Landmark study generates first genomic atlas for global wheat improvement

Landmark study generates first genomic atlas for global wheat improvement
Curtis Pozniak in wheat field. Credit: Christina Weese/USask

In a landmark discovery for global wheat production, a University of Saskatchewan-led international team has sequenced the genomes for 15 wheat varieties representing breeding programs around the world, enabling scientists and breeders to much more quickly identify influential genes for improved yield, pest resistance and other important crop traits.

The research results, just published in Nature, provide the most comprehensive atlas of wheat genome sequences ever reported. The 10+ Genome Project collaboration involved more than 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the U.K., Saudi Arabia, Mexico, Israel, Australia, and the U.S.

“It’s like finding the missing pieces for your favorite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the USask Crop Development Centre (CDC). “By having many complete gene assemblies available, we can now help solve the huge puzzle that is the massive wheat pan-genome and usher in a new era for wheat discovery and breeding.”

Scientific groups across the global wheat community are expected to use the new resource to identify genes linked to in-demand traits, which will accelerate breeding efficiency.

“This resource enables us to more precisely control breeding to increase the rate of wheat improvement for the benefit of farmers and consumers, and meet future food demands,” Pozniak said.

One of the world’s most cultivated cereal crops, wheat plays an important role in global food security, providing about 20 percent of human caloric intake globally. It’s estimated wheat production must increase by more than 50 percent by 2050 to meet an increasing global demand.

In 2018 as part of another international consortium, USask researchers played a key role in decoding the genome for the bread wheat variety Chinese Spring, the first complete wheat genome reference and a significant technical milestone. The findings were published in the journal Science.

“Now we have increased the number of wheat genome sequences more than 10-fold, enabling us to identify genetic differences between wheat lines that are important for breeding,” Pozniak said. “We can now compare and contrast the full complement of the genetic differences that make each variety unique.”

Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and project co-leader from Germany said, “Given the significant impact of the Chinese Spring reference genome on research and application, it is a major achievement that just two years later we are providing additional sequence resources that are relevant to wheat improvement programs in many different parts of the world.”

The 10+ Genome study represents the start of a larger effort to generate thousands of genome sequences of wheat, including genetic material brought in from wheat’s wild relatives.

The research team was able to track the unique DNA signatures of genetic material incorporated into modern cultivars from several of wheat’s undomesticated relatives by breeders over the century.

“These wheat relatives have been used by breeders to improve disease resistance and stress resistance

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Genomic data ‘catches corals in the act’ of speciation and adaptation

Genomic data 'catches corals in the act' of speciation and adaptation
A) Porites lobata (yellow massive morphology) shown next to Porites compressa (blue-grey branching morphology) side by sidein the same habitat; (B) example of variation in bleaching susceptibility of P. compressa in Kāne’ohe Bay. Credit: Forsman, et al. (2020)

A new study led by the University of Hawai’i at Mānoa’s Hawai’i Institute of Marine Biology (HIMB) revealed that diversity in Hawaiian corals is likely driven by co-evolution between the coral host, the algal symbiont, and the microbial community.

As coral reef ecosystems have rapidly collapsed around the globe over the past few decades, there is widespread concern that corals might not be able to adapt to changing climate conditions, and much of the biodiversity in these ecosystems could be lost before it is studied and understood. Coral reefs are among the most highly biodiverse ecosystems on earth, yet it is not clear what drives speciation and diversification in the ocean, where there are few physical barriers that could separate populations.

The team of researchers used massive amounts of metagenomic sequencing data to try to understand what may be some of the major drivers of adaptation and variation in corals.

“Corals have incredible variation with such a wide range of shapes, sizes, and colors that it’s really hard for even the best trained experts to be able to sort out different species,” said Zac Forsman, lead author of the study and HIMB assistant researcher. “On top of that, some corals lose their algal symbionts, turning stark white or ‘bleached’ and die during marine heatwaves, while a similar looking coral right next to it seems fine. We wanted to try to better understand what might be driving some of this incredible variation that you see on a typical coral reef.”

Forsman and colleagues examined genetic relationships within the coral genus Porites, which forms the foundation and builds many coral reefs around the world. They were able to identify genes from the coral, algal symbionts, and bacteria that were most strongly associated with coral bleaching and other factors such as the shape (morphology) of the coral colony. They found relatively few genes associated with bleaching, but many associated with distance from shore, and colony morphologies that dominate different habitats.

“We sought out to better understand coral bleaching and place it in the context of other sources of variation in a coral species complex. Unexpectedly, we found evidence that these corals have adapted and diverged very recently over depth and distance from shore. The algal symbionts and microbes were also in the process of diverging, implying that co-evolution is involved. It’s like we caught them in the act of adaptation and speciation.”

“These corals have more complex patterns of variation related to habitat than we could have imagined and learning about how corals have diversified over various habitats can teach us about how they might adapt in the future,” he explained. “Since variation is the raw material for adaptation, there is hope for the capacity of these corals to adapt to future conditions, but only

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The genomic basis of adaptations, the differences between species, and the mechanisms of speciation

Credit: CC0 Public Domain

How do new species arise, and how quickly does this happen? Evolutionary biologist Professor Axel Meyer from the University of Konstanz and his team have come one decisive step closer to answering fundamental questions in biology. Upon evaluation of an extensive data set collected during extensive research on extremely young species of cichlids in crater lakes in Nicaragua, empirical evidence suggests that the evolutionary divergence of a population in the same geographical area into a new species is more likely to occur when many genes across the genome are involved in producing species-distinguishing characteristics. Additionally, new species can emerge within only a few hundred years This contradicts the hitherto established theory that speciation is a slow process and that ecologically important interspecies differences with simple, genetically locally limited architecture are more likely to result in the formation of a new species than those on a so-called polygenic basis are. Ultimately, it is about the question that Darwin already asked: What is a species, and how and why do new species arise? The results of this large-scale multidisciplinary study have been published in the scientific journal Nature.

Which genes, and how many of them are involved in speciation?

In genetics, the question of emergence of new species translates into: What is the pattern of changes in the genome that leads to the emergence of new species? What happens genetically during the continuum from initially no differences within a population up to the completed speciation of reproductively separate species? Since his doctoral thesis in the 1980s at the University of California, in Berkeley, U.S., and since the end of the 1990s at the University of Konstanz, Axel Meyer has been researching the question of which and how many genes or genetic loci—i.e. regions on the genome—are involved in the development of adaptations and new species. Here, the focus is on the study of very young species of cichlids, often only a few hundred generations old, living in crater lakes in Nicaragua. Although all these fishes descended from the same older original populations in the two large lakes of Nicaragua, Lake Managua and Lake Nicaragua, there are fish populations or even small species complexes of several species in each of the crater lakes that live exclusively in the respective lake, with specific phenotypic differences that are sometimes found in very similar fashion in several lakes, i.e. seem to have developed independently several times.

Multiple phenotypes in the same crater lake

There are fishes with pronounced lips and others without lips, gold-colored and black and white fishes, fishes that differ from others by having particularly slender bodies or certain delicate or robust tooth shapes. These phenotypes originated within the crater lakes, thus in the same geographical area (sympatric speciation), without external barriers such as rivers or mountains favoring this by limiting gene flow by gene exchange through reproduction. Thus, this is not allopatric speciation.

The variations regarding the lips, color, body and tooth shape of the fishes are genetically

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