number of genetic characteristics that are different among individuals, is very low. “This is remarkable given that their population size is very large – there can, for example, be millions of individuals in a single pond”, says Shuqing Xu, professor for plant evolutionary ecology at the University of Münster and lead author of the study.

To understand the reason behind this mystery, a team of plant researchers headed by Dr. Meret Huber from the Max Planck Institute for Chemical Ecology in Jena and the University of Münster measured the mutation rate of this duckweed under outdoor conditions, i.e. how many mutations accumulate per generation. The result: low genetic diversity in this plant was accompanied by an extremely low mutation rate. “Our study emphasizes that accurate estimates of mutation rates are important for explaining patterns of genetic diversity among species”, says Meret Huber. The results are not only relevant for future studies on the evolution of plants, including many crops that have similar reproductive strategies like duckweeds, they will also accelerate the use of duckweeds both for basic research and industrial applications. The study was published in the journal “Nature Communication”.

Background

Although mutations are the raw materials for evolutionary changes, they are often accompanied by fitness impairments. Evolutionary researchers have hypothesized that natural selection in species with large populations drives the mutation rate to as low as possible. According to this hypothesis, a species with a very large population size may under certain conditions evolve an extremely low mutation rate – which in turn can result in a very low genetic diversity. Until now, however, scientists had not been able to show this connection in eukaryotes, i.e. organisms whose cells have a nucleus. One reason for this is that mutation rates are difficult to measure experimentally.

The researchers took samples of the giant duckweed (Spirodela polyrhiza) from 68 waterbodies distributed all over the world and read the DNA sequences of their entire genomes. They found that in congruence with their geographic origin the samples fall into four genetic clusters: America, Europe, India and Southeast Asia. Based on the genome sequence information, they found that the genetic diversity of the species is among the lowest values reported in multicellular eukaryotes.

Because genetic diversity is determined by mutation rate and effective population size, the scientists then experimentally estimated the mutation rates and calculated effective population size. Since external conditions can influence the mutation rate, they performed the experiments under outdoor conditions. The result: by sequencing genomes, they found that the mutation rate in the giant duckweed was the lowest ever determined for multicellular eukaryotes. The estimated effective population size, as expected, is rather large.

The researchers suspect that the enormous population size of the giant duckweed, and therefore the large possibilities of selection in the course of evolution, has led to the reduction of mutations to a minimum. This in turn can explain the low genetic diversity. “Our study provides new insights into why and how genetic diversity differs among different species”, says Shuqing Xu.

Together with their collaborators, the scientists are currently working on analyzing genomes of even more duckweed samples and plan to carry out outdoor selection experiments. They wish to discover which other factors might have played roles in shaping the evolution of this plant.

Read the paper: Nature Communication

Article source: University of Münster

Image: Close-up of the giant duckweed. Credit: Klaus J. Appenroth

Crops just can’t do without phosphorus.

Globally, more than 45 million tons of phosphorus fertilizer are expected to be used in 2019. But only a fraction of the added phosphorus will end up being available to crops.

The impact is two-fold: financial and environmental. “Fertilizer costs are significant for farmers in south Florida,” says Tiedeman. “And phosphorus rock, the most widely used source of phosphorus fertilizer, is in low supply across the globe. It is thought that phosphorus rock resources will only be available for the next 50 to 200 years.”

Tiedeman is exploring whether a rarely-studied process involving soil fungi could contribute to low phosphorus availability to plants in south Florida. This research could also help unravel how land use influences fungal communities in soil. It may also help us better understand vital soil-phosphorus dynamics.

“In general, fungi play a tremendous role in cycling phosphorus within soils,” Tiedeman says. “They can release phosphorus from mineral (rock) and organic (decaying matter) sources. From there, plants take up the released phosphorus.”

But under specific environmental conditions, like those found in south Florida soils, fungi may be contributing to the problem of phosphorus unavailability. Some fungi are capable of making minerals out of elements dissolved in soil water. This process is called “bioprecipitation”. Tiedeman wonders if fungi can take dissolved (plant-available) phosphorus and convert it to less available mineral forms.

The soils of south Florida add another layer to the puzzle. “Agricultural soils in south Florida are quite unique,” says Tiedeman. “They were created by pulverizing limestone bedrock to create rocky calcareous soil.”

“Over time, this coating can become a ‘seed’ for more stable, less available forms of phosphorus.” says Tiedeman.

Without freed-up phosphorus, crops can’t grow successfully. So many farmers in south Florida have kept adding phosphorus to soils. In a continuing cycle, most of this phosphorus becomes unavailable to plants. Over time, large amounts of unavailable phosphorus have collected in these soils. “Some agricultural soils in the area have 100-200 times more phosphorus than what was naturally present. Along with high concentrations of P, the types of P compounds present in these soils are perplexing. Recent studies have documented the presence of apatite – a phosphorus crystal that generally requires intense heat and pressure in order to form. One hypothesis, which is driving Tiedeman’s research, is that microorganisms in the soil are creating stable phosphorus minerals.

To investigate whether fungi are able to create phosphorus minerals, Tiedeman is bringing the fungi into the lab. This allows her to explore several questions: How do local soil fungi respond to doses of available phosphorus while living in limestone soils? Do fungi contribute to the crystallization of phosphorus?

“We plan to analyze fungal samples and any biproducts of their growth using a scanning electron microscope,” says Tiedeman. “That would allow us to actually look for crystal forms of phosphorus. It may also help us better understand how fungi get crystals to form.”

“Investigating south Florida’s limestone soils may have implications beyond a regional scale,” says Tiedeman. “Identifying all processes involved in phosphorus unavailability in calcareous soils will be useful in developing strategies to improve fertilizer use efficiency. This could be of great benefit to producers and the environment.”

Tiedeman presented her research at the International Meeting of the Soil Science Society of America, Jan. 6-9, San Diego.

Article source: American Society of Agronomy

Image credit: Mary Tiedeman.

Salinity stress is considered one of the most important abiotic factors that limits the productivity of crop plants, and the estimated global cost due to salinity is more than $12 billion annually. This is due to the extensive use of irrigation and high rates of evapotranspiration, which result in increased salt accumulation in the soil.

A study out of The USDA Agricultural Research Service at the University of Wisconsin has evaluated the response of diverse carrot germplasm to salinity stress, identified salt-tolerant carrot germplasm that may be used by breeders, and defined appropriate screening criteria for assessing salt tolerance in germinating carrot seed.

Adam Bolton and Philipp Simon focused on carrots in their research of glycophytic plants. Most crops, including cultivated carrots, are categorized as glycophytic plants. The growth of glycophytes is greatly reduced in saline soils because they lack physiological mechanisms such as the salt glands and bladders that allow halophytes, or salt-loving plants, to thrive in high salinity.

Bolton and Simon postulate that this type of extensive evaluation is needed to develop varieties that are considered fully salt-tolerant at each developmental stage for carrots.

Their research is explained in the article “Variation for Salinity Tolerance During Seed Germination in Diverse Carrot Germplasm”, found in HortScience, published by The American Society for Horticultural Science.

Bolton and Simon note that one approach to combating the negative effects of salinity stress in glycophytic crops is identifying new genetic sources of tolerance and efficient phenotypic methods to develop salinity-tolerant cultivars.

Data collected from many crop species suggest that the level of salinity tolerance is highly dependent on the developmental stage of the plant. This life stage-specific tolerance means that a genotype that has tolerance at one life stage may not be tolerant at any other of its life stages. Therefore, to more efficiently identify tolerant genotypes, their evaluations needed to continue throughout the varying stages of ontogeny of the plant, from germination through the reproductive phase.

Screening for salt tolerance at the germination stage is the first step in identifying tolerant genotypes because it is a critical stage for plant development. Fortunately, the researchers discovered, screening at this stage is among the most rapid and economical stages of development to evaluate a large number of diverse germplasm accessions.

Bolton and Simon used multiple criteria for quantifying salt tolerance. This broad approach demonstrated wide phenotypic variations during the seed germination stage among diverse carrot accessions. Significant differences in the percent of seed germination under nonstress conditions and for all salt tolerance germination measurements were observed among the 14 different regions of carrot accession origin.

Ultimately, this study identified a wide range of phenotypic variations for salt tolerance during the germination stage in a collection of diverse carrot accessions. These accessions could serve as potential parents for creating mapping populations to identify the specific genotype associated with salt tolerance. This discovery is promising for breeders as it suggests a route for them to move toward generating healthy plant crop cultivars with additional tools for growing on salt-affected soil.

Simon adds, “In previous studies, carrots have been characterized as a crop that is sensitive to salinity. This study evaluated a large collection of wild and cultivated carrot germplasm and confirmed that, in fact, many carrot cultivars are saline-sensitive during seed germination, but that many germplasm accessions evaluated were quite saline-tolerant. Interestingly, many of the more saline-tolerant carrots evaluated were cultivated carrots, perhaps reflecting unintentional selection by farmers that have been growing the crop with saline irrigation water. This study provides an optimistic outlook for breeding carrots with improved salinity tolerance during germination. Tolerance during seeding and later plant development will also be needed as salinity becomes a more serious challenge for farmers.”

Read the paper: HortScience

Article source: American Society for Horticultural Science

Image credit: Markus Spiske / Pixabay

California produces 99 percent of the walnuts grown in the United States. New research could provide a major boost to the state’s growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California’s 4,800 growers.

In a new study, a team of scientists at the University of California, Davis, and USDA’s Agricultural Research Service, ARS used a unique approach to sequence the genomes of the English walnut and its wild North American relative by tapping into the capabilities of two state-of-the-art technologies: long-read DNA sequencing and optical genome mapping. The resulting genome sequences are believed to be of the highest quality ever assembled of any woody perennial.

“By sequencing the genome of a walnut hybrid, we produced complete genome sequences for both parents in the time normally required to produce the sequence of one genome,” said Ming-Cheng Luo, leading genomics investigator on the project and a research geneticist in the Department of Plant Sciences at UC Davis.

This approach could be applied to genome sequencing of trees and many other woody perennials, opening the door to a better understanding of the genetic blueprints of almonds, pecans, pistachios and grapes.

“Like walnut, these other crops naturally cross-pollinate and are therefore highly variable,” said Jan Dvorak, co-principle investigator and genetics professor at the Department of Plant Sciences at UC Davis. “Variability has always greatly complicated our ability to produce a high-quality genome sequence for such crops, but these new technologies now make it possible,” Dvorak added.

In California, walnuts are grown commercially using rootstocks chosen specifically for their ability to tolerate various soil-borne diseases.

“We chose to cross the widely used English walnut specifically with the wild Texas Black walnut because of its native resistance to several soil-borne diseases and root nematodes, which are serious pests of walnut in California,” said Dan Kluepfel,a USDA-ARS scientist and principal investigator of the walnut-rootstock development project.

The assembled genome sequences of the two walnut species also will now help researchers identify genetic markers that breeders can use to develop new varieties with improved pathogen and pest resistance.

Major contributors to the project included UC Davis scientists Tingting Zhu, Le Wang, and Agriculture and Agri-Food Canada scientist Frank You.

Read the paper: Horticulture Research

Article source: USDA’s Agricultural Research Service (ARS)

Image credit: Suju/ Pixabay

A national-scale study of U.S. forests found strong relationships between the diversity of native tree species and the number of nonnative pests that pose economic and ecological threats to the nation’s forests.

“Every few years we get a new exotic insect or disease that comes in and is able to do a number on our native forests,” says Kevin Potter, a North Carolina State University research associate professor in the Department of Forestry and Environmental Resources and co-author of an article about the research in Proceedings of the National Academy of Sciences.

“Emerald ash borer is clobbering a number of ash species in the Midwest and increasingly in the South. The chestnut, a magnificent tree that had immense ecosystem value as well as economic value in the South and North, is pretty much gone because of a pathogen. And hemlocks are under attack by the hemlock woolly adelgid from the Northeast along the Appalachian Mountains into the South.”

To better understand how nonnative insects and diseases invade U.S. forests, researchers tested conflicting ideas about biodiversity. The first is that having more tree species can facilitate the diversity of pests by providing more places for them to gain a toehold. Another possibility is that tree biodiversity can have protective effects for forests, such as by diluting the pool of host trees and making it harder for pests to become established.

“We found that both facilitation and dilution seem to be happening at the same time,” Potter says. “What we found is that native tree biodiversity really is important, but it’s important in different ways at different times.”

Combining two national county-level data sets, researchers found that relationships between tree diversity and pest diversity follow a hump-shaped curve.

“As you have an increasing number of tree species, you have an increasing number of pest species, up to an inflection point where that relationship changes,” Potter says. “Then you have a decreasing number of pest species as the number of host tree species increases.”

Overall, counties where forests have 30 to 40 different host tree species tend to have the most nonnative pests. But the effects depend on whether the invader is a specialist that can infest only a single tree species or whether it’s a generalist, like the gypsy moth, which can spread to more than 60 different hosts.

“What we see is that forests in the Midwest and up into New England are at the middle part of that hump-shaped curve in terms of the number of host tree species, and those are places where there have been a lot of insect and disease problems,” Potter says.

“Out West we have fewer insect and disease pests, but in some cases they still do a lot of damage because the forests are not diverse. If you have a specialist pest come in and knock back one of the major components of your biodiversity, then that can have a greater impact. An example of how that works would be Sudden Oak Death, a disease in California that’s affecting oaks there.”

Researchers with the U.S. Forest Service, Purdue, NC State, Czech University of Life Sciences and Duke collaborated on the study, which used two large datasets. The U.S. Forest Inventory and Analysis, a national forest census, contains information from 135,000 forested plots across the U.S. where crews regularly measure trees and check environmental conditions. For this study, the FIA data were used to compile counts of tree species for each of 2,098 counties. The Alien Forest Pest Explorer database offers a county-level record of the presence or absence of nonnative insects and diseases, including 66 used for this study.

Researchers also examined other factors that could affect pest invasions, such as human population density and environmental conditions, including precipitation, elevation and average temperature. Tree biodiversity was a better predictor of nonnative pests, Potter says.

Results could help prioritize monitoring efforts for forests most at risk for future pest invasions, he says.

“The unfortunate reality is that a lot of times we don’t notice these exotic pests and diseases until they’ve gotten established and start having an impact on our native species, when it’s almost too late.”

Read the paper: PNAS

Article source: NC State University

Image credit: Kevin M. Potter, NC State University

Crop models are parameterization schemes that simulate the processes of crop development and production. Their inclusion in climate models can promote the simulation ability of climate models, according to Dr. Zou Jing at the Institute of Oceanographic Instrumentation, Qilu University of Technology.

ZOU and his co-researchers from the Institute of Atmospheric Physics, Chinese Academy of Sciences/Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences/Zhejiang Institute of Meteorological Sciences, developed a new crop–climate coupled model and published their results on its evaluation in Advances of Atmospheric Sciences.

“Most previous studies coupled a single crop model into a climate model,” explains Dr. Zou, “but we considered three crop types with different farming systems in this study. We chose rice, wheat and maize, which cover 81% of the cereal-crop planting area in China. We further distinguished these crops in terms of different farming systems to provide more detailed descriptions about the actual crop planting. For example, winter wheat and spring wheat are different in our model,” he adds.

According to their findings, the new crop–climate model has an excellent ability in simulating crop phenology, and offers a slight correction of the bias in the original climate model in some typical areas.

“Our new model provides a good tool to investigate the relationship between crop development and climate change for global change studies,” says Dr. Zou. “The expectation is that the model can be applied in food production or agricultural research, if further promotion of the model’s accuracy and parameter optimization is achieved in future work,” he adds.

Read the paper: Advances of Atmospheric Sciences

Article source: Institute of Atmospheric Physics, Chinese Academy of Sciences

Image credit: WikiImages/ Pixabay

A new study by UAlberta biologists shows the first evidence of apoptosis, or programmed cell death in algae. The outcomes have broad-reaching implications, from the development of targeted antibiotics to the production of biofuels in industry.

“It sounds odd, but programmed cell death is important to all large organisms. For any cells to differentiate, they have to be able to kill cells. For example, if you injure yourself, your scab is formed with these killed-off cells,” explained Rebecca Case, associate professor in UAlberta ’s Department of Biological Sciences. “Here at the single-cell level, we’ve found that small molecules are passed from bacteria into the host algae. By doing that, the bacteria are able to tell the algae to kill itself.”

Until now, programmed cell death, also known as apoptosis, was thought to only occur in large, multicellular organisms such as animals and humans. This research shows that bacteria that live on single-cellular algae can cause programmed cell death. “It is the first documentation of true apoptosis via bacterial pathogens in microorganisms like algae,” said Case, who conducted the work with PhD graduate Anna Bramucci.

Major potential

One potential application of this research is in drug discovery and development. Unlike traditional antibiotics, which kill all bacteria, this research can be applied to develop drugs with a more fine-tuned approach, turning individual bacteria or cells on and off. Previously Case and colleagues have used this approach to find antibiotics that are effective at concentrations up to 1,000 times lower than traditional antibiotics.

“In interactions like these that occur in close proximity you can find molecules that are effective in very small concentrations,” said Case. “Going forward, that’s what we want—really potent molecules.”

Another area of interest is in natural fuels derived from living matter, called biofuels. “Algae can also be used to create lipids for biofuels,” explained Case. “If we can better understand their life cycles, we can find ways to keep them alive for longer, to produce more fuel for industry.”

Read the paper: Scientific Reports

Article source: University of Alberta

Image credit: Anna Bramucci/ University of Alberta