Biomimicry

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Genetics of AdaptationFrom Model Organism to
Model Ecosystems
Genetics of AdaptationFrom Model Organism to
Model Ecosystems
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//borevitzlab.uchicago.edu/
Indiana Dunes National Lakeshore
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Genetics of Adaptation

• Transgenetics 1
• Mutants 10
• Families 100
• Ancestral Populations 1000
• Compatible Species 10000
• Communities 100000
• Ecosystems 1000000000
• Biosphere 1000000000000

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Talk Outline
Talk Outline
SNP/Tiling microarrays SFP/SNP Genetic Diversity
biodiverisity Population structure, migration,
admixture Whole Genome Association Phenotyping in
Natural environments Seasonal Variation in the
Lab Next Species Aquilegia, Switchgrass Ecological
plant communities Indiana Dunes, Tall Grass
Prairies
SNP/Tiling microarrays SFP/SNP Genetic Diversity
biodiverisity Population structure, migration,
admixture Whole Genome Association Phenotyping in
Natural environments Seasonal Variation in the
Lab Next Species Aquilegia, Switchgrass Ecological
plant communities Indiana Dunes, Tall Grass
Prairies
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Universal Whole Genome Array
DNA
RNA
Gene/Exon Discovery Gene model correction Non-codi
ng/ micro-RNA
Chromatin Immunoprecipitation ChIP chip
Alternative Splicing
Methylation
Antisense transcription
Polymorphism SFPs Discovery/Genotyping
Transcriptome Atlas Expression levels Tissues
specificity
Comparative Genome Hybridization
(CGH) Insertion/Deletions Copy Number
Polymorphisms
RNA Immunoprecipitation RIP chip
Allele Specific Expression
Control for hybridization/genetic
polymorphisms to understand TRUE expression
variation
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Which arrays should be used?
Gene array
Exon array
Tiling array
35bp tile, 25mers 10bp gaps
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Which arrays should be used?
SNP array
How about multiple species? Microbial
communities?
Pst,Psm,Psy,Psx, Agro, Xanthomonas, H parasitica,
15 virus,
Ressequencing array
Tiling/SNP array 2007 250k SNPs, 1.6M
tiling probes
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Genomic profile of cellular systems responding to
the environment
ORFa
Transcriptome Atlas
ORFb
start
AAAAA
deletion
M
M
M
M
M
M
SFP
M
M
M
M
M
M
SNP
SNP
SFP
SFP
conservation
Chromosome (bp)
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Potential Deletions
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SFPs and CCGG Methylome
Genomic DNA
Col
HpaII digestion
Random labeling
Col
Genomic DNA
MspI digestion
Random labeling
Genomic DNA
Van
HpaII digestion
Random labeling
Van
Genomic DNA
MspI digestion
Random labeling
Full model Intensity genotype enzyme
genotype x enzyme
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SFP detection on tiling arrays
Xu Zhang
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Additive, dominant and maternal effects on
annotated gene expression
Xu Zhang
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de novo transcriptome variation
Xu Zhang
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Genetic Structure

• Family Structure
• 100-1000 SNPs
• Deep racial historical population structure
• 10,000 SNPs
• Genetic Association
• causative gene
• 100k, 1M SNPs

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Local adaptation under strong selection
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Seasonal Variation
Matt Horton
Megan Dunning
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Variation within a field http//naturalvariation.o
rg/hapmap
Variation within a field http//naturalvariation.o
rg/hapmap
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Diversitywithin andbetween populations
80 Major Haplotypes
Google Earth Fly By
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Distribution of the common haplotype in USA
43/6368 of the sites in USA has this most
common haplotypeAmong big sites(nlinesgt10)
36/4286
Common haplotype sharing across sites in USA
Yan Li
of colors 629
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Distribution of haplotype clone size
87 of haplotypes occur in just a single
population (1km level) lt1 haplotypes are
invasive present in gt10 populations
5 haplotypes present in 19 or more populations.
They are each globally distributed
Yan Li
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Genetic Variation within aMidwest Field (PNA)

• Haplotype frequency differs across collection
  dates

Yan Li
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Geoff Morris
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Selecting mapping population
All data 5309 lines at 142 SNPs
1841 lines at 142 SNPs after removing clones
384 diverse lines (1 line from each of the 384
group)
Redundancy randomly chosen 25 lines from the
1680 unique lines (data1_5) will have 282
alleles141 SNPs x 2
Final 360 lines in seasonal flowering time
Yan Li
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Begin with regions spanning the Native Geographic
range
Lund Sweden
Nordborg et al PLoS Biology 2005 Li et al PLoS
ONE 2007
Tossa Del Mar Spain
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Sweden Spain
Seasons in the Growth Chamber
Seasons in the Growth Chamber

• Changing Day length
• Cycle Light Intensity
• Cycle Light Colors
• Cycle Temperature

• Changing Day length
• Cycle Light Intensity
• Cycle Light Colors
• Cycle Temperature

Geneva Scientific/ Percival
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Solar Calc II
Kurt Spokas Version 2.0a June 2006
USDA-ARS Website Midwest Area (Morris,MN) http//
www.ars.usda.gov/mwa/ncscrl
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Seasonal Flowering Time Response
Seasonal Flowering Time Response
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Kas/Col floweringtime QTL
FLM
FRI
Yan Li
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Whole Genome Association MappingFlowering Time
Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
Magnus Nordborg
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Disease Resistance (HR) LD mapping
Data from Aranzana, PLoS 2006 Brian Traw, Katrin
Jakob
RPS5
RPT2
250k SNP array, Yan Li, Susi
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Comparing Association Mapping with BSA Mapping
0.4
1
Chromosome
Zhao et al., 2006
Ivan Baxter
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Next Species.
Next Species.
Eco region diversity plant community population
genomics. Genetic variation within and between
species and locations Remnant, restored,
reconstructed, prairies savannahs Comparative
population structure, in species assemblages
Differential effects on annuals, perennials,
selfers, outcrossers Categorize existing genetic
diversity- Conservation Genetics Restore with
maximal regional diversity samples to allow
natural selection breeding.
Eco region diversity plant community population
genomics. Genetic variation within and between
species and locations Remnant, restored,
reconstructed, prairies savannahs Comparative
population structure, in species assemblages
Differential effects on annuals, perennials,
selfers, outcrossers Categorize existing genetic
diversity- Conservation Genetics Restore with
maximal regional diversity samples to allow
natural selection breeding.
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Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
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Aquilegia and pollinators
Humming Bird Hawkmouth
Bumble Bee
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Christos Noutsos
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Genetics of Speciationalong a Hybrid Zone
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Indiana Dunes Collection site
Christos Noutsos
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Short, mixed, and Tall grass Prairie
Tall Grass Prairies. 99.9 plowed under 464
species declined long term survival is in
danger 328 (71) are endemic
http//climate.konza.ksu.edu/
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www.uni.edu/ceee/foodproject/mud.jpg
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People Cause 10X More Soil Erosion Than All
Natural Processes Combined...
Human activity causes 10 times more erosion of
continental surfaces than all natural processes
combined, an analysis by a University of Michigan
geologist shows. "If you ask how fast erosion
takes place over geologic timesay over the last
500 million yearson average, you get about 60
feet every million years," Wilkinson said. In
those parts of the United States where soil is
being eroded by human agricultural activity,
however, the rate averages around 1,500 feet per
million years,
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Global Soil Degradation
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Environmental Shakeup

• Specialists can
• Migrate
• Adapt
• or Go Extinct
• Generalists
• are Advantaged
• Invasive species
• Bioclimatic mapping
• 32 of the European plant species in a given cell
  in 1990 would disappear by 2050
• Bakkenes et al. (2002)

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Lake Michigan sand dunes
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The Next Generation of Biofuels Greenhouse-Neutra
l Biofuels from High-Diversity Low-Input
Prairie Ecosystems by David Tilman University
of Minnesota
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Nielsen and Hole, 1963
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Total Carbon (LPJ)
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Carbon in Vegetation (LPJ)
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Carbon in Soil (LPJ)
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Real Time Ecosystem Monitoring

• HPWREN
• San Diego wireless ecological data sensing.

Fermilab AmeriFlux site, provided by Timothy J.
Martin (ANL-EVS)
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Remote Sensing (micro NEON)
Real time sensing 100s of cameras Temperature Humi
dity Light spectrum/intensity Wind speed
direction Air quality (CO2, NOX..) Water levels,
quality (salts etc) Soil temp, moisture
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Ecological Genomics

• 1) Target Foundation Prairie Species
• 454 expressed gene sequencing
• 250k sequences, 10,000s SNPs
• Macro and Micro evolutionary importance
• 2) Landscape Genetics
• Sample 1000s of genotypes across tallgrass region
• Identify population structure and diversity mix
• 3) Use Diversity Mix for Restoration
• Monitor local adaptation, genetic/community level

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http//borevitzlab.uchicago.edu
http//borevitzlab.uchicago.edu
Arabidopsis Yan Li Megan Dunning Joy
Bergelson Magnus Nordborg Paul Marjoram Aquilegia
Christos Noutsos Scott Hodges Tall Grass
Prairie Geoff Morris Mike Miller
Arabidopsis Yan Li Megan Dunning Joy
Bergelson Magnus Nordborg Paul Marjoram Aquilegia
Christos Noutsos Scott Hodges Tall Grass
Prairie Geoff Morris Mike Miller
Arrays Xu Zhang Shinhan Shiu Ivan Baxter
Arrays Xu Zhang Shinhan Shiu Ivan Baxter