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Advancing Science with DNA Sequence
Genomics and BioenergyGenomics and Bioenergy
Gerald A. TuskanDOE Joint Genome InstituteFAO SeminarOctober 12, 2007
Advancing Science with DNA Sequence
U.S. Energy Consumption U.S. Energy Consumption and the Economyand 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 & U.S. Energy Production & ConsumptionConsumption
Source: http://www.eia.doe.gov/Energy Flow 2005
(104 Quadrillion Btu)
Advancing Science with DNA Sequence
U.S. Energy Consumption by U.S. Energy Consumption by Source and SectorSource and Sector
Source: http://www.eia.doe.gov/
Advancing Science with DNA Sequence
U.S. Crude Oil Production 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/
Advancing Science with DNA Sequence
Increases in Atmospheric COIncreases in Atmospheric CO22
Source: http://cdiac.ornl.gov/ftp/trends/co2/maunaloa.co2
Advancing Science with DNA Sequence
World COWorld CO22 Emissions Emissions
Source: http://www.eia.doe.gov/
Advancing Science with DNA Sequence
Renewable Energy in the U.S.Renewable Energy in the U.S.
Source: http://www.eia.doe.gov/
Advancing Science with DNA Sequence
Long-term Supply OptionsLong-term Supply Options
Source: Steven Koonin, 2006, BP
Advancing Science with DNA Sequence
How do we . . . 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 Closed–loop domestic production of lignocellulosic biofuelsof lignocellulosic biofuels
createcreate
??
Advancing Science with DNA Sequence
Sun
Role of BiologyRole of Biology
Poplar Termite Pichia stipitis
FermentersFeedstocks
•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 Sugar Alcohol
Biomass converting organisms
Advancing Science with DNA Sequence
Brachypodium
Dedicated Energy Crops – Dedicated Energy Crops –
The MonocotsThe Monocots
Foxtail Millet
Maize
Potential Energy Crop
Model GenomeSwitchgrassMiscanthus
Informative GenomeMonocots
Sorghum
Oryza
Potential Energy Crop
Model GenomeSwitchgrassMiscanthus
Informative GenomeMonocots
Model GenomeWheat
Informative GenomeMonocots
Musa
Advancing Science with DNA Sequence
Dedicated Energy Crops – Dedicated Energy Crops – The DicotsThe Dicots
Glycine
Eucalyptus
Populus
Populus
Arabidopsis
Potential Energy Crop
Model GenomeOil production
Informative GenomeLegumesPrunus
Glycine
Potential Energy Crop
Model GenomeWoody Perennial
Informative GenomeEurosid I
Model GenomeEurosid II
Informative GenomePopulus
Prunus
LG X269 predicted gene models
▬ 83 LG X-unique gene models
▬ 4 related to drought tolerance
LG VIII210 predicted gene models
G_2425_A0.0O_393S4_393.1O_349O_356O_374_CO_3945.1STS1_ASTS37.8G_9619.7G_53912.0G_239012.2P_204_E17.0G_343723.2G_356423.6G_156025.2S1_731.0S15_1132.6T7_1135.9
PtAG_137.3G_233746.7O_12748.8O_52049.2T3_1849.9S1_23r50.0S8_1954.8S8_2055.4O_52157.7G_141458.8S5_1661.1S8_961.6G_1809S4_766.6O_381_B67.9G_126968.2O_54168.6P_288169.0G_1235G_4041_BS13_26T3_7r69.6T5_19T5_1870.3G_1835G_2332P_282670.4P_2272_A73.4P_223575.4G_1382S4_1579.8O_547_B82.3O_54592.2O_66299.1S17_5O_661103.7S13_15112.2O_594O_663113.4P_2020_Ar115.5G_3847117.0O_670125.2S15_9129.5O_517131.3S3_18S3_19133.0O_671141.7
IV
G_3602S17_370.0T12_10r2.7S8_184.0
S8_1010.0G_1941G_2425_B13.9G_295115.8G_1250_A19.3S6_17O_58321.0G_246524.7S7_2133.4P_204.1145.6P_252047.6O_56049.8G_103751.8G_1815G_2565P_2392G_397353.8P_276554.3P_201154.6
PtAG_255.3P_240756.3T2_2256.5G_2562G_3101G_3206S13_2856.9T7_1257.2O_2959.3G_51462.5P_286665.1G_94665.2G_901S7_24r67.5S8_2669.9O_59377.3S13_679.0G_94387.4P_253191.4P_333P_2574O_33392.7G_3981100.4G_3037105.7P_204.05106.0
XI
Gender0.0G_791.0O_5502.4O_5423.2G_1917G_249S17_14O_5437.4O_276G_231915.6S3_819.7O_27721.7G_2829O_26328.6U_R728.7T4_330.2S13_11S2_1930.6S1_835.6O_20635.8S4_1736.2S5_2837.0S2_337.2P_204_Gr41.8S6_21r42.2G_604G_4063G_1278G_1131G_4000
44.2
P_204_H45.5T5_21rS17_7r46.3S3_4O_43347.0S17_24O_59749.1T4_651.9T11_10r61.2T6_4r69.1O_53678.3S3_2084.5
S13_3698.2S12_27r101.1G831104.8
XIX
Eucalyptus
Populus Genome
Advancing Science with DNA Sequence
Accelerated DomesticationAccelerated 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 DomesticationCorn Domestication
• Teosinte
Timeline:
5000 ybp
• Corn Landraces
2000 ybp
• Modern Hybrids
Today
Advancing Science with DNA Sequence
Modern Corn AttributesModern 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 - 200 ybp 120 ybp
Wild Stands
Today
PopulusPopulus Domestication Domestication
Clonal Selection
Improved Hybrids
Domesticated Trees
The Future?
Advancing Science with DNA Sequence
Cost
($/t
on)
Yield (ton/ac/yr)
Current conventional approach
Functional Relationship Between Functional Relationship Between Yield & Cost of Energy CropsYield & 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 PoplarFully Domesticated Poplar
Advancing Science with DNA Sequence
0.1
ARF5PoptrARF5.1PoptrARF5.2
10001000
ARF6PoptrARF6.2
PoptrARF6.1748
747
PoptrARF6.4PoptrARF6.5
1000
743
PoptrARF6.3PoptrARF16.6394
166
ARF8PoptrARF8.1
PoptrARF8.21000
1000
393
ARF19ARF7
PoptrARF7.1PoptrARF7.2
1000983
1000
PoptrARF7.3PoptrARF7.4
1000
1000
342
393
ARF3PoptrARF3.1
PoptrARF3.21000
PoptrARF3.3PoptrARF3.4961
634645
ARF4PoptrARF4
1000
636
ARF13ARF23
ARF14ARF12ARF22
516
ARF15ARF20
ARF21975
696994
9981000
1000
ARF1PoptrARF1.1PoptrARF1.2
10001000
ARF9PoptrARF9.1
PoptrARF9.21000
PoptrARF9.3PoptrARF9.4
1000785
451
ARF11ARF18
1000
886
422
ARF2PoptrARF2.1PoptrARF2.2
10001000
PoptrARF2.3PoptrARF2.4
1000
985
PoptrARF26PoptrARF25
1000
435
280
1000
572
ARF10PoptrARF10.1PoptrARF10.2
1000874
ARF16PoptrARF16.1
PoptrARF16.21000
PoptrARF16.3PoptrARF16.4
PoptrARF16.51000
1000634
860
995
ARF17PoptrARF17.1PoptrARF17.2
10001000
474
Novel Gene Function: Novel Gene Function: ARF & Aux/IAA genesARF & Aux/IAA genes
Arabidopsis-specific
Populus-specific
Arabidopsis – 23 genesPopulus – 40 genes
Activator domain13:5 Populus: Arabidopsis
Kalluri et al., 2006
Advancing Science with DNA Sequence
Novel Gene Function: Novel Gene Function: The Aux/IAA7 subgroupThe Aux/IAA7 subgroup
PoptrIAA7.1 and PoptrIAA7.2 closely group with AtIAA7 and AtIAA14.
IAA7.1
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 Sequence
IAA16.3IAA16.3
ControlControl 90-day-old Populus cuttings
stem cross sectional area (cm2)
transgenic
control
7.14.4
Novel Gene Function: Novel Gene Function: The Aux/IAA16 subgroupThe 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 CandidatesFungal 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 & ConclusionsSummary & 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
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