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

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

Advancing Science with DNA Sequence U.S. Energy Production & Consumption Source: Energy Flow 2005 (104 Quadrillion Btu)

Advancing Science with DNA Sequence U.S. Energy Consumption by Source and Sector Source:

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:

Advancing Science with DNA Sequence Increases in Atmospheric CO 2 Source:

Advancing Science with DNA Sequence World CO 2 Emissions Source:

Advancing Science with DNA Sequence Renewable Energy in the U.S. Source:

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

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?

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

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

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_ O_349O_356 O_374_CO_ STS1_ASTS3 7.8 G_ G_ G_ P_204_E 17.0 G_ G_ G_ S1_ S15_ T7_ PtAG_ G_ O_ O_ T3_ S1_23r 50.0 S8_ S8_ O_ G_ S5_ S8_ G_1809S4_ O_381_B 67.9 G_ O_ P_ G_1235G_4041_B S13_26T3_7r 69.6 T5_19T5_ G_1835G_2332 P_ P_2272_A 73.4 P_ G_1382S4_ O_547_B 82.3 O_ O_ S17_5O_ S13_ O_594O_ P_2020_Ar G_ O_ S15_ O_ S3_18S3_ O_ IV G_3602S17_ T12_10r 2.7 S8_ S8_ G_1941G_2425_B 13.9 G_ G_1250_A 19.3 S6_17O_ G_ S7_ P_ P_ O_ G_ G_1815G_2565 P_2392G_ P_ P_ PtAG_ P_ T2_ G_2562G_3101 G_3206S13_ T7_ O_ G_ P_ G_ G_901S7_24r 67.5 S8_ O_ S13_ G_ P_ P_333P_2574 O_ G_ G_ P_ XI Gender 0.0 G_ O_ O_ G_1917G_249 S17_14O_ O_276G_ S3_ O_ G_2829O_ U_R T4_ S13_11S2_ S1_ O_ S4_ S5_ S2_ P_204_Gr 41.8 S6_21r 42.2 G_604G_4063 G_1278G_1131 G_ P_204_H 45.5 T5_21rS17_7r 46.3 S3_4O_ S17_24O_ T4_ T11_10r 61.2 T6_4r 69.1 O_ S3_ S13_ S12_27r G XIX Eucalyptus Populus Genome

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.

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

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)

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

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

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

Advancing Science with DNA Sequence 0. 1 ARF5 PoptrARF5.1 PoptrARF ARF6 PoptrARF6.2 PoptrARF PoptrARF6.4 PoptrARF PoptrARF6.3 PoptrARF ARF8 PoptrARF8.1 PoptrARF ARF19 ARF7 PoptrARF7.1 PoptrARF PoptrARF7.3 PoptrARF ARF3 PoptrARF3.1 PoptrARF PoptrARF3.3 PoptrARF ARF4 PoptrARF ARF13 ARF23 ARF14 ARF12 ARF ARF15 ARF20 ARF ARF1 PoptrARF1.1 PoptrARF ARF9 PoptrARF9.1 PoptrARF PoptrARF9.3 PoptrARF ARF11 ARF ARF2 PoptrARF2.1 PoptrARF PoptrARF2.3 PoptrARF PoptrARF26 PoptrARF ARF10 PoptrARF10.1 PoptrARF ARF16 PoptrARF16.1 PoptrARF PoptrARF16.3 PoptrARF16.4 PoptrARF ARF17 PoptrARF17.1 PoptrARF 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

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.

Advancing Science with DNA SequenceIAA16.3 Control 90-day-old Populus cuttings stem cross sectional area (cm 2 ) transgenic control 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.

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.

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.

Advancing Science with DNA Sequence