Biomass

Summary
Bigger, Better Plants
High Throughput Phenotyping
Lignin Levers
Visualizing Genomes
Translation to Other Crops
Project Leads and Collaborators
Funding
Publications
Publicity

Summary
One aspect of research in the Leach Lab has focused on biomass and bioenergy and how plants can be optimized for food, forage, and energy.
This page serves to compile and synthesize various components of this research in one place.

Generally our objectives are:

  1. To identify and characterize plant genes influencing total biomass
  2. To develop more efficient ways to measure key plant traits in field conditions (the phenotypes)
  3. To characterize the relationships between plant composition and forage/bioenergy traits
  4. To better visualize genetic information on different plant species, varieties and more
  5. To translate what we learn in model crops such as rice, to dedicated crops such as switchgrass

Bigger, Better Plants
By screening a rice recombinant inbred line population (RIL) between two varieties that express different biomass and bioenergy phenotypes, we aim to discover genes for example, that make the “big” plants “big”.  Additionally, by screening a separate population of mutant rice lines, we have identified a mutation that leads to additional grain and biomass production in a specific rice variety.

High Throughput Phenotyping
With the advent of next generation sequencing, genetic information is plentiful and inexpensive. However linking genetic information to phenotypes – how plant genes are expressed in an environment – remains a challenge and depends on our ability to accurately measure many important phenotypes on large numbers of plants.  To this end, we are developing a tractor based, GPS positioned array of sensors to measure many plants in a field at once.

Paul Tanger, a graduate student in the Leach Lab, after training as a Sustainability Leadership Fellow, was inspired to produce a video highlighting the high throughput phenotyping system we developed.  IRRI has plans to expand the use of this system to many other studies and measurement of useful traits.  IRRI is generously hosting the video via Youtube:

Lignin Levers
This project aims to determine the role of two important genes in lignin biosynthesis. Lignin is a critical lever in downstream bioenergy processes through its abundance in the complex matrix of plant cell walls. If the amount of lignin can be optimized, enzymatic digestion of cellulose or thermochemical conversion of lignin can be made more sustainable. We propose to use rice as our model plant, then translate our findings to its close relative, switchgrass, a strong perennial, drought tolerant bioenergy feedstock. This research was recently funded by the Colorado Center for Biorefining and Biofuels and begins January 2014.

Visualizing Genomes
Comparative genomics approaches are uniquely powerful for the identification of functional elements of genomes that have been conserved over longer evolutionary timescales.  We have used comparative genomic approaches to reveal important patterns of conservation in whole genome plant alignments.  We have assembled a genome browser to visualize and compare this information:
http://genome.genetics.rutgers.edu/

Translation to Other Crops
We have developed populations of switchgrass, a potential bioenergy crop, to link the genetics between switchgrass and other model crop species such as rice.  We are investigating gene expression differences between these populations as a means to identify key genes responsible for biomass and other important traits.

Project Leads and Collaborators
Principal Investigators:

Collaborators:

  • Courtney Jahn, CSU
  • Steve Klassen, IRRI
  • Jillian Lang, CSU
  • Ken McNally, IRRI
  • Julius Mojica, CSU
  • Paul Tanger, CSU
  • Brad Tonnessen, CSU

Funding
Funding for the projects described here is generously provided by these institutions and grants:

  • U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, grant DE-FG02-08ER64629 and U.S. Department of Agriculture, National Institutes of Food and Agriculture, USDA-NIFA award 2008-35504-0485 to Leach, Bush, Kern, Leung, McKay and Zhao
  • U.S. Agency for International Development, IRRI-USAID Linkage grant DRPC2011-42 to Leach and Leung
  • CSU Clean Energy Supercluster seed grant to Tanger, Jahn, Leach
  • Colorado Center for Biorefining and Biofuels (C2B2) seed grant to Lang, Tanger, Tonnessen, Leach
  • U.S. National Science Foundation IGERT fellowship to Tanger

Publications

  • Tanger, P., Vega-Sánchez, M.E., Fleming, M., Tran, K., Singh, S., Abrahamson, J.B., Jahn, C.E., Santoro, N., Naredo, E.B., Baraoidan, M., Danku, J.M.C., Salt, D.E., McNally, K.L., Leung, H., Ronald, P.C., Bush, D.R., McKay, J.K., Leach, J.E. 2015. Cell wall composition of rice straw varies among environments, varieties, and tissue types: impacts on bioenergy potential. BioEnergy Research. DOI: 10.1007/s12155-014-9573-y.
  • Tanger, P., Field, J. L., Jahn, C. E., DeFoort, M. W., and Leach, J. E. (2013). Biomass for thermochemical conversion: targets and challenges. Front. Plant Sci. 4:, 218
  • Yang Z, Z Shen, H Tetreault, L Johnson, B Friebe, T Frazier, LK Huang, B Xu, C Burklew, X-Q  Zhang, B Zhao, 2013. Production of autopolyploid lowland switchgrass lines through in vitro chromosome doubling. Bioenergy Research
  • Sathitsuksanoh N, B Xu, B Zhao, YH Zhang, 2013. Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment. PLoS ONE 8(9): e73523
  • Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoña E, Leung H. 2013. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding Rice  doi: 10.1186/1939-8433-6-11
  • Xu B, N Sathitsuksanoh, Y Tang, MK Udvardi, JY Zhang, Z Shen, M Balota, K Harich, PY-H Zhang, B Zhao, 2012. Overexpression of AtLOV1 in switchgrass alters plant architecture, lignin content, and flowering time. PLoS One, 7(12): e47399
  • Hupalo D, AD Kern. Conservation and functional element discovery in 20 angiosperm plant genomes. 2013. Mol Biol Evol Mar 11 doi:pii:g3.113.005637v1
  • Jahn, C. E., Mckay, J. K., Mauleon, R., Stephens, J., McNally, K. L., Bush, D. R., Leung, H., and Leach, J. E. (2011). Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties. Plant Physiology 155, 157–168

Publicity

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