DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

    More

    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

    More

    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

    More:

    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

    Read more

    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

    More

    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

    More

    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

    Read more

    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

    Read more

    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos and Templates
    • Photos
    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

    More

    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

    More

    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

    Read more

News & Publications
Home › News Releases › Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet

October 5, 2020

Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet

Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)

A green millet (Setaria viridis) plant along a highway in Illinois. (Courtesy of the Kellogg lab)

For years, Elizabeth (Toby) Kellogg and other researchers at the Danforth Plant Science Center (Danforth Center) drove up and down the highways of the continental United States, occasionally pulling over to the side of the road to collect small weedy plants and bring them back to the lab. The weedy grass was green millet (Setaria viridis), a small model grass with a short lifecycle that uses a carbon fixation process known as the C4 pathway, which particularly helps plants thrive in warm, arid environments. Corn and sugarcane are among the major high-yield C4 crops, as are the candidate biofuel feedstocks Miscanthus and switchgrass.

Innumerable road trips and hundreds of plants have resulted in a paper published October 5, 2020, in Nature Biotechnology. Kellogg and her colleagues, along with researchers at the HudsonAlpha Institute for Biotechnology 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), generated genome sequences for nearly 600 green millet plants and released a very high quality reference S. viridis genome sequence. Analysis of these plant genome sequences also led researchers to identify a gene related to seed dispersal in wild populations for the first time.

“To our knowledge, nobody has ever discovered a dispersal gene that way,” said Kellogg, a senior author of the paper. “This paper is the first one to survey a huge amount of natural diversity and say, ‘Yeah, there are genes out there that affect this phenotype.’”

Results from A “Massive Amount” of Sequencing

Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)

Green millet plants growing at the Danforth Center. (Bruton Stroube/ Donald Danforth Plant Science Center)

Seed dispersal is critical for plants in the wild, but it is an undesirable trait for domesticated crops because it leads to reduced harvest yields. Over thousands of years, farmers have selected for cereal plants without this shattering trait – referring to the moment when the cluster of seeds at the tip of each branch breaks apart so the seeds can disperse – so that the seeds remain atop the plant to be collected.

Association mapping led the team to identify a gene called Less Shattering 1 (SvLes1); gene editing studies led by co-first author Pu Huang confirmed that it was involved in shattering by turning it off. “It’s a new shattering gene variant identified in a natural population. Not very many of these shattering genes have been discovered that let a plant go all the way to seed but prevent the seeds from falling,” said JGI Plant Program head Jeremy Schmutz, who is also a HudsonAlpha Faculty Investigator. “This could be another mechanism to turn off shattering and domesticate crops.” How shattering occurs varies widely between crops, Kellogg added, and shattering genes may be specific to species or groups of species.

The genome data also revealed that green millet was introduced into the United States multiple times from Eurasia. The team also identified a gene associated with leaf angle, which determines how much sunlight leaves can get and in turn serves as a predictor of yield. The gene is an ortholog of known genes, “The gene has now been mapped back in maize as involved in leaf angle,” noted Schmutz. “It’s a nice example of de novo discovery and then mapping back to identify candidate genes.”

Every dot on this map represents the location of a green millet (Setaria viridis) plant collected by Danforth Center researchers. (Courtesy of the Kellogg lab)

Every dot on this map represents the location of a green millet (S. viridis) plant collected by Danforth Center researchers. (Courtesy of the Kellogg lab)

Through JGI’s Community Science Program, sequences of several hundred green millet plant genomes were generated, though the final analyses focused on 598 individuals. Schmutz and his team assembled and annotated the genomes at HudsonAlpha. Sujan Mamidi and Adam Healey, two of the co-first authors, led the data analyses and assembled the green millet “pan-genome” (a set of 51,000 genes that represent all the genes that are present in a given species).

“This is a great example of developing a large-scale genome infrastructure with a reasonably accessible system,” said Schmutz. “Building the pan-genome and accessions allow us to see presence/absence variation easily and to find genes missing in particular accessions, and to confirm phenotypes, which validate traits.”

“The number of lines sequenced is not trivial, and they were all assembled de novo, which let the team look at presence/absence of whole genes,” Kellogg agreed. “Getting that information is hard. There’s a good reason nobody’s done it; it’s a heck of a lot of work. I wouldn’t have done it without the contribution of Jeremy’s group. It’s just a massive amount of sequencing.”

A Resource for Many Applications

Kellogg noted that C4 crops have gotten a lot of interest because they’re very productive even in high heat while C3 crops have become less efficient at photosynthesis, a concern as extreme weather events become more frequent. “A big part of the Danforth Center’s mission is to feed the hungry and improve human health. So there’s a major question: how to turn a C3 crop into a C4 crop. There should be a master regulator but no one has found it,” Kellogg mused. “[The S. viridis genome] is a resource for many different applications. The JGI group has been wonderful to collaborate with, and this [project] wouldn’t have been possible without their involvement; it’s something we wouldn’t have even started.”

The reference genome of Setaria viridis is available on JGI’s plant portal Phytozome.

Researchers from the RIKEN Center for Sustainable Resource Science (Japan) and Chinese Academy of Agricultural Sciences (China) were also involved in this work.

Publication: Mamidi S et al. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nature Biotechnology. 2020 Oct 5. doi:10.1038/s41587-020-0681-2

 

Byline: Massie Santos Ballon

***

About The Donald Danforth Plant Science Center: Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research, education and outreach aim to have impact at the nexus of food security and the environment, and position the St. Louis region as a world center for plant science. The Center’s work is funded through competitive grants from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation, and the Bill & Melinda Gates Foundation. Follow us on Twitter at @DanforthCenter.

About HudsonAlpha: HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to developing and applying scientific advances to health, agriculture, learning, and commercialization. Opened in 2008, HudsonAlpha’s vision is to leverage the synergy between discovery, education, medicine, and economic development in genomic sciences to improve the human condition around the globe. The HudsonAlpha biotechnology campus consists of 152 acres nestled within Cummings Research Park, the nation’s second largest research park. The state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. HudsonAlpha has become a national and international leader in genetics and genomics research and biotech education and fosters more than 40 diverse biotech companies on campus. To learn more about HudsonAlpha, visit hudsonalpha.org.

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
  • Podcasts
  • CSP Plans
  • Featured Profiles

Related Content:

An Automated Tool for Assessing Virus Data Quality

Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)

A One-Stop Shop for Analyzing Algal Genomes

Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)

Uncovering Novel Genomes from Earth’s Microbiomes

Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)

2021 JGI Proposal Call Brings New Investigators into Community Science Program

Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)

The More the Merrier: Making the Case for Plant Pan-genomes

Brachypodium distachyon, the model species for temperate cereals and biofuel crop grasses with a growing pangenome of one hundred genomes. Spain: Huesca, Ibieca, San Miguel de Foces. (Photography credits: Pilar Catalán)

Picking Up Threads of Cotton Genomics

cotton boll G. hirsutum (Cotton Inc)
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • 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

© 1997-2021 The Regents of the University of California