1. Advancing Science with DNA Sequence Genomics and Bioenergy Gerald A. Tuskan DOE Joint Genome Institute FAO Seminar October 12, 2007

2. Advancing Science with DNA Sequence U.S. Energy Consumption and the Economy ● 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

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

4. Advancing Science with DNA Sequence U.S. Energy Consumption by Source and Sector Source: http://www.eia.doe.gov/

5. Advancing Science with DNA Sequence U.S. Crude Oil Production ● 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 Source: http://www.eia.doe.gov/

6. Advancing Science with DNA Sequence Increases in Atmospheric CO 2 Source: http://cdiac.ornl.gov/ftp/trends/co2/maunaloa.co2

7. Advancing Science with DNA Sequence World CO 2 Emissions Source: http://www.eia.doe.gov/

8. Advancing Science with DNA Sequence Renewable Energy in the U.S. Source: http://www.eia.doe.gov/

9. Advancing Science with DNA Sequence Long-term Supply Options Source: Steven Koonin, 2006, BP

10. Advancing Science with DNA Sequence How do we... ● 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? Closed–loop domestic production of lignocellulosic biofuels create?

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

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

13. Advancing Science with DNA Sequence Dedicated Energy Crops – The Dicots Glycine Eucalyptus Populus Arabidopsis Potential Energy Crop Model Genome Oil production Informative Genome Legumes Prunus Glycine Potential Energy Crop Model Genome Woody Perennial Informative Genome Eurosid I Model Genome Eurosid II Informative Genome Populus Prunus LG X 269 predicted gene models ▬83 LG X-unique gene models ▬4 related to drought tolerance LG VIII 210 predicted gene models G_2425_A 0.0 O_393S4_39 3.1 O_349O_356 O_374_CO_394 5.1 STS1_ASTS3 7.8 G_961 9.7 G_539 12.0 G_2390 12.2 P_204_E 17.0 G_3437 23.2 G_3564 23.6 G_1560 25.2 S1_7 31.0 S15_11 32.6 T7_11 35.9 PtAG_1 37.3 G_2337 46.7 O_127 48.8 O_520 49.2 T3_18 49.9 S1_23r 50.0 S8_19 54.8 S8_20 55.4 O_521 57.7 G_1414 58.8 S5_16 61.1 S8_9 61.6 G_1809S4_7 66.6 O_381_B 67.9 G_1269 68.2 O_541 68.6 P_2881 69.0 G_1235G_4041_B S13_26T3_7r 69.6 T5_19T5_18 70.3 G_1835G_2332 P_2826 70.4 P_2272_A 73.4 P_2235 75.4 G_1382S4_15 79.8 O_547_B 82.3 O_545 92.2 O_662 99.1 S17_5O_661 103.7 S13_15 112.2 O_594O_663 113.4 P_2020_Ar 115.5 G_3847 117.0 O_670 125.2 S15_9 129.5 O_517 131.3 S3_18S3_19 133.0 O_671 141.7 IV G_3602S17_37 0.0 T12_10r 2.7 S8_18 4.0 S8_10 10.0 G_1941G_2425_B 13.9 G_2951 15.8 G_1250_A 19.3 S6_17O_583 21.0 G_2465 24.7 S7_21 33.4 P_204.11 45.6 P_2520 47.6 O_560 49.8 G_1037 51.8 G_1815G_2565 P_2392G_3973 53.8 P_2765 54.3 P_2011 54.6 PtAG_2 55.3 P_2407 56.3 T2_22 56.5 G_2562G_3101 G_3206S13_28 56.9 T7_12 57.2 O_29 59.3 G_514 62.5 P_2866 65.1 G_946 65.2 G_901S7_24r 67.5 S8_26 69.9 O_593 77.3 S13_6 79.0 G_943 87.4 P_2531 91.4 P_333P_2574 O_333 92.7 G_3981 100.4 G_3037 105.7 P_204.05 106.0 XI Gender 0.0 G_79 1.0 O_550 2.4 O_542 3.2 G_1917G_249 S17_14O_543 7.4 O_276G_2319 15.6 S3_8 19.7 O_277 21.7 G_2829O_263 28.6 U_R7 28.7 T4_3 30.2 S13_11S2_19 30.6 S1_8 35.6 O_206 35.8 S4_17 36.2 S5_28 37.0 S2_3 37.2 P_204_Gr 41.8 S6_21r 42.2 G_604G_4063 G_1278G_1131 G_4000 44.2 P_204_H 45.5 T5_21rS17_7r 46.3 S3_4O_433 47.0 S17_24O_597 49.1 T4_6 51.9 T11_10r 61.2 T6_4r 69.1 O_536 78.3 S3_20 84.5 S13_36 98.2 S12_27r 101.1 G831 104.8 XIX Eucalyptus Populus Genome

14. Advancing Science with DNA Sequence Accelerated Domestication  Apply advanced, modern genetic and genomics techniques to accelerate the domestication rate in fast growing short-rotation tree species.

15. Advancing Science with DNA Sequence Corn Domestication Teosinte Timeline: 5000 ybp Corn Landraces 2000 ybp Modern Hybrids Today

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

17. Advancing Science with DNA Sequence Timeline: 30 M - 200 ybp120 ybp Wild Stands Today Populus Domestication Clonal Selection Improved Hybrids Domesticated Trees The Future?

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

19. Advancing Science with DNA Sequence 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 Fully Domesticated Poplar

20. Advancing Science with DNA Sequence 0. 1 ARF5 PoptrARF5.1 PoptrARF5.2 1000 ARF6 PoptrARF6.2 PoptrARF6.1 748 747 PoptrARF6.4 PoptrARF6.5 1000 743 PoptrARF6.3 PoptrARF16.6 394 166 ARF8 PoptrARF8.1 PoptrARF8.2 1000 393 ARF19 ARF7 PoptrARF7.1 PoptrARF7.2 1000 983 1000 PoptrARF7.3 PoptrARF7.4 1000 342 393 ARF3 PoptrARF3.1 PoptrARF3.2 1000 PoptrARF3.3 PoptrARF3.4 961 634 645 ARF4 PoptrARF4 1000 636 ARF13 ARF23 ARF14 ARF12 ARF22 516 ARF15 ARF20 ARF21 975 696 994 998 1000 ARF1 PoptrARF1.1 PoptrARF1.2 1000 ARF9 PoptrARF9.1 PoptrARF9.2 1000 PoptrARF9.3 PoptrARF9.4 1000 785 45 1 ARF11 ARF18 1000 886 422 ARF2 PoptrARF2.1 PoptrARF2.2 1000 PoptrARF2.3 PoptrARF2.4 1000 985 PoptrARF26 PoptrARF25 1000 435 280 1000 572 ARF10 PoptrARF10.1 PoptrARF10.2 1000 874 ARF16 PoptrARF16.1 PoptrARF16.2 1000 PoptrARF16.3 PoptrARF16.4 PoptrARF16.5 1000 634 860 995 ARF17 PoptrARF17.1 PoptrARF17.2 1000 474 Novel Gene Function: ARF & Aux/IAA genes Arabidopsis-specific Populus-specific Arabidopsis – 23 genes Populus – 40 genes Activator domain 13:5 Populus: Arabidopsis Kalluri et al., 2006

21. Advancing Science with DNA Sequence Novel Gene Function: The Aux/IAA7 subgroup PoptrIAA7.1 and PoptrIAA7.2 closely group with AtIAA7 and AtIAA14. IAA7.1 Control RNAi-mediated down-regulation of PoptrIAA7.1 results in severe dwarf phenotype in Populus with exaggerated lateral shoot growth. 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.

22. Advancing Science with DNA SequenceIAA16.3 Control 90-day-old Populus cuttings stem cross sectional area (cm 2 ) transgenic control 7.1 4.4 Novel Gene Function: The Aux/IAA16 subgroup AtIAA16 loss-of- function mutants expressed no visible phenotype. RNAi-mediated down- regulation of PoptrIAA16.31 results in radial growth in Populus.

23. Advancing Science with DNA Sequence Fungal Genomics Candidates 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.

24. Advancing Science with DNA Sequence 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.

25. Advancing Science with DNA Sequence