DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

    More

News & Publications
Home › News Releases › Fields of Breeders’ Dreams: A Team Effort Toward Targeted Crop Improvements

January 27, 2021

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

Community effort yields reference switchgrass genome, environmental adaptations data

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

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 three DOE Bioenergy Research Centers (BRCs)—the Great Lakes Bioenergy Research Center (GLBRC), the Center for Bioenergy Innovation, 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.

Harvesting switchgrass under field rainout shelters for drought tolerance studies. (David Lowry)

Harvesting switchgrass under field rainout shelters for drought tolerance studies. (David Lowry)

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

Logo of Genome Insider, podcast of the Joint Genome Institute

Click on the logo or go here to listen to Tom Juenger and David Lowry in the JGI Genome Insider podcast.

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

A field technician wrestling a large switchgrass plant during fall harvest. (Jason Bonnette)

A field technician wrestling a large switchgrass plant during fall harvest. (Jason Bonnette)

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.

Switchgrass in front of a white rock growing along a river (background) in central Texas Hill Country. (David Lowry)

Switchgrass growing along a river in central Texas Hill Country. (David Lowry)

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.

Man in front of truck with bagged switchgrass plants. This is from one of many switchgrass collecting trips around the state of Texas in 2010. (David Lowry)

One of many switchgrass collecting trips around the state of Texas in 2010. (David Lowry)

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.”

Tour of switchgrass farming at Arlington Research Station in Wisconsin during a switchgrass community meeting.(David Lowry)

Tour of switchgrass farming at Arlington Research Station in Wisconsin during a switchgrass community meeting.(David Lowry)

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.

 

 

Byline: Massie S. Ballon

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

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.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

SPRUCE-ing Up Science

mentors and interns for JGI-UC Merced internship program

JGI at 25: Studying Sorghum’s Survival Skills

A graphic showing citations of the Sorghum bicolor reference genome

Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts

Single filament of Ca. Thiomargarita magnifica (Jean-Marie Volland)

Polar Phytoplankton Need Zinc to Cope with the Cold

Photograph of a stream of diatoms beneath Arctic sea ice.

JGI at 25: Solving the Mystery of the Missing Oil

A surface slick in the Gulf of Mexico, taken ~1.5 km from the Deepwater Horizon wellhead (Olivia Mason, LBNL).

JGI at 25: The Human Genome Project, or the JGI’s Origin Story

JGI contributions detailed in DOE Human Genome Project poster
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2022 The Regents of the University of California