Plant Genetics
Real-time DNA sequencing, anywhere, anytime, is one step closer to making the jump from science fiction to science fact, according to researchers at the Royal Botanic Gardens, Kew. A recent paper published in Scientific Reports outlined how the team used a MinION portable DNA sequencer to analyze plant species in the field.
Published in Genetics/Traits
Australian researchers at the University of Adelaide have identified a naturally occurring wheat gene that, when turned off, eliminates self-pollination but still allows cross-pollination - opening the way for breeding high-yielding hybrid wheats.

Published in the journal Nature Communications, and in collaboration with U.S.-based plant genetics company DuPont Pioneer, the researchers say this discovery and the associated breeding technology have the potential to radically change the way wheat is bred in Australia and internationally. To read the full story, click here.
Published in Genetics/Traits
Cereal breeders continue to focus on improved yields, developing varieties that stand up to the pest and disease challenges producers face across the Prairies. Seed companies have supplied Top Crop Manager with the following information on new cereal varieties for 2018.
Published in Cereals
The area seeded to barley in Ontario has been trending downwards over the past two decades, from 325,000 acres in 1998 to only 85,000 acres in 2017. That decline has happened despite the upsurge in the province’s craft brewing industry, which prefers locally grown ingredients. So, in a three-year project, University of Guelph researchers are using several strategies to develop improved malting and feed cultivars suited to the needs of producers in Ontario.
Published in Cereals
Scientists from the International Barley Hub have discovered a genetic pathway to improved barley grain size and uniformity, a finding which may help breeders develop future varieties suited to the needs of growers and distillers.

Cereal genetics researchers working with professor Robbie Waugh and Dr. Sarah McKim, at the James Hutton Institute and the University of Dundee’s Division of Plant Sciences, published work examining the genetic control of grain formation in barley, specifically the role of a gene called VRS3. Researchers found that a mutation in this gene improved grain uniformity in six-rowed barley. To read the full story, click here.
Published in Genetics/Traits
When it comes to fighting Fusarium graminearum, our crops may soon have some new tiny but powerful allies. Research by Manish Raizada at the University of Guelph is providing the foundation for commercializing some anti-Fusarium bacteria as biocontrol products. As well, a student in his lab discovered an amazing mechanism that a bacterial strain called M6 uses to stop the fungus dead in its tracks.
Published in Diseases
Blackleg levels on the Prairies have been going up, but research information on blackleg races and cultivar resistance, plus a new cultivar labelling system and a new diagnostic test, can help bring those disease levels back down.
Published in Diseases
Researchers have discovered a way to boost the nutritional value of corn—the world’s largest commodity crop—by modifying the plant with a bacterial gene that causes it to produce methionine, a key nutrient.

The discovery could benefit millions of people in developing countries, such as in South America and Africa, who depend on corn as a staple. It could also significantly reduce worldwide animal feed costs. READ MORE
Published in Corn
A team of University of Guelph researchers at the cutting edge of discovering how plants communicate with one another has proven the stress of “seeing” weed competition causes a plant to significantly change growth patterns and drop yield.  
Published in Weeds
Not many farmers can say they’ve had a hand in early-stage selection of the very crops they’re growing in their fields, but the University of Manitoba’s Participatory Plant Breeding Program is making this possible for producers coast-to-coast.
Published in Plant Breeding
Some diet books have claimed modern wheat breeding has produced changes in wheat varieties that are causing harmful effects to human health. But University of Saskatchewan researchers have already determined that some key nutritional characteristics in wheat have actually changed very little from the varieties grown 150 years ago to today’s varieties. Now these researchers are teaming up with a University of Alberta colleague to delve into another important aspect of this issue: Have wheat gluten proteins changed over time?
Published in Plant Breeding
On Canada’s fertile Prairies, dominated by the yellows and golds of canola and wheat, summers are too short to grow corn on a major scale.

But Monsanto Co. is working to develop what it hopes will be North America’s fastest-maturing corn, allowing farmers to grow more in Western Canada and other inhospitable climates, such as Ukraine.

The seed and chemical giant projects that western Canadian corn plantings could multiply 20 times to 10 million acres by 2025 - adding some 1.1 billion bushels, or nearly 3 percent to current global production. For the full story, click here.
Published in Plant Breeding
It’s been almost 15 years since the Human Genome Project was declared complete. The publicly funded research project was established in 1990, kicking off an international effort to identify and map all of the DNA sequences in the human genome by 2005.
Published in Genetics/Traits
Dr. Anfu Hou is a leading plant breeder. He works at Agriculture and Agri-Food Canada’s Research and Development Centre in Morden, Man.

Hou was born in China and his research took him through several countries before he settled in Morden, which is located just north of the U.S. border. Geography is not insignificant here. Hou and his team develop crop varieties specifically suited to grow and grow well in the unique soil and weather conditions in Manitoba and Western Canada. For the full story, click here.
Published in Plant Breeding
Scientists at Cold Spring Harbor Laboratory (CSHL) have harnessed the still untapped power of genome editing to improve agricultural crops. Using tomato as an example, they have mobilized CRISPR/Cas9 technology to rapidly generate variants of the plant that display a broad continuum of three separate, agriculturally important traits: fruit size, branching architecture and overall plant shape.

All are major components in determining how much a plant will yield. The method is designed to work in all food, feed, and fuel crops, including the staples rice, maize, sorghum and wheat.

"Current rates of crop yield increases won't meet the planet's future agricultural demands as the human population grows," says CSHL Professor Zachary Lippman, who led the research. "One of the most severe limitations is that nature hasn't provided enough genetic variation for breeders to work with, especially for the major yield traits that can involve dozens of genes. Our lab has now used CRISPR technology to generate novel genetic variation that can accelerate crop improvement while making its outcomes more predictable."

The team's experiments, published in Cell, involve using CRISPR to make multiple cuts within three tomato genome sequences known as a promoters -- areas of DNA near associated genes which help regulate when, where, and at what level these "yield" genes are active during growth. In this way generating multiple sets of mutations within each of these regulatory regions, the scientists were able to induce a wide range of changes in each of the three targeted traits.

"What we demonstrated with each of the traits," explains Lippman, "was the ability to use CRISPR to generate new genetic and trait variation that breeders can use to tailor a plant to suit conditions. Each trait can now be controlled in the way a dimmer switch controls a light bulb."

By using CRISPR to mutate regulatory sequences -- the promoters of relevant "yield" genes rather than the genes themselves - the CSHL team finds that they can achieve a much subtler impact on quantitative traits.

Fine-tuning gene expression rather than deleting or inactivating the proteins they encode is most likely to benefit commercial agriculture because of the flexibility such genetic variation provides for improving yield traits.

"Traditional breeding involves great time and effort to adapt beneficial variants of relevant genes to the best varieties, which must continuously be improved every year," says Lippman. "Our approach can help bypass this constraint by directly generating and selecting for the most desirable variants controlling gene activity in the context of other natural mutations that benefit breeding. We can now work with the native DNA and enhance what nature has provided, which we believe can help break yield barriers."

Each of the mutated areas creates what are known as quantitative trait loci (QTL). In any given plant, QTL have arisen naturally over thousands of years, the result of spontaneous mutations that caused subtle changes in yield traits.

Searching for and exploiting QTL from nature has been an objective of plant breeders for centuries, but the most valuable QTL - those that cause subtle changes in traits - are rare. Lippman and his team have now shown that CRISPR-generated QTL can be combined with existing QTL to create "toolkits" of genetic variation that exceed what is found in nature.

The research discussed here was supported by a PEW Latin American Fellowship; a National Science Foundation Postdoctoral Research Fellowship in Biology grant (IOS- 1523423); a National Science Foundation Plant Genome Research Program grant (IOS-1732253); and a National Science Foundation Plant Genome Research Program grant (IOS-1546837).

"Engineering quantitative trait variation for crop improvement by genome editing" appears online in Cell September 14, 2017. The authors are: Daniel Rodríguez-Leal, Zachary H. Lemmon, Jarrett Man, Madelaine E. Bartlett, and Zachary B. Lippman. The paper can be viewed at: http://www.cell.com/cell/newarticles
Published in Genetics/Traits
Domesticating plants to grow as crops can turn out to be a double-edged scythe.

On one hand, selecting specific desirable traits, such as high yields, can increase crop productivity. But other important traits, like resistance to pests, can be lost. That can make crops vulnerable to different stresses, such as diseases and pests, or the effects of climate change.

To reduce these vulnerabilities, researchers often turn to the wild relatives of crops. These wild relatives continue to evolve in nature, often under adverse conditions. They possess several useful genes for desirable traits. These traits include high levels of resistance to diseases and tolerance to environmental stresses.

In a new study, scientists report significant strides in transferring disease- and stress-resistance traits from wild relatives of several legumes to their domesticated varieties. This research was conducted at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Patancheru, India.

Legumes, such as chickpea, pigeonpea, and groundnut, are among the few crops that grow well in the scant rainfall and marginal soils of the semi-arid tropics. But they are facing significant challenges, says Shivali Sharma, lead author.

“Legume crops are hit hard by diseases, insect-pests, drought, heat stress, and salinity,” says Sharma. “Also, semi-arid regions are highly vulnerable to climate change.” These factors limit legume crops.

There are several wild relatives of these crops that are resistant to pests and diseases. “There is an urgent need to find and introduce these useful genes from wild relatives into crop cultivars,” says Sharma. That would improve the resilience of domestic legume varieties and sustain agriculture in these regions.

It can be highly challenging – and often impossible – to directly breed domesticated crops with their wild relatives. For example, of the eight wild annual species of chickpea, only one is readily crossable with cultivated chickpea and yields fertile offspring.

Similarly, wild varieties of groundnut are resistant to fungal infections. But direct crossing of wild and domesticated groundnut is challenging because of differences in how the DNA in their cells is packaged. Additionally, these species do not cross well with cultivars.

Most wild varieties of groundnut are diploid: their DNA is organized in two sets of chromosomes per cell, much like in humans. During reproduction, one set comes from the male parent and the other set from the female parent.

Domesticated groundnut plants, on the other hand, are tetraploid. Their cells contain four sets of chromosomes. The sets of chromosomes in each cell, called ploidy, makes it difficult to directly interbreed wild and domestic varieties of groundnut.

“It takes a lot of time and resources to overcome challenges like these,” says Sharma. “That often makes breeders reluctant to directly use wild species in breeding programs.”

Pre-breeding programs, such as the one at ICRISAT, invest their time and skill in the wild crop relatives. Sharma and her colleagues bred wild groundnut varieties whose cells have four sets of chromosomes. Then they identified which of these tetraploid wild varieties were also resistant to fungal infections. These were then crossed with cultivated groundnut varieties to develop new breeding lines with good resistance and yields. Plant breeders can now directly cross these fungal-resistant lines with domesticated groundnut to create new varieties.

“Crop wild relatives are the reservoir of many useful genes and traits,” says Sharma. “It is our responsibility to use this hidden treasure for future generations.”

It’s especially important in the context of legumes because they provide a bevy of benefits. For instance, bacteria in their root nodules pull in valuable atmospheric nitrogen. That increases soil fertility and reduces the need for fertilizers.

Legumes are also vital for food security in the semi-arid tropics and other parts of the world. They are an important source of protein and micronutrients. Combined with cereals, they are a sustaining diet for people across the world.

And “pre-breeding programs are the first step to improve the nutrition and resilience of modern legume varieties,” says Sharma.

Read more about this research in Crop Science.
Published in Other Crops
Researchers have used a supercontinuum laser to analyze whole grains with long near-infrared wavelengths.

By measuring each grain you can more accurately observe the variation that naturally exists among grains from the same field and even from the same straw. READ MORE
Published in Cereals
Researchers have made a significant breakthrough that could make barley more tolerant to waterlogging and wet conditions.

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
Published in Genetics/Traits
Innovative research is shedding new light on grain filling in oat, including the oft-overlooked occurrence of unfilled kernels. The research has overturned some common assumptions about oat grain filling and is opening the way to faster development of higher yielding and better quality oat varieties.
Published in Plant Breeding
Just like you inoculate legume seeds with a rhizobial inoculant, one day you might inoculate canola seeds with a plant-growth-promoting fungus. Greenhouse experiments in Alberta are showing that a fungus called Piriformospora indica can boost canola performance, providing benefits like increased yields, reduced fertilizer needs, and increased tolerance to cold and drought. Now the research team is testing this promising inoculant in the field.

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.
Published in Other Crops
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