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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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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Front End Cyber

• Sample tracking..
• Meta Data
• Field. GPS, Time/Date, Species
• Phenology/ Developmental Stage
• Environmental Data
• Light (quality/ quantity), temp, humidity
• Wind (speed/ direction), soil - temp moisture
• Data Archival

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Trait x Environmental Disection

• Yield. Growth, development, harvest index,
  partitioning
• Environmental partitioning -- microclimate
  mapping
• Genetic variation can specify trait/environment
  networks.

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Back End Cyber

• Quality control - filtering
• Real Time data visualization
• Google Earth layers, animation
• Subset summary data
• Statistical analysis
• Population and Quantitative genetic
• QTL / Association mapping
• Community structure
• Environmental Filtering / Overdispersion
• Longitudinal and clinal patterns

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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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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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\Kas/Col floweringtime QTL
Seasonal Flowering Time Response
Seasonal Flowering Time Response
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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..Ecosystem Genomics
Next Species..Ecosystem Genomics

• From the field to web page.. TOOLS
• Cataloging Natures Genetic Library
• Eco region diversity/ Plant community population
  genomics.
• Genetic variation within and between species and
  locations
• 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.

• From the field to web page.. TOOLS
• Cataloging Natures Genetic Library
• Eco region diversity/ Plant community population
  genomics.
• Genetic variation within and between species and
  locations
• 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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Lake Michigan sand dunes
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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
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Organisms

• Audience -- Plant biologists,
• Citizen scientists especially farmers
• Priority Database schema - ontology
• Start with species with the most data and large
  community
• Emerging species with new types of data
• Species
• Growth chamber species (Arab)
• Crop species (maize, rice)
• Natural area species
• wild flowers
• trees

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Traits

• Phenology
• Development - integration of quantitative and
  qualitative traits
• Read out of environmental cues
• Life history
• Floral traits
• morphological variation
• Mating system
• Yield/ Fitness
• Development plant architecture/ Plasticity
• Physiology
• Rapid responses to environment (stress),
  photosynthesis, ion leakage
• Omics

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Spatial Temporal Data

• Preserve raw individual point GPS data
• Key index for species identification
• Will be genotype referenced
• Population Definition
• Archival
• Herbarium voucher
• Scans or Photographs

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aBiotic Environmental Data

• Sampled at a hierarchical scale
• Plot, microclimate, regional
• Soils, nutrient profiles -gt soil types
• Water content, remote sensing
• Where the weather meets the climate
• Integrated real time weather stations
• Historical
• Model prediction
• iPlant will query across available data sets

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Biotic Environment

• Plant as host (Plant phenotype)
• Microbial community
• Above and below ground
• Pollination
• Herbivores
• Neighbor density
• shade
• Community composition
• Landscape disturbance Regimes
• Shape files layers as treatments
• Land use type, history (aerial photographs)
• Farmer records quality control

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Outreach

• Citizen scientists
• Farmers, naturalists, students, teachers
• Project budburst, International Science Fair
• Summary data online
• Public, land managers
• Diversity awareness