Indiana Dunes National Lakeshore

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From Molecular Systems to EcoSystems Biology
From Molecular Systems to EcoSystems Biology
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//borevitzlab.uchicago.edu/
Indiana Dunes National Lakeshore
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Talk Outline
Talk Outline
SNP/Tiling microarrays SFP/Methylation Transcripti
on variation Whole Genome Association Genetic
Diversity biodiverisity Population structure,
migration, admixture 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/Methylation Transcripti
on variation Whole Genome Association Genetic
Diversity biodiverisity Population structure,
migration, admixture 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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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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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?
BAC array
cDNA array
Long oligo array
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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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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
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Methylation polymorphisms are extensive
a Features of constitutive CG methylation bc
Features of Col- or Van-specific methylation df
cDNAs or promoters with feature(s) of enzyme
effect (p lt 0.1) or genotype enzyme
interaction (p lt 0.05) eg cDNAs or promoters
containing CCGG feature(s) h Intergenic
features (excluding cDNAs or promoters) of enzyme
effect (p lt 0.1) or genotype enzyme interaction
(p lt 0.05) i Intergenic (excluding cDNAs or
promoters) CCGG-containing features
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Additive, dominant and maternal effects of gene
expression
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Gene expression variation between genotypes
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An example of HMM detected segments
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Whole Genome Association MappingFlowering Time
Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
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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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Global and Local Population Structure
Olivier Loudet
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Local adaptation under strong selection
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Seasonal Variation
Matt Horton
Megan Dunning
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Local Population Structure
common haplotypes
142 Non singleton SNPs gt6400 accessions
Yan Li, et al
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Diversity within and between populations
80 Major Haplotypes
Google Earth Fly By
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Diversity within and between populations
17 Major Haplotypes
80 Major Haplotypes
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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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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
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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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Genetics of Speciationalong a Hybrid Zone
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Aquilegia (Columbine) NSF Genome Complexity

• Microarray floral development
• QTL candidates
• Physical Map (BAC tiling path)
• Physical assignment of ESTs
• QTL for pollinator preference
• 400 RILs, map abiotic stress
• QTL fine mapping/ LD mapping
• Develop transformation techniques
• VIGS
• Whole Genome Sequencing (JGI 2007)

Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus
Nordborg (USC) Justin Borevitz (U Chicago) Jeff
Tompkins (Clemson)
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Nielsen and Hole, 1963
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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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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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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