advancing science with dna sequence genomics and bioenergy gerald a. tuskan doe joint genome...

Advancing Science with DNA Sequence

Genomics and BioenergyGenomics and Bioenergy

Gerald A. TuskanDOE Joint Genome InstituteFAO SeminarOctober 12, 2007


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


U.S. Energy Production & U.S. Energy Production & ConsumptionConsumption

Source: http://www.eia.doe.gov/Energy Flow 2005

(104 Quadrillion Btu)


U.S. Energy Consumption by U.S. Energy Consumption by Source and SectorSource and Sector

Source: http://www.eia.doe.gov/


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



Increases in Atmospheric COIncreases in Atmospheric CO22

Source: http://cdiac.ornl.gov/ftp/trends/co2/maunaloa.co2


World COWorld CO22 Emissions Emissions



Renewable Energy in the U.S.Renewable Energy in the U.S.



Long-term Supply OptionsLong-term Supply Options

Source: Steven Koonin, 2006, BP


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

??


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


Brachypodium

Dedicated Energy Crops – Dedicated Energy Crops –

The MonocotsThe Monocots

Foxtail Millet

Maize

Potential Energy Crop

Model GenomeSwitchgrassMiscanthus

Informative GenomeMonocots

Sorghum

Oryza


Model GenomeSwitchgrassMiscanthus


Model GenomeWheat


Musa


Dedicated Energy Crops – Dedicated Energy Crops – The DicotsThe Dicots

Glycine

Eucalyptus

Populus

Populus

Arabidopsis


Model GenomeOil production

Informative GenomeLegumesPrunus

Glycine


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


Accelerated DomesticationAccelerated Domestication

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


Corn DomesticationCorn Domestication

• Teosinte

Timeline:

5000 ybp

• Corn Landraces

2000 ybp

• Modern Hybrids

Today


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)


Timeline:

30 M - 200 ybp 120 ybp

Wild Stands

Today

PopulusPopulus Domestication Domestication

Clonal Selection

Improved Hybrids

Domesticated Trees

The Future?


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


• 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


0.1

ARF5PoptrARF5.1PoptrARF5.2

10001000

ARF6PoptrARF6.2

PoptrARF6.1748

747

PoptrARF6.4PoptrARF6.5

1000

743


166

ARF8PoptrARF8.1

PoptrARF8.21000

1000

393

ARF19ARF7


1000983

1000


1000

1000

342

393

ARF3PoptrARF3.1

PoptrARF3.21000


634645

ARF4PoptrARF4

1000

636

ARF13ARF23

ARF14ARF12ARF22

516

ARF15ARF20

ARF21975

696994

9981000

1000


10001000

ARF9PoptrARF9.1

PoptrARF9.21000


1000785

451

ARF11ARF18

1000

886

422


10001000


1000

985

PoptrARF26PoptrARF25

1000

435

280

1000

572


1000874

ARF16PoptrARF16.1

PoptrARF16.21000


PoptrARF16.51000

1000634

860

995


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


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.


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.


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.


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 genomics and bioenergy gerald a. tuskan doe joint genome...

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