DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

    Read more

    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

    Read more

    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

  • 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
    screencap long reads webinar_ Metagenome Program
    Utilizing long-read sequencing for metagenomics and DNA modification detection webinar
    Watch the webinar on how the JGI employs single-molecule, long-read DNA sequences to aid with genome assembly and transcriptome analysis of microbial, fungal, and plant research projects.

    More

    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

    Read more

    martin-adams-unsplash
    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

    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)
    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

Our Science
Home › Science Highlights › Dealing with Drought: Uncovering Sorghum’s Secrets

December 2, 2019

Dealing with Drought: Uncovering Sorghum’s Secrets

Over 40 percent of the cereal crop’s genes respond to drought stress.

The Science

2016 sorghum field with blue and red streamers to discourage bird predation. (Peggy G. Lemaux)

Sorghum field in 2016, with blue and red streamers to discourage bird predation. (Peggy G. Lemaux)

Fields of drooping stalks and cracked earth are becoming common images in many regions due to more extreme weather events such as heat waves, droughts and floods. The planet’s resources are being stretched by a growing human population and increasing demand for agricultural products. Sorghum bicolor (L.) Moench is an African grass that adroitly handles droughts, floods and poor soils. This is the first paper that describes sorghum’s response to drought, from a large-scale field experiment to uncover the mechanisms behind sorghum’s capacity to produce high yields despite drought conditions. The field experiment is led by a consortium involving researchers from the University of California (UC), Berkeley, UC Agriculture and Natural Resources (ANR), US Department of Agriculture P­­lant Gene Expression Center, Pacific Northwest National Laboratory, and the U.S. Department of Energy Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab).

The Impact

Half a billion people consider sorghum a staple food in their diet, and the Department of Energy (DOE) also considers this to be a candidate bioenergy crop for its potential production of biomass on marginal lands not usable for conventional food crops. For that reason, its genome was sequenced by the JGI in 2009 and it is considered to be a Flagship Plant. By uncovering and characterizing the mechanisms through which sorghum is equipped to deal with adverse environmental conditions, researchers hope to improve yields for other crops under water-limited conditions.

Summary

Field lab set up and torn down each week – with centrifuges, vortexers, liquid nitrogen and dry ice – to fast freeze all root, leaf and rhizosphere samples. Pictured left to right: Jeff Dahlberg, Cheng Gao, Julie Sievert, Joy Hollingsworth. (Peggy G. Lemaux)

Field lab set up and torn down each week – with centrifuges, vortexers, liquid nitrogen and dry ice – to fast freeze all root, leaf and rhizosphere samples. Pictured left to right: Jeff Dahlberg, Cheng Gao, Julie Sievert, Joy Hollingsworth. (Peggy G. Lemaux)

In humans, traits such as height or susceptibility to certain diseases are well known to be partially due to the DNA sequence that makes up an individual’s genome. The genes of sorghum plants are likely responsible for the crop’s ability to produce good yields under water limiting conditions. Epigenetic Control of Drought Response in Sorghum (EPICON) is a five-year, multi-institution project funded by the DOE Office of Biological and Environmental Research to determine what genes respond to drought conditions, and how these conditions impact the crop and its microbiome. For three consecutive years (2016-2018), researchers conducted large-scale experiments in the field at the UC Kearney Agricultural Research and Extension Center (KARE) in Parlier, Calif. They grew two sorghum cultivars under three watering conditions, and then collected root, leaf and rhizosphere (soil surrounding the root) samples from the plants at the same time each week over the full life cycle of the plant. The first year’s gene expression results were published in the Proceedings of the National Academy of Science the week of December 2, 2019.

Sorghum variety BTx642 grown in Central Valley at temperatures around 100 degrees for 65 days without water. It is still green and filling grain to almost the same extent as plants that were watered weekly. (Jeffrey Dahlberg, UC ANR Agricultural Research and Extension Center)

The sorghum “stay-green” variety BTx642, grown in Central Valley at temperatures around 100 degrees for 65 days without water. (Jeffrey Dahlberg, UC ANR Agricultural Research and Extension Center)

While sorghum is drought-tolerant, the crop’s precise response is dependent on when exactly water becomes a limiting factor – before or after flowering. For the study, the team grew two sorghum varieties: one that tolerates better pre-flowering drought stress and a “stay-green” variety that tolerates drought conditions better after flowering. All plants were subjected to one of three conditions during their lifecycles. In the pre-flowering drought condition, no water was given during weeks 3 to 8 before flowering. In the post-flowering period drought was implemented by halting irrigation after the weekly watering was applied before week 9 (flowering); and a control condition, with water being applied weekly throughout the duration of the experiment, equal to the amount of water lost through evaporation in the leaves. Each week the team would set up a makeshift lab powered by a generator at the KARE field site and then collect and process the samples starting at 10am Pacific time.

JGI researchers helped develop the overall experimental design, sequenced the RNA from nearly 400 root and leaf samples and helped analyze the sequencing datasets. The results from the first year showed that 10,727 genes or 44% of expressed genes respond to drought stress regardless of whether drought was applied before or after the plants flower. More genes responded to drought in the roots than in the leaves, suggesting that roots are more affected by the lack of water than the leaves. The team found sets of genes that change their expression in the same manner in the two cultivars and some differently. Some different responses relate to functioning of the photosynthetic machinery, which requires water to function. Other responses help the plant deal with excess solar radiation.

Once collected, 30-40 gram leaf samples are frozen and then pulverized to provide homogenous samples to multiple labs. Study co-author Mary Madera uses the freezer mill that is used to grind the samples in a bath of liquid nitrogen after frozen samples are first pounded to fit into the canister that is inserted into the freezer mill. (Peggy G. Lemaux)

Once collected, 30-40 gram leaf samples are collected and frozen. After pounding the frozen samples  to fit into the canister above, study co-author Mary Madera uses the freezer mill to grind the samples in a bath of liquid nitrogen to provide homogenous samples to multiple labs. (Peggy G. Lemaux)

Additionally, in both cultivars, the team found that a large set of genes impacted by drought is associated with the symbiotic relationship between plant roots and arbuscular mycorrhizal fungi (AMF), known to provide plants with nutrients and pathogen protection. Specifically, gene expression in that set, implicated in AMF interactions, was dramatically reduced as a result of pre-flowering drought stress.

The first year’s results will be compared to data from additional years of sampling, which are currently being analyzed. All EPICON data collected, along with methodology and results, will ultimately be published on the JGI plant data portal Phytozome.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Ramana.Madupu@science.doe.gov

PI Contacts
Peggy Lemaux
University of California, Berkeley
lemauxpg@berkeley.edu

John Vogel
DOE Joint Genome Institute
jpvogel@lbl.gov

Funding:

This research was funded in part by DOE Grant DE-SC0014081 (to N.V., B.C., C.G., G.P., M.M., J.H., J.S., Y.Y., J.A.O., V.R.S., S.D., L.X., M.J.B., A.V., C.J., R.H., D.C.-D., R.O., J.W.T., J.D., J.P.V., P.G.L., and E.P.); Gordon and Betty Moore Foundation Grant GBMF3834 and Alfred P. Sloan Foundation Grant 2013-10-27 (to the University of California, Berkeley [N.V.]); L’Ecole Normale Superieure-CFM Data Science Chair (E.P.); and the Office of Science (BER), DOE Grant DE-SC0012460 (to M.J.H.). Work conducted by the DOE Joint Genome Institute is supported by the Office of Science of the DOE Contract DE-AC02-05CH11231. D.P. is supported in part by the Berkeley Fellowship and NSF Graduate Research Fellowship Program Grant DGE 1752814. K.K.N. is an investigator of the Howard Hughes Medical Institute.

Publication:

  • Varoquax N et al. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc. Natl. Acad. Sci. U.S.A. 2019 Dec 5. doi:10.1073/pnas.1907500116.

Related Links:

  • UC Berkeley News Release: “Genomic gymnastics help sorghum plant survive drought“
  • UCANR News Release: “Genomic gymnastics help sorghum plant survive drought“
  • ABC30 Story: “Drought tolerant crop being studied in the Valley”
  • EPICON on JGI Phytozome portal
  • JGI Plant Flagship Genomes
  • JGI News Release: Scientists Publish Genetic Blueprint of Key Biofuels Crop
  • Sorghum bicolor genome on JGI Phytozome portal
  • JGI Feature: Studying Drought Tolerance in Sorghum

 

 

by 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)

Filed Under: Science Highlights

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Podcasts
  • Webinars
  • 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)

How Maize Makes An Antibiotic Cocktail

Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)

From Competition to Cooperation

The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)

A Grass Model to Help Improve Giant Miscanthus

Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)

In Hot Spring Microbial Mat, Viruses Ride “Piggyback”

Microbial mat under the microscope. Visible layers contain different microbial communities and minerals. The team characterized viruses in a subset of the mat layers. (John Spear)
  • 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