Ecological GenomicsUnderlying Plant Evolution

Deer mouse burrow

Birds/insects in a cotton wood

Fresh water and marine invasives

Aquilegia, Arabidopsis, Mimulus? Indiana Dunes National Lakeshore

Justin BorevitzEcology & EvolutionUniversity of Chicagohttp://naturalvariation.org/

Ecological GenomicsUnderlying Plant Evolution

Talk OutlineTalk Outline

• Genetic Diversity ~ biodiverisity– Population structure, migration, admixture

• Phenotyping in Natural environments– Seasonal Variation in the Lab

• Next Species, Aquilegia

• SNP/Tiling microarrays– Methylation

– Deletions

• Ecological Conservation Genomics

• Genetic Diversity ~ biodiverisity– Population structure, migration, admixture

• Phenotyping in Natural environments– Seasonal Variation in the Lab

• Next Species, Aquilegia

• SNP/Tiling microarrays– Methylation

– Deletions

• Ecological Conservation Genomics

Global and Local Population Structure

Olivier Loudet

Local adaptation

under strong

selection

Seasonal Variation

Matt Horton

Megan Dunning

149 Non singleton SNPs >6000 accessions

Global, Midwest, and UK

common haplotypes

Local Population Structure

Megan Dunning, Yan Li

80 Major Haplotypes

Diversity within and between populations

Google EarthFly By

17 Major Haplotypes

80 Major Haplotypes

Diversity within and between populations

Variation within a field http://naturalvariation.org/hapmapVariation within a field http://naturalvariation.org/hapmap

Begin with regions spanning the Native Geographic range

Nordborg et al PLoS Biology 2005Li et al PLoS ONE 2007

Tossa Del MarSpain

LundSweden

Seasons in the Growth Chamber

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

Sweden Spain

Seasons in the Growth Chamber

• Changing Day length

• Cycle Light Intensity

• Cycle Light Colors

• Cycle Temperature

GenevaScientific/ Percival

Day Length

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sep

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apr

may jun jul

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month

hour

s

Sweden

Spain

standard

standard

Light Intensity

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standard

Temperature

-10

-5

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Spain Low

Sweden High

Sweden Low

standard

Kurt Spokas

Version 2.0a June 2006

USDA-ARS Website Midwest Area (Morris,MN)http://www.ars.usda.gov/mwa/ncscrl

Seasonal Flowering Time ResponseSeasonal Flowering Time Response

Kas/Col RILsVan/Col RILs384 diverse Accessions

Spain/Sweden Spring (early late) Fall (early late)

Kas/Col RILsVan/Col RILs384 diverse Accessions

Spain/Sweden Spring (early late) Fall (early late)

**

**

**

**

10 Days 1000X10 Days 1000X

Aquilegia (Columbines)

Recent adaptive radiation, 350Mb genome

Genetics of Speciationalong a Hybrid Zone

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)

SNP SFP MMMMM MSFP

SFP

MMMMM M

Chromosome (bp)

con

serv

atio

n

SNP

ORFa

start AAAAA

Tra

nsc

ripto

me

Atla

s

ORFb

deletion

The Genomic ResponseMediating the Environment

Which arrays should be used?

cDNA array

Long oligo array

BAC array

Which arrays should be used?

Gene array

Exon array

Tiling array35bp tile, 25mers 10bp gaps

Which arrays should be used?

Tiling/SNP array 2007 250k SNPs, 1.6M tiling probes

SNP array

Ressequencing array

How about multiple species? Microbial communities?

Pst,Psm,Psy,Psx, Agro, Xanthomonas, H parasitica, 15 virus,

RNA DNA

Universal Whole Genome Array

Transcriptome AtlasExpression levelsTissues specificity

Transcriptome AtlasExpression levelsTissues specificity

Gene/Exon DiscoveryGene model correctionNon-coding/ micro-RNA

Gene/Exon DiscoveryGene model correctionNon-coding/ micro-RNA

Alternative SplicingAlternative Splicing

Comparative GenomeHybridization (CGH)

Insertion/DeletionsCopy Number Polymorphisms

Comparative GenomeHybridization (CGH)

Insertion/DeletionsCopy Number Polymorphisms

MethylationMethylation

ChromatinImmunoprecipitation

ChIP chip

ChromatinImmunoprecipitation

ChIP chip

Polymorphism SFPsDiscovery/Genotyping

Polymorphism SFPsDiscovery/Genotyping

Control for hybridization/genetic polymorphismsto understand TRUE expression variation

RNA ImmunoprecipitationRIP chip

RNA ImmunoprecipitationRIP chip

Antisense transcription

Allele Specific Expression

Potential Deletions

Delta p0 FALSE Called FDR

1.00 0.95 18865 160145 11.2%

1.25 0.95 10477 132390 7.5%

1.50 0.95 6545 115042 5.4%

1.75 0.95 4484 102385 4.2%

2.00 0.95 3298 92027 3.4%

SFP detection on tiling arrays

SFPs and CC*GG Methylome

HpaII digestion

Random labeling

Random labeling

MspI digestion

Col

Col

Genomic DNA

Genomic DNA

HpaII digestion

Random labeling

Random labeling

MspI digestion

Van

Van

Genomic DNA

Genomic DNASFP

Hpa msp

Inte

nsit

y

Col

Col

Hpa msp

Van

Van

*

SFP*

*

*

Hpa msp

Col

Col

Hpa msp

Van

Van

mSFP

*

*

* *

* *

* *Hpa msp

Col

Col

Hpa msp

Van

Van

* *

Full model: Intensity ~ genotype + enzyme + genotype x enzyme

Enzyme Genotype x enzyme

p-value HpaII > MspIa p-value Col-specificb Van-specificc

<0.01 2373 <0.01 1062 407

<0.05 4522 <0.03 2389 944

<0.1 6324 <0.05 3700 1515

Gened 3628 (20%) Gened 3498 (20%)

Total genee 17760 Total genee 17760

Promoterf 305 (6%) Promoterf 455 (9%)

Total promoterg 5041 Total promoterg 5041

Intergenich 1298 (16%) Intergenich 782 (9%)

Total intergenici 8264 Total intergenici 8264

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 < 0.1) or genotype × enzyme

interaction (p < 0.05) eg cDNAs or promoters containing CCGG feature(s)h Intergenic features (excluding cDNAs or promoters) of enzyme effect (p < 0.1) or

genotype × enzyme interaction (p < 0.05)i Intergenic (excluding cDNAs or promoters) CCGG-containing features

Verification of methylation polymorphisms

Verification of methylation polymorphisms

ColColColVanVanVan

Col♂ x Van♀Col♂ x Van ♀

Van♂ x Col♀Van ♂ x Col ♀Van♂ x Col ♀

CC*GG

chromomethylase 2 (CMT2) exon19

0

1

2

3

4

5

6

hpaII mspI

log

inte

nsity

col van col♂xvan♀ van♂xcol♀

epiTyper

Genic distribution of constitutive and polymorphic methylation sites

bp

Co-methylation of pericentromere regions

Natural Copy Variation on Tiling Arrays

Segregating self seed from wild ME isolate (Early – Late)

Potential Deletions Suggest Candidate Genes

FLOWERING1 QTL

Chr1 (bp)

Flowering Time QTL caused by a natural deletion in FLM

FLM

FLM natural deletion

(Werner et al PNAS 2005)

Chip genotyping of a Recombinant Inbred Line

Van x Col RIL 23

 logLK

20

AA 20198

AB 587

BB 13064

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 GeneticsRestore 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 GeneticsRestore with maximal regional diversity samples to allow natural selection breeding.

Next Species….

Root system of the prairie grassesRoot system of the prairie grasses

Picture Courtesy of Chicago Wilderness

Nielsen and Hole, 1963

Are Biofuels the Answer?...

The Next Generation of Biofuels:The Next Generation of Biofuels:Greenhouse-Neutral Biofuels from Greenhouse-Neutral Biofuels from

High-Diversity Low-Input High-Diversity Low-Input Prairie EcosystemsPrairie Ecosystems

bybyDavid TilmanDavid Tilman

University of MinnesotaUniversity of Minnesota

http://www.plosone.org/

NaturalVariation.orgNaturalVariation.orgUSC

Magnus NordborgPaul Marjoram

Max Planck

Detlef Weigel

Scripps

Sam Hazen

University of Michigan

Sebastian Zoellner

USC

Magnus NordborgPaul Marjoram

Max Planck

Detlef Weigel

Scripps

Sam Hazen

University of Michigan

Sebastian Zoellner

University of Chicago

Xu ZhangYan Li

Peter RoycewiczEvadne Smith

Megan DunningJoy Bergelson

Michigan State

Shinhan Shiu

PurdueIvan Baxter

University of Chicago

Xu ZhangYan Li

Peter RoycewiczEvadne Smith

Megan DunningJoy Bergelson

Michigan State

Shinhan Shiu

PurdueIvan Baxter