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)

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.