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Fields of breeders’ dreams: A team effort toward targeted crop improvements

Community effort yields reference switchgrass genome, environmental adaptations dataCredit: David Lowry Gardeners and farmers around the country recognize that crop

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Community effort yields reference switchgrass genome, environmental adaptations data

Gardeners and farmers around the country recognize that crop varieties grow best in certain regions. Most plant species have adapted to their local environments; for example, crop and ornamental seeds sold for the upper Midwest are often very different than those bred for Texas. Identifying and breeding varieties that have high productivity across a range of environments is becoming increasingly important for food, fuel and other applications, and breeders aren’t interested in waiting decades to develop new crops.

One example is an ongoing collaborative effort to improve the emerging bioenergy crop switchgrass (Panicum virgatum), which has established 10 experimental gardens located in eight states spread across 1,100 miles. Switchgrass is a perennial grass that quickly grows in a variety of soils and water conditions, standing taller than basketball star LeBron James. In each garden, switchgrass plants clonally propagated from cuttings represent a diverse collection sourced from half of the United States.

As reported January 27, 2021 in Nature, the team led by researchers at the University of Texas (UT) at Austin, the HudsonAlpha Institute for Biotechnology (HudsonAlpha), and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), has produced a high-quality reference sequence of the complex switchgrass genome using samples collected at these gardens. Building off this work, researchers at all four DOE Bioenergy Research Centers (BRCs)–the Great Lakes Bioenergy Research Center (GLBRC), the Center for Bioenergy Innovation, the Center for Advanced Bioenergy & Bioproducts Institute, and the Joint BioEnergy Institute–have expanded the network of common gardens and are exploring improvements to switchgrass through more targeted genome editing techniques to customize the crop for additional end products.

The genetic diversity within this set of plants, each with a fully-sequenced genome, and these gardens allow researchers to test what genes affect the plant’s adaptability to various environmental conditions. “To accelerate breeding for bioenergy, we need to make connections between the plant’s traits and genetic diversity,” said John Lovell, an evolutionary biologist at HudsonAlpha and first author of the study. “For that, it’s necessary to have the plant’s genome as a reference. Additionally, having the gardens as a resource helps breeders find genetic regions of interest.” The combination of field data and genetic information has allowed the research team to associate climate adaptations with switchgrass biology, information that could be useful toward the DOE’s interest in harnessing the crop as a versatile candidate biomass feedstock for producing sustainable alternative fuels.

Common Gardens Are A Community Effort

The common gardens began nearly a decade ago with a proposal from UT-Austin’s Tom Juenger, a longtime JGI collaborator and a senior author on this study. The use of switchgrass as a feedstock for biomass-based fuels was initially fostered by DOE’s Bioenergy Research Centers, which initiated the sequencing of the switchgrass genome. DOE’s Billion Ton Report, identified potential switchgrass production areas across the U.S., guiding the location of the common gardens. “Gardeners and farmers fully understand that when you move plants outside of their native habitat or cold hardiness zones, they have different levels of performance,” Juenger said. “The novelty here is that we’re trying to actually figure out what’s causing those differences rather than just observing them. Can we quantify them? Can we tie them to the genome? We can use common garden plantings of clonally propagated plants to address these questions.”

Multiple collection methods were applied to gather the diversity of switchgrass plants represented in the gardens. “Tom gave me a truck and I drove all over Texas with a shovel,” recalled study co-author David Lowry, who started as a postdoctoral fellow in the Juenger lab and continues to work on the project from a lab at Michigan State University that is affiliated with the GLBRC. Additional samples came from U.S. Department of Agriculture stock centers, collaborators, and collections at other field sites. “This paper is a combination of really cutting-edge genomics and genetic analysis with large scale data collection,” he added.

Jeremy Schmutz, head of the JGI Plant Program, drew parallels between these common gardens and those previously grown for the DOE candidate feedstock poplar. “You’re collecting natural diversity and you’re planting natural diversity in multiple locations, and then you are extracting links between the genetic variation and phenotypic performance,” he said. Both switchgrass and poplar are JGI Flagship Plants.

Reaping Long-Term Investment Benefits

Switchgrass has a large polyploid genome, which means most genes are found as multiple copies across the chromosomes. “In the past, we needed model systems to test genetic hypotheses in species with large and complex genomes,” said Lovell. “However, new sequencing technologies have allowed us to build the necessary genome resources to directly test for genes involved in biomass yield and climate adaptation in switchgrass, despite its physical size and genome complexity.”

Work on the switchgrass genome sequence started more than a decade ago. As sequencing technologies have advanced, assembly and annotation of the genome sequence has improved in parallel. For example, the current version of the genome is assembled into sequences of 5.5 million basepair (bp) in length, while the previous version had an average of 25,000 bp pieces. That’s the difference between assembling a 10,000-piece puzzle and doing the same puzzle with just 50 pieces.

The combination of new genetic tools and experimental gardens allow researchers to detect climate-gene matches, which can be exploited for accelerated crop improvement. “Because of the DOE’s long-term investment and the effort that has gone into this, people are going to be able to model further research on this complex species and also at the same time, take advantage of what we can do now with genomics to really make inroads into plant biology and improvements of switchgrass as the crop species,” Schmutz said.

The switchgrass genotypes that were planted into the common gardens were sequenced and assembled by the JGI, allowing the research team to conduct association mapping, linking genes to traits. One of the team’s findings is that the performance of switchgrass across the garden sites depended on the origin or collection location of the individual switchgrass plants. They were able to identify many regions in the switchgrass genome that are associated with genetic differences that lead to productivity in different environments.

For example, many plants collected from native habitats in Texas and other southern locales did not survive the cold winter of 2019 at the most northern common garden in South Dakota. Conversely, upper Midwest native switchgrass plants performed poorly at the southern common gardens in Texas. This reciprocal home site advantage is direct evidence of climatic adaptation. The team’s database of genes that underlie adaptation to climate provides breeders with a strong foundation to improve crop productivity under specific climates.

Sourcing plants from so many parts of the country also helped the team understand why some switchgrass plants from the Northeast have traits similar to those from the Midwest, even though their genomes were very different.

The high quality reference genome sequence of switchgrass is available on the JGI plant data portal Phytozome. This version can help breeders identify genomic regions of interest and directly introduce these features into new crop varieties. “It’s going to be important to have all this information in order to facilitate breeding going forward,” noted Lowry.

The team has received additional DOE funding to continue maintaining the gardens, which excites Juenger. “There will be a continuation of collecting data and information from these existing plantings, and then trying to leverage these discoveries to better understand how plants tolerate stresses and challenges in the natural environment,” he said. “There aren’t many efforts that have been able to study native perennial plants with these genetic and genomic resources, interweaved with this long longitudinal study perspective. Although it’s been this enormous investment to set up these gardens, we have them to study for a number of years. And that’s a real benefit for the research program.”

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Researchers from the University of California (UC), Berkeley, Rutgers University, USDA-ARS, Arizona Genomics Institute, University of Georgia, Athens, Clemson University, Marshall University, Jawaharlal Nehru University (India), Noble Research Institute, University of Nebraska, Lincoln, South Dakota State University, University of Missouri, Argonne National Laboratory, USDA-NRCS, Texas A&M University, UC Davis, Oklahoma State University, University of Oklahoma, and Washington State University were also involved in this work.

Publication: Lovell J et al. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature. 2021 Jan 27. doi: 10.1038/s41586-020-03127-1.

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Fields of Breeders’ Dreams: A Team Effort Toward Targeted Crop Improvements

As reported January 27, 2021 in Nature, the team led by researchers at the University of Texas (UT) at Austin, the HudsonAlpha Institute for Biotechnology (HudsonAlpha), and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), has produced a high-quality reference sequence of the complex switchgrass genome using samples collected at these gardens. Building off this work, researchers at all four DOE Bioenergy Research Centers (BRCs)–the Great Lakes Bioenergy Research Center (GLBRC), the Center for Bioenergy Innovation, the Center for Advanced Bioenergy & Bioproducts Institute, and the Joint BioEnergy Institute–have expanded the network of common gardens and are exploring improvements to switchgrass through more targeted genome editing techniques to customize the crop for additional end products.

Source: https://bioengineer.org/fields-of-breeders-dreams-a-team-effort-toward-targeted-crop-improvements/

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Bioengineer

Diving into devonian seas: Ancient marine faunas unlock secrets of warming oceans

Credit: Syracuse University Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one

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Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one that is millions of years in the making.

A team of paleontologists led by Professor Cathryn Newton has increased scientists’ understanding of whether Devonian marine faunas, whose fossils are lodged in a unit of bedrock in Central New York known as the Hamilton Group, were stable for millions of years before succumbing to waves of extinctions.

Drawing on 15 years of quantitative analysis with fellow professor Jim Brower (who died in 2018), Newton has continued to probe the structure of these ancient fossil communities, among the most renowned on Earth.

The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Such persistence, Newton says, is a longstanding scientific enigma. She and her colleagues tested the hypothesis that these ancient communities displayed coordinated stasis–a theory that attempts to explain the emergence and disappearance of species across geologic time.

Newton and Brower, along with their student Willis Newman G’93, found that Devonian marine communities vary more in species composition than the theory predicts. Newton points out that they sought not to disprove coordinated stasis but rather to gain a more sophisticated understanding of when it is applicable. “Discovering more about the dynamics of these apparently stable Devonian communities is critical,” she says. “Such knowledge has immediate significance for marine community changes in our rapidly warming seas.”

Since geologist James Hall Jr. first published a series of volumes on the region’s Devonian fossils and strata in the 1840s, the Hamilton Group has become a magnet for research scientists and amateur collectors alike. Today, Central New York is frequently used to test new ideas about large-scale changes in Earth’s organisms and environments.

During Middle Devonian time (approximately 380-390 million years ago), the faunal composition of the region changed little over 4-6 million years. “It’s a significant amount for marine invertebrate communities to remain stable, or ‘locked,’” explains Newton, a professor in the Department of Earth and Environmental Sciences.

She, Brower and student researchers spent years examining eight communities of animals that once dwelled in a warm, shallow sea on the northern rim of the Appalachian Basin (which, eons ago, lay south of the equator). When the organisms died, sediment from the seafloor began covering their shells and exoskeletons. Minerals from the sediment gradually seeped into their remains, causing them to fossilize. The process also preserved many of them in living position, conserving original shell materials at some sites.

These fossils currently populate exposed bedrock throughout Central New York, ranging from soft, dark, deep-water shale to hard, species-rich, shelf siltstone. “Communities near the top of the bedrock exhibit more taxonomic and ecological diversity than those at the bottom,” Newton says. “We can compare the community types and composition through time. They are remarkable sites.”

Coordinated stasis has been a source of contention since 1995, when it was introduced. At the center of the dispute are two model-based explanations: environmental tracking and ecological locking.

Environmental tracking suggests that faunas follow their environment. “Here, periods of relative stasis are flanked by coordinated extinctions or regional disappearances. When the environment changes, so do marine faunas,” says Newton, also Professor of Interdisciplinary Sciences and Dean Emerita of Arts and Sciences.

Ecological locking, in contrast, views marine faunas as tightly structured communities, resistant to large-scale taxonomic change. Traditionally, this model has been used to describe the stability of lower Hamilton faunas.

Newton and her colleagues analyzed more than 80 sample sites, each containing some 300 specimens. Special emphasis was placed on the Cardiff and Pecksport Members, two rock formations in the Finger Lakes region that are part of the ancient Marcellus subgroup, famed for its natural gas reserves.

“We found that lower Hamilton faunas, with two exceptions, do not have clear counterparts among upper ones. Therefore, our quantitative tests do not support the ecological locking model as an explanation for community stability in these faunas,” she continues.

Newton considers this project a final tribute to Newman, a professor of biology at the State University of New York at Cortland, who died in 2014, and Brower, who fell seriously ill while the manuscript was being finalized. “Jim knew that he likely would not live to see its publication,” says Newton, adding that Brower died as the paper was submitted to GSA.

She says this new work extends and, in some ways, completes the team’s earlier research by further analyzing community structures in the Marcellus subgroup. “It has the potential to change how scientists view long-term stability in ecological communities.”

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The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Source: https://bioengineer.org/diving-into-devonian-seas-ancient-marine-faunas-unlock-secrets-of-warming-oceans/

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Pioneering research unravels hidden origins of Eastern Asia’s ‘land of milk and honey’

Credit: Dr Shufeng Li A study has revealed for the first time the ancient origins of one of the world’s

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A study has revealed for the first time the ancient origins of one of the world’s most important ecosystems by unlocking the mechanism which determined the evolution of its mountains and how they shaped the weather there as well as its flora and fauna.

It was previously thought Southern Tibet and the Himalaya were instrumental in turning the once barren land of eastern Asia into lush forests and abundant coastal regions which became home to a rich array of plant, animal and marine life, including some of the world’s rarest species. But new findings, published today in the journal Science Advances, conversely show Northern Tibet played the more influential role in this transformation which began more than 50 million years ago.

Scientists from a UK-China partnership used an innovative climate model to simulate vegetation and plant diversity, combined with spectacular new fossil finds, to discover how this unique biodiversity hotspot evolved.

Lead author, Dr Shufeng Li, a visiting scientist at the University of Bristol in the UK and associate professor at Xishuangbanna Tropical Botanical Garden (XTBG) Institute in Yunnan, China, said: “Until now it was unknown why the climate changed from that of a dry, arid, almost desert-like ecosystem to that of a lush, wet ecosystem where a vast array of plant, animal, and marine life can be found, including some of the world’s rarest species.

“We conducted 18 sensitivity experiments using different Tibetan topographies representing various late Paleogene to early Neogene conditions, which test almost all possible Tibetan growth evolution scenarios.”

The findings showed that from the late Paleogene to the early Neogene age, some 23-40 million years ago, the growth of the north and northeastern portion of Tibet was the most important factor because it increased rainfall, especially winter rainfall, over eastern Asia where dry winter conditions existed before.

This allowed the development of a stable, wet and warm climate, conducive to the evolution of vast and varied plants and animal species which formed the biodiversity hotspot known today for supplying more than a billion people with fresh water and providing ingredients used for lifesaving pharmaceutical drugs. Rare species of monkey, tiger, leopard, bear, fox, mongoose, hedgehog, seal, dolphin, and sea lion all live in this abundant ecosystem.

Earlier research has mainly investigated the impact of Tibetan mountain building much further to the South when India collided with Asia around 55 million years ago, leading to the rise of the Himalaya mountains and, eventually, the vast arid Tibetan Plateau. However, recent work is increasingly showing the creation of the modern Tibetan plateau was complex, and did not rise as one monolithic block as originally believed.

Co-author Professor Paul Valdes, Professor of Physical Geography at the University of Bristol who led the modelling group, said: “Most previous studies have focused on Southern Tibet and the Himalaya, but our results indicate it is the growth of northern Tibet which is really important.

“The topography of northern Tibet decreases the East Asian winter monsoon winds in the southern part of China, causing wetter winters in eastern Asia and this allows the expansion of vegetation and biodiversity.”

So enigmatic was the drastic change that even in Chinese folklore this area is known as the ‘Land of Fish and Rice’, due to its immense productivity.

“Without the growth in Northern Tibetan mountains, none of this would exist. But our research should also be taken as a cautionary tale,” Professor Valdes explained.

“A unique set of tectonic and stable climatic conditions over millions of years allowed the development of this rare species rich region of South East Asia. However, global warming, harmful intensive agricultural techniques, forest clearing and lack of integrated conservation to preserve this unique ecosystem means once it is gone, it is gone for good.”

Professor Zhekun Zhou, of the Chinese Academy of Sciences’ XTBG, who led on the fossil analysis, said: “So effectively, without northern Tibetan growth, there would be no ‘land of milk and honey’ in eastern Asia. This research represents a significant breakthrough in understanding how this remarkably rich region of mountainous terrain and diverse plant life formed.”

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Paper

‘Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia’ by Shufeng Li et al in Science Advances

Notes to editors:

A selection of images, including captions and credit details, can be found here: Dr Li Shufeng and Professor Paul Valdes are available for interview:

https://drive.google.com/drive/folders/1jS58Q9m2kAzoj1mrrtHhvhRbdWa-CG08?usp=sharing

Lead and corresponding author: Dr Li Shufeng – Xishuangbanna Tropical Botanical Garden (XTGB) Institute, Chinese Academy of Sciences, Yunnan.

Email – XTGB: [email protected] and Bristol: [email protected]

Co-author: Prof. Paul Valdes – University of Bristol, School of Geographical Sciences

Email: [email protected]

Source: https://bioengineer.org/pioneering-research-unravels-hidden-origins-of-eastern-asias-land-of-milk-and-honey/

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Focusing on field analysis

Microscopy systems using customized chips could expand on-site identification of pathogensCredit: Viri et al. The development of cost-efficient, portable microscopy

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Microscopy systems using customized chips could expand on-site identification of pathogens

Credit: Viri et al.

The development of cost-efficient, portable microscopy units would greatly expand their use in remote field locations and in places with fewer resources, potentially leading to easier on-site analysis of contaminants such as E. coli in water sources as well as other practical applications.

Current microscopy systems, like those used to image micro-organisms, are expensive because they are optimized for maximum resolution and minimal deformation of the images the systems produce. But some situations do not require such optimization–for instance, simply detecting the presence of pathogens in water. One potential approach to developing a low-cost portable microscopy system is to use transparent microspheres in combination with affordable low-magnification objective lenses to increase image resolution and sensitivity.

A group of researchers from Ecole Polytechnique Federale de Lausanne (EPFL) in Switzerland published a study on such an assembly composed of barium titanate spheres that are partially embedded in thin polymeric membranes. The result of their work, appearing in SPIE’s new Journal of Optical Microsystems, is a proposed method to fabricate microfluidic chips using the assembly for enhanced detection of bacteria. Such customized chips with fluidic and optical components already integrated have many benefits when combined with portable low-end imagers for analyses at remote sites or in resource-limited regions.

“Cost reduction and portability are of benefit to the proliferation of analytical devices, especially in limited-resource contexts, and the integration of affordable micro-optical elements directly onto microfluidic chips can highly contribute to this,” said Martin Gijs, a professor at EPFL and an author of the published work.

The assembly’s ability to enhance bacteria detection paves the way for other applications friendly to use at remote sites. Additionally, the researchers revealed an opportunity to customize specific functional microfluidic elements. Such integrations could bring to fruition applications such as on-site antibiotic testing.

Given falling costs of the components and fabrication methods, the researchers’ proposed fabrication protocol could be adapted easily for a wide variety of microfluidic chips with integrated optical elements. Considered along with the lower cost of low-end imaging systems, the approach could sharply increase the use of such microscopy systems in low-resource locations for on-site analyses.

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Read the open access paper: Vittorio Viri, Daniel Migliozzi, and Martin A.M. Gijs, “Integration of polymeric membrane/dielectric sphere assemblies in microfluidic chips for enhanced-contrast imaging with low-magnification systems,” J. Opt. Microsys. 1(1), 014001 (2021) doi 10.1117/1.JOM.1.1.014001.

A group of researchers from Ecole Polytechnique Federale de Lausanne (EPFL) in Switzerland published a study on such an assembly composed of barium titanate spheres that are partially embedded in thin polymeric membranes. The result of their work, appearing in SPIE’s new Journal of Optical Microsystems, is a proposed method to fabricate microfluidic chips using the assembly for enhanced detection of bacteria. Such customized chips with fluidic and optical components already integrated have many benefits when combined with portable low-end imagers for analyses at remote sites or in resource-limited regions.

Source: https://bioengineer.org/focusing-on-field-analysis/

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