Texas Switchgrass Collaborative

About us


The Texas Switchgrass Collaborative is a group of researcher funded by the National Science Foundation and centered at the University of Texas at Austin. We are studying various aspects of the ecology, physiology, and genetics of switchgrass, a major candidate bioenergy crop. Our primary focus is to understand the mechanisms of drought tolerance in switchgrass.

Background and Justification
A critical challenge of the 21st century is to discover large-scale sources of sustainable energy. While various alternatives to fossil fuels are currently being developed for electricity production (e.g. solar, nuclear, wind), there will also be a continuing need for combustible liquid fuels. Currently, biofuels, either ethanol or biodiesel derived from agricultural crops or dedicated cellulosic feedstocks represent a small fraction of our domestic energy demands. However, the Energy Security and Independence Act of 2007 (P.L. 110-140) has mandated 36 billion gallons of biofuel production by 2022. These mandates cannot be met through corn-based ethanol without reductions in global food security. As an alternative, cellulosic ethanol derived from perennial feedstocks, such as switchgrass (Panicum virgatum), are predicted to bring higher returns on energy inputs (>500%), have greater potential in reducing greenhouse gasses, and are less damaging to ecosystems than corn-based ethanol. Switchgrass requires far fewer fertilizer and water inputs than corn and can be grown on marginal lands. As only limited breeding has been completed in switchgrass, there is enormous potential for improvement in abiotic stress tolerance, yield, and biofuel capacity.

Understanding genetic variation of drought tolerance in switchgrass




The effects of climate change during the next 50-100 yrs will largely determine shifts in habitat type and quality, as well as the potential to use habitats for biofuel production. Although decreasing precipitation is expected to reduce plant productivity, the severity of impact will depend on the magnitude and frequency of altered rainfall, physiological tolerance envelopes of species, as well as the ability of switchgrass to acclimate or adapt. As such, a major goal of climate change ecology is to determine responses of target plant species under realistic field conditions. Here, we will use sophisticated field rainout shelters and realistic planting densities to explore switchgrass responses to predicted climate. To understand gene expression responses to drought we will implement RNA-sequencing on various switchgrass varieties under different drought regimes.

We are currently screening multiple cultivars of switchgrass for their tolerance to drought at multiple sites in Central Texas. This research will be conducted at the Lady Bird Johnson Wildflower Center and the Brackenridge Field Laboratory in Austin, TX, as well as the USDA Grassland Soil and Water Research Laboratory in Temple, TX.

The primary goals of this project will be to estimate the environmental and genetic variability for drought-related traits, overall physiology, and performance among diverse Panicum virgatum varieties grown under future climate environments; identify drought-tolerant P. virgatum varieties for further study and potential biofuel use; and determine gene expression response to drought across switchgrass ecotypes.

We are currently developing computational tools to study the association between genetic and climate variation. We can use genotype-climate correlations to identify climatic gradients that are potentially important for local adaptation. We also plan to identify loci where alleles covary with climate as a means of identifying genes important for adaptation to climate stress. We have incorporated information from additional experiments into this genotype-climate association study to further refine our search for candidate genes.

Development of diploid switchgrass as a model genomic system




The agronomic development of switchgrass as a biofuel crop has focused primarily on Panicum virgatum. Unfortunately, P. virgatum is a complex polyploid (both tetraploid and octaploid series exist), has a large genome (1C > 1500 Mbp) and is thus not easily amenable to traditional molecular genetic studies. In contrast, the closely related diploid species Panicum hallii has a much simpler genome (~500 Mbp) and can provide a genetic reference to support and interpret parallel studies in P. virgatum. Importantly, P. hallii occurs over the same moisture gradient as P. virgatum in the southern Great Plains and has locally adapted mesic (var. filipes) and xeric (var. hallii) ecotypes.

We are currently developing P. hallii as a model genomic system through high-throughput genomic and transcriptome sequencing in collaboration with the Department of Energy Joint Genome Institute. Our goal is to understand the genetic basis of natural variation in drought tolerance and biofuel related traits through a combination of high-density genetic mapping with RNA-sequencing. This aim will be achieved by leveraging distribution of natural drought adaptations distributed along the steep cline in soil moisture across Texas and the desert Southwest.

Switchgrass Field Trials




A large agronomic community is implementing field trials of switchgrass (Panicum virgatum) across current and future expected growing regions of the USA. This infrastructure provides a unique opportunity for collaborative research.

Our focus is on 10 sites across the southern US: USDA-GSW, Temple, TX; USDA-ARS, Weslaco, TX; Texas A&M University, Kingsville, TX; USDA-NRCS, Nacogdoches, TX; USDA-NRCS, Knox City, TX; Konza Prairie Biological Station, Manhattan, KS; USDA-NRCS, Elsberry, MO; and three sites in AR.

Overall, the selected sites provide a range of variation in temperatures, day length, rainfall regimes, and soil series, and will complement the Temple and Austin precipitation manipulation experiments and bolster data for climatic envelope modeling. The physiological stress responses of the varieties are being quantified using the physiology and growth measurements. These data provide realistic values of plant parameters needed for the ALMANAC (see below), which will be used to simulate leaf area growth, nutrient uptake, and biomass production. Leaf samples will be collected from these sites as a source of additional material for genomics.

Spatial Modeling
The Agriculatural Land Management Alternatives with Numerical Assessment Criteria model (ALMANAC) is a process-oriented simulation that was developed by the USDA. It contains explicit functions for water balance, nutrient cycling, and plant growth and requires detailed environmental data on soil, weather, and wind conditions. The model was parametrized and validated by field trials performed in 11 states. We extended the ALMANAC software interface to run spatially across the eastern US to predict the current and future yields of switchgrass under extreme climate change scenarios reported by the IPCC. These simulated switchgrass yields are being used to answer several questions about the long-term potential and effect of switchgrass for biofuel production.

Collections and Germplasm



 * [[Media:Panicum_Collections_5_29_11.xls‎‎‎‎‎|Plant material]] currently growing at Brackenridge Biological Research Station.


 * Map of collections of Panicum hallii in herbarium on SEINet

Protocols

 * Switchgrass Field Protocols
 * Genotyping through University of Georgia
 * M13 labeling
 * Pig-tailing to reduce stutter
 * Diploid Panicum crossing technique
 * CTAB DNA Extraction
 * Switchgrass Lab Protocols

Literature collection
The following link contains a list of Relevant Publications

Academic Labs

 * Tom Juenger, University of Texas at Austin
 * Christine Hawkes, University of Texas at Austin
 * Tim Keitt, University of Texas at Austin

USDA

 * Philip Fay, USDA Temple, TX
 * James Kiniry, USDA Temple, TX
 * Mari-Vaughn Johnson, USDA Temple, TX

Postdocs

 * David Lowry
 * Eli Meyer
 * Mike Aspinwall
 * Samuel Taylor

Graduate Students

 * Taylor Quedensley
 * Jesse R. Lasky
 * Kate Behrman

Contact
This wiki page is primarily maintained by David Lowry, who can be contacted with questions at davidbryantlowry@gmail.com