The Western Barley Genetics Alliance announced it had identified new molecular markers to target waterlogging-tolerant genes in barley, while field trials in Western Australia last year showed promising yield results.
The Alliance is a partnership between Western Australia’s Department of Primary Industries and Regional Development, Murdoch University, University of Tasmania and the Zhejiang and Yangzhou universities in China.
Alliance director Chengdao Li said they worked with two universities in China, which were both located in regions prone to flooding and waterlogging. READ MORE
“Piriformospora indica was discovered relatively recently in northwest India, and since then has been found in other parts of the world,” notes Janusz Zwiazek, a professor of plant physiology at the University of Alberta, who is leading the research. Since Piriformospora indica’s discovery about two decades ago, researchers have been learning more and more about this interesting fungus. Zwiazek expects it will likely be classified as a type of mycorrhizal fungi.
He explains that Mycorrhizal fungi are a group of fungi that colonize plant roots, forming mutually beneficial relationships with their hosts. “Mycorrhizal fungi are very common. Probably more than 90 per cent of plant species are associated with mycorrhizal fungi in nature. Especially in soils that are poor in nutrients such as phosphorus and nitrogen, these fungi can mobilize these nutrients in the soil and make them available to plants. Mycorrhizal fungi can also protect plants against different environmental stresses such as drought, pathogens, and so on,” says Zwiazek.
“But the exception is the family of Brassicaceae, the cabbage family of plants, to which canola belongs. Cabbage family plants typically don’t form mycorrhizal associations. So they don’t have the added benefit that many other plants receive from having these helpful fungi that can do so much good.”
Luckily for canola growers, Piriformospora indica is a bit different from the average mycorrhizal fungus in a couple of ways.
“Researchers have discovered that Piriformospora indica is capable of forming associations with the roots of a number of cabbage family species,” notes Zwiazek.
Also, most mycorrhizal fungi have to be cultured in a plant host, but Piriformospora indica can be grown in a pure culture without a plant host, so it is easier to grow for commercial production of inoculants. And previous research has shown that Piriformospora indica has the ability to provide multiple benefits to host plant species, such as improving nutrient uptake, increasing stress tolerance, improving disease resistance, and enhancing plant performance.
With all those things going for Piriformospora indica, Zwiazek was keen to see how it might work with canola.
The first phase of the project was done in growth rooms where all the environmental conditions, such as temperature, light and moisture, were strictly controlled. The experiments were done under sterile conditions to exclude the possible effects of any other microbes.
“We inoculated canola plants with a fungal culture of Piriformospora indica, and we studied the effects on plant growth under different environmental conditions, which we controlled in the growth rooms,” he says. Zwiazek’s team evaluated the effects of such things as temperature stress, low nitrogen and phosphorus levels, drought and flooding stress, and salinity stress on canola growth characteristics and yields, with and without the fungus.
The biggest challenge in the project’s first phase was to develop a practical way to inoculate canola plants with the living fungus. Zwiazek explains, “In many cases, [commercial] mycorrhizal associations and mycorrhizal technology have failed because it is very difficult to inoculate the plants on a large scale, to maintain the inoculum alive long enough and develop the conditions which could be used on a commercial level and applied in practice.”
After testing various Piriformospora indica inocula and procedures, the project team has developed an innovative inoculum and protocol that are practical for applying the fungus to seeds in commercial operations. They are currently applying for a patent for this technology.
The project’s first phase is largely completed, and the results are very promising.
“The most important findings are that the fungus can colonize canola plants quite easily and quite effectively, and it can be quite effective in increasing the growth and yield of canola, especially under lower phosphorus levels,” says Zwiazek. “Also, the fungus makes the plants more resistant to low soil temperatures and low air temperatures, and to drought stress conditions.”
Now the next step is to see how well Piriformospora indica works under field conditions. So in 2016 the project team started testing the inoculant in field trials.
In these trials, Zwiazek’s team will be looking at the effects of different soil amendments (including different soil organic matter and growth-promoting bacteria) on canola growth and yield, with and without the inoculant. As well, they are doing some tests in collaboration with Mary Ruth McDonald from the University of Guelph and Habibur Rahman from the University of Alberta to see how the fungus affects the canola plant’s ability to resist clubroot and possibly other canola pathogens.
“The results of the greenhouse studies are very exciting. But everything has to be really tested in the field – this is the ultimate test. Hopefully in two or three years we’ll have a pretty good idea of how the fungus performs under field conditions, and how much farmers can actually benefit from it.”
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Funders for this research include the Agriculture Funding Consortium (AFC), Alberta and Saskatchewan canola producer groups, Alberta Innovates – Bio Solutions, and Western Grains Research Foundation.
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The GAPP funds research and development projects that address industry opportunities in order to accelerate the application of genomics-derived solutions and sustainable innovations that are beneficial to Canadians. Canola is a major driver of the Canadian economy representing $7.4 billion in farm cash receipts and over $9 billion in exports, primarily to China, Japan, Mexico and the United States. Canola also serves a critical role in our global food system. Seeds are crushed into a cooking oil that is one of the lowest in saturated fats, making it a popular choice for food services seeking to lower trans fats in their products. The remaining canola meal provides a high protein livestock feed.
Benson Hill, using its proprietary CropOS cognitive computational platform, has identified a portfolio of trait candidates demonstrated to improve photosynthesis, one of the most complex systems in plants that is responsible for all agriculture production. In collaboration with the University of Guelph, researchers will validate these and other trait candidates in canola for further testing and development.
Benson Hill's platform combines vast datasets and biological knowledge with big data analytics and scalable cloud-based computing – an intersection of disciplines known as cloud biology – to predict biological outcomes for any target crop using any genomics tool, from breeding to gene editing to transgenics. The ability to more accurately predict gene targets that are linked to certain phenotypic outcomes with CropOS enables Benson Hill to accelerate identification of promising trait candidates, reducing product development costs and increasing speed to market.
Timothy Close, a professor of genetics at UC Riverside says the research will make it easier for researchers working with barley to develop new varieties through breeding and the unlock the mechanisms of barley genes.
The research will also aid scientists working with other “cereal crops,” including rice, wheat, rye, maize, millet, sorghum, oats and even turfgrass, which like the other food crops, is in the grass family, Close said.
The report in Nature provides new insights into gene families that are key to the malting process. The barley genome sequence also enabled the identification of areas of the genome that have been vulnerable to genetic bottlenecking during domestication, knowledge that helps to guide breeders to optimize genetic diversity in their crop improvement efforts.
Ten years ago, the International Barley Genome Sequencing Consortium, which is led by Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany, set out to assemble a complete reference sequence of the barley genome.
The barley genome is almost twice the size of the human genome and 80 per cent of it is composed of highly repetitive sequences, which cannot be assigned accurately to specific positions in the genome without considerable extra effort.
Multiple novel strategies were used in this paper to circumvent this fundamental limitation. Major advances in sequencing technology, algorithmic design and computing made it possible. Still, this work kept teams around the world – in Germany, Australia, China, Czech Republic, Denmark, Finland, Sweden, Switzerland, United Kingdom and the United State – occupied for a decade. This work provides knowledge of more than 39,000 barley genes.
During malting, amylase proteins are produced by germinated seeds to decompose energy-rich starch that is stored in dry grains, yielding simple sugars. These sugars then are available for fermentation by yeast to produce alcohol. The genome sequence revealed much more variability than was expected in the genes that encode the amylase enzymes.
About a year ago, a group of researchers discovered Palmer is resistant to the herbicide class known as PPO-inhibitors, due to a mutation —known as the glycine 210 deletion — on the PPX2 gene.
“We were using a quick test that we originally developed for waterhemp to determine PPO-resistance based on that mutation. A lot of times, the test worked. But people were bringing in samples that they were fairly confident were resistant, and the mutation wasn’t showing up. We started to suspect there was another mechanism out there,” says University of Illinois molecular weed scientist Patrick Tranel.
Tranel and his colleagues decided to sequence the PPX2 gene in plants from Tennessee and Arkansas to see if they could find additional mutations. Sure enough, they found not one, but two, located on the R98 region of the gene.
“Almost all of the PPO-resistant plants we tested had either the glycine 210 deletion or one of the two new R98 mutations. None of the mutations were found in the sensitive plants we tested,” Tranel says.
Furthermore, some of the resistant plants had both the glycine 210 deletion and one of the new R98 mutations. Tranel says it is too early to say what that could mean for those plants. In fact, there is a lot left to learn about this resistance mechanism.
“We don’t know what level of resistance the new mutations confer relative to glycine 210,” Tranel says. “There are a lot of different PPO-inhibiting herbicides. Glycine 210 causes resistance to all of them, but we don’t know yet if the R98 mutations do.”
The team is now growing plants to use in follow-up experiments. Tranel hopes they will be able to determine how common the three mutations are in any given population. “That way,” he says, “when a farmer sends us a resistant plant and it doesn’t come back with the glycine 210 deletion, we will be able to tell him how likely it is that he’s dealing with another one of these mutations.”
In the meantime, other research groups or plant testing facilities could use the new genetic assay to detect the mutations in Palmer samples. Tranel hopes they will. “The more labs testing for this, the more we learn about how widespread the mutation is,” he says.
The article, “Two new PPX2 mutations associated with resistance to PPO-inhibiting herbicides in Amaranthus palmeri,” is published in Pest Management Science. The work was supported by a grant from the USDA’s National Institute of Food and Agriculture.
Wheat and other edible grasses have developed pores that make them more drought tolerant. Stanford scientists have studied these pores with an eye toward future climate change.
These plants, which make up about 60 percent of the calories people consume worldwide, have a modified stoma that experts believe makes them better able to withstand drought or high temperatures. Stanford University scientists have now confirmed the increased efficiency of grass stomata and gained insight into how they develop. Their findings, reported in the March 17 issue of Science, could help us cultivate crops that can thrive in a changing climate.
“Ultimately, we have to feed people,” said Dominique Bergmann, professor of biology and senior author of the paper. “The climate is changing and, regardless of the cause, we’re still relying on plants to be able to survive whatever climate we do have.”
Adjusting an ancient system
Grasses – which include wheat, corn and rice – developed different stomata, which may have helped them spread during a prehistoric period of increased global dryness. Stomata usually have two so-called “guard cells” with a hole in the middle that opens and closes depending on how a plant needs to balance its gas exchange. If a plant needs more CO2 or wants to cool by releasing water vapour, the stomata open. If it needs to conserve water, they stay closed.
The protein in yellow moves out of the guard cells into cells on both sides. By recruiting these cells, grass stomata become better suited to hot and dry environments.
Grasses improved on the original structure by recruiting two extra cells on either side of the guard cells, allowing for a little extra give when the stoma opens. They also respond more rapidly and sensitively to changes in light, temperature or humidity that happen during the day. Scientists hope that by knowing more about how grass developed this system, they may be able to create or select for edible plants that can withstand dry and hot environments, which are likely to become more prevalent as our climate changes.
“We take our food and agriculture for granted. It’s not something the ‘first world’ has to deal with, but there are still large areas of the world that suffer from famine and this will increase,” said Michael Raissig, a postdoctoral researcher in the Bergmann lab and lead author of the paper. “The human population is going to explode in the next 20 to 30 years and most of that is in the developing world. That’s also where climate change will have the biggest effect.”
Growing a better mouth
Scientists have assumed grasses’ unusual stomata make these plants more efficient “breathers.” But, spurred by curiosity and a passion for developmental biology, these researchers decided to test that theory.
Thanks to a bit of luck, they found a mutant of the wheat relative Brachypodium distachyon that had two-celled stomata. Partnering with the Berry lab at the Carnegie Institution for Science, the group compared the stomata from the mutant to the normal four-celled stomata. They not only confirmed that the four-celled version opens wider and faster but also identified which gene creates the four-celled stomata – but it wasn’t a gene they expected.
“Because it was a grass-specific cell-type, we thought it would be a grass-specific factor as well,” said Raissig, “but it’s not.”
Instead of relying on a completely new mechanism, the recruitment of the extra cells seems to be controlled by a well-studied factor which is known to switch other genes on and off. In other plants, that factor is present in guard cells, where it is involved in their development. In grasses, the team found that the factor migrated out of guard cells and directly into two surrounding cells, recruiting them to form the four-celled stomata.
Feeding the world
Over evolutionary time, humans have bred and propagated plants that produce the kinds of foods we like and that can survive extreme weather.
“We’re not consciously breeding for stomata but we’re unconsciously selecting for them,” said Bergmann, who is also a Howard Hughes Medical Institute investigator. “When we want something that’s more drought resistant, or something that can work better in higher temperatures, or something that is just able to take in carbon better, often what we are actually doing is selecting for various properties of stomata.”
The adaptability and productivity of grass makes understanding this plant family critical for human survival, the scientists said. Someday, whether through genetic modification or selective breeding, scientists might be able to use these findings to produce other plants with four-celled stomata. This could also be one of many changes – to chloroplasts or enzymes, for example – that help plants photosynthesize more efficiently to feed a growing population.
Annually, diseases, weeds, and insects are estimated to cause more than $1.3 billion in losses for sunflower growers. To combat this, researchers are preserving the genetic diversity of wild sunflowers. Wild plants retain the genes needed to resist pests and survive in different environments.
Only three plant species -- rice, wheat, and maize -- account for most of the plant matter that humans consume, partly because of the mutations that made these crops the easiest to harvest. But with CRISPR technology, we don't have to wait for nature to help us domesticate plants, argue researchers.
Some scientists say the solution could lie in crops' DNA and are making “gene catalogs” to help farmers grow healthier produce that can withstand climate change. | READ MORE
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