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Genomics and Bioenergy

Gerald A. Tuskan DOE Joint Genome Institute FAO Seminar October 12, 2007. Genomics and Bioenergy. The U.S. consumes roughly 26% of the worlds energy; yet we represent about 6% of the world’s population There is a linear relationship between energy consumption and gross domestic product

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Genomics and Bioenergy

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  1. Gerald A. Tuskan DOE Joint Genome Institute FAO Seminar October 12, 2007 Genomics and Bioenergy

  2. The U.S. consumes roughly 26% of the worlds energy; yet we represent about 6% of the world’s population There is a linear relationship between energy consumption and gross domestic product Many developing countries are adopting the U.S. social, economic and energy-use model U.S. Energy Consumption and the Economy

  3. U.S. Energy Production & Consumption Energy Flow 2005 (104 Quadrillion Btu) Source: http://www.eia.doe.gov/

  4. U.S. Energy Consumption by Source and Sector Source: http://www.eia.doe.gov/

  5. Domestic production has declined over the past 20 years and is expected to continue to decline Consumption is growing and imported oil is meeting this demand Continuing with business as usual has economic, environmental and national security consequences U.S. Crude Oil Production Source: http://www.eia.doe.gov/

  6. Increases in Atmospheric CO2 Source: http://cdiac.ornl.gov/ftp/trends/co2/maunaloa.co2

  7. World CO2 Emissions Source: http://www.eia.doe.gov/

  8. Renewable Energy in the U.S. Source: http://www.eia.doe.gov/

  9. Long-term Supply Options Source: Steven Koonin, 2006, BP

  10. Reduce our need for imported sources of energy? Maintain our standard of living? Reduce our carbon emissions? Preserve our energy security? Maintain our reliance on affordable transportation fuels? create ? How do we . . . Closed–loop domestic production of lignocellulosic biofuels

  11. Role of Biology Sun Cellulose Sugar Alcohol Biomass converting organisms Fermenters Feedstocks Poplar Termite Pichia stipitis Soybean, Maize, Switchgrass, Miscanthus, Sorghum, Cotton, Brachypodium • White Rot Fungus • Clostridium thermocellum • Saccharophagus degradans • Acidothermus cellulolyticus • Tamar wallaby forestomach • Poplar biomass degraders • Asian Longhorned Beetle gut • Elephant Grass decomposers • Thermoanaerobacter • Ethanolicus • Pichia stipitis

  12. Brachypodium Oryza Foxtail Millet Maize Musa Sorghum Dedicated Energy Crops – The Monocots Potential Energy Crop Model Genome Switchgrass Miscanthus Informative Genome Monocots Potential Energy Crop Model Genome Switchgrass Miscanthus Informative Genome Monocots Model Genome Wheat Informative Genome Monocots

  13. IV G_2425_A 0.0 O_393 S4_39 3.1 O_349 O_356 5.1 O_374_C O_394 STS1_A STS3 7.8 G_961 9.7 G_539 12.0 G_2390 12.2 XIX P_204_E 17.0 G_3437 23.2 G_3564 23.6 G_1560 25.2 Gender S1_7 31.0 0.0 S15_11 32.6 Populus Genome G_79 1.0 T7_11 35.9 O_550 2.4 PtAG_1 37.3 O_542 3.2 G_2337 46.7 G_1917 G_249 7.4 O_127 48.8 S17_14 O_543 O_520 49.2 O_276 G_2319 15.6 T3_18 49.9 269 predicted gene models S3_8 19.7 S1_23r 50.0 O_277 21.7 S8_19 54.8 G_2829 O_263 28.6 S8_20 55.4 U_R7 28.7 LG X O_521 57.7 T4_3 30.2 G_1414 58.8 S13_11 S2_19 30.6 S5_16 61.1 S1_8 35.6 S8_9 61.6 O_206 35.8 • 83 LG X-unique gene models • 4 related to drought tolerance G_1809 S4_7 66.6 S4_17 36.2 O_381_B 67.9 S5_28 37.0 G_1269 68.2 S2_3 37.2 O_541 68.6 P_204_Gr 41.8 P_2881 69.0 Arabidopsis S6_21r 42.2 G_1235 G_4041_B 69.6 G_604 G_4063 S13_26 T3_7r G_1278 G_1131 44.2 T5_19 T5_18 70.3 G_4000 G_1835 G_2332 70.4 P_204_H 45.5 P_2826 T5_21r S17_7r 46.3 Prunus P_2272_A 73.4 S3_4 O_433 47.0 P_2235 75.4 S17_24 O_597 49.1 G_1382 S4_15 79.8 T4_6 51.9 O_547_B 82.3 T11_10r 61.2 O_545 92.2 T6_4r 69.1 O_662 99.1 O_536 78.3 S17_5 O_661 103.7 S3_20 84.5 S13_15 112.2 O_594 O_663 113.4 P_2020_Ar 115.5 G_3847 117.0 S13_36 98.2 Populus O_670 125.2 S12_27r 101.1 S15_9 129.5 G831 104.8 O_517 131.3 S3_18 S3_19 133.0 O_671 141.7 210 predicted gene models XI LG VIII G_3602 S17_37 0.0 T12_10r 2.7 S8_18 4.0 S8_10 10.0 G_1941 G_2425_B 13.9 G_2951 15.8 G_1250_A 19.3 Eucalyptus S6_17 O_583 21.0 G_2465 24.7 Glycine S7_21 33.4 P_204.11 45.6 P_2520 47.6 O_560 49.8 G_1037 51.8 G_1815 G_2565 53.8 P_2392 G_3973 P_2765 54.3 P_2011 54.6 PtAG_2 55.3 P_2407 56.3 T2_22 56.5 G_2562 G_3101 56.9 G_3206 S13_28 T7_12 57.2 O_29 59.3 G_514 62.5 P_2866 65.1 G_946 65.2 G_901 S7_24r 67.5 S8_26 69.9 O_593 77.3 S13_6 79.0 G_943 87.4 P_2531 91.4 P_333 P_2574 92.7 O_333 G_3981 100.4 G_3037 105.7 P_204.05 106.0 Dedicated Energy Crops – The Dicots Potential Energy Crop Model Genome Oil production Informative Genome Legumes Glycine Populus Prunus Eucalyptus Potential Energy Crop Model Genome Woody Perennial Informative Genome Eurosid I Model Genome Eurosid II Informative Genome Populus

  14. Accelerated Domestication • Apply advanced, modern genetic and genomics techniques to accelerate the domestication rate in fast growing short-rotation tree species.

  15. Modern Hybrids • Corn Landraces • Teosinte Timeline: 2000 ybp Today 5000 ybp Corn Domestication

  16. Non-dehiscing seed head No lateral branching Soft seed coat Pest resistance 25,000 plants per acre High yields (135 bushels/acre) Modern Corn Attributes

  17. Domesticated Trees Improved Hybrids Clonal Selection Wild Stands Populus Domestication Timeline: 30 M - 200 ybp 120 ybp Today The Future?

  18. Accelerated domestication approach Current conventional approach Cost ($/ton) 1st 10 Generations 2nd 10 Generations Yield (ton/ac/yr) Functional Relationship Between Yield & Cost of Energy Crops

  19. Fully Domesticated Poplar • Reduced recalcitrance of cellulose degradation • Reduced height growth • Compact crown • Higher productivity per unit area • Greater number of stems per unit area • Compact root system • Drought/Stress tolerance • Enhanced radial growth • Nutrient use efficiency • Greater product yield • Reduced flowering

  20. ARF5 1000 PoptrARF5.1 1000 PoptrARF5.2 ARF6 747 PoptrARF6.2 748 PoptrARF6.1 743 PoptrARF6.4 393 1000 166 PoptrARF6.5 PoptrARF6.3 393 394 PoptrARF16.6 ARF8 1000 PoptrARF8.1 1000 PoptrARF8.2 342 ARF19 1000 ARF7 983 PoptrARF7.1 1000 1000 PoptrARF7.2 PoptrARF7.3 1000 PoptrARF7.4 ARF3 PoptrARF3.1 645 1000 PoptrARF3.2 634 PoptrARF3.3 636 961 PoptrARF3.4 ARF4 1000 PoptrARF4 Arabidopsis – 23 genes Populus – 40 genes ARF13 ARF23 1000 ARF14 1000 ARF12 998 516 ARF22 994 ARF15 696 ARF20 975 ARF21 ARF1 1000 PoptrARF1.1 1000 PoptrARF1.2 Arabidopsis-specific ARF9 PoptrARF9.1 451 1000 PoptrARF9.2 785 PoptrARF9.3 1000 PoptrARF9.4 ARF11 Populus-specific Activator domain 13:5 Populus: Arabidopsis 0.1 572 1000 474 422 886 1000 280 ARF18 ARF2 1000 PoptrARF2.1 1000 PoptrARF2.2 985 PoptrARF2.3 1000 435 PoptrARF2.4 PoptrARF26 1000 PoptrARF25 ARF10 874 PoptrARF10.1 1000 PoptrARF10.2 995 ARF16 PoptrARF16.1 860 1000 PoptrARF16.2 634 PoptrARF16.3 1000 PoptrARF16.4 1000 PoptrARF16.5 ARF17 1000 PoptrARF17.1 1000 PoptrARF17.2 Novel Gene Function: ARF & Aux/IAA genes Kalluri et al., 2006

  21. PoptrIAA7.1 and PoptrIAA7.2 closely group with AtIAA7 and AtIAA14. AtIAA7: Loss of function mutant (axr2-5) has phenotype similar to wild-type but has slightly longer hypocotyl and altered shoot gravitropism. AtIAA14: Loss of function mutant appears normal. IAA7.1 RNAi-mediated down-regulation of PoptrIAA7.1 results in severe dwarf phenotype in Populus with exaggerated lateral shoot growth. IAA7.1 Control Novel Gene Function: The Aux/IAA7 subgroup

  22. 7.1 transgenic control 4.4 stem cross sectional area (cm2) Novel Gene Function: The Aux/IAA16 subgroup RNAi-mediated down-regulation of PoptrIAA16.31 results in radial growth in Populus. AtIAA16 loss-of-function mutants expressed no visible phenotype. IAA16.3 Control 90-day-old Populus cuttings

  23. Cochliobolus heterostrophus (A) Tremella mesenterica (B) Puccinia graminis (B) Acaulospora longula or Gigaspora spp. or Glomus versiforme (G) Basidiomycota Ascomycota Glomeromycota Zygomycota Chytridiomycota Phylogenetic representation of the Kingdom Fungi phyla. The Zygomycota and Blastocladiales of the Chytridiomycota appear paraphyletic. The rest of Chytridiomycota form a single basal fungal clade. Fungal Genomics Candidates

  24. Summary & Conclusions • The U.S. consumes approximately 25% of the world’s energy. • 85% of the U.S. total is from fossil fuels. • Short-rotation Populus systems offer a plausible means of supplying biomass for conversion to liquid transportation fuels. • Increases in average productivity will require accelerated domestication approaches. • Access to the complete catalog of Populus genes will facilitate the development of domesticated tree systems through functional genomics approaches.

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