Toward the Ecological Genomics Underlying Plant Adaptation

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Toward the Ecological GenomicsUnderlying Plant
Adaptation
Toward the Ecological GenomicsUnderlying Plant
Adaptation
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//naturalvariation.org/
Indiana Dunes National Lakeshore
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Talk Outline
Talk Outline

• Genetic Diversity biodiverisity
• Population structure, migration, admixture
• Phenotyping in Natural environments
• Seasonal Variation in the Lab
• Next Species/ Ecological plant communities
• Aquilegia
• SNP/Tiling microarrays
• Methylation
• Deletions

• Genetic Diversity biodiverisity
• Population structure, migration, admixture
• Phenotyping in Natural environments
• Seasonal Variation in the Lab
• Next Species/ Ecological plant communities
• Aquilegia
• SNP/Tiling microarrays
• Methylation
• Deletions

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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
149 Non singleton SNPs gt6000 accessions Global,
Midwest, and UK
Megan Dunning, Yan Li
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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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Migration of Clonal Lines
Cluster 2
Cluster 26
Cluster 10
Cluster 20
PopName CS LAK LR MAP MDN MNFPIN
MNFPOT MNFRIV MSGA MUSKSP PAW
PENT RIV YNG NumLines 14 13 1
15 12 19
9 13 26 14
26 29 33 2
Cluster2 128 lines from diff pops Cluster10
16/17 lines are MNFPIN Cluster20 all 13 lines
from MNFRIV Cluster 26 all 18 lines from PENT
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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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The Genomic Response Mediating 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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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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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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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
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 0.9
5 3298 92027 3.4
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Methylation polymorphisms are extensive
Enzyme Genotype x enzyme Genotype x enzyme
p-value HpaII gt MspIa p-value Col-specificb Van-specificc
lt0.01 2373 lt0.01 1062 407
lt0.05 4522 lt0.03 2389 944
lt0.1 6324 lt0.05 3700 1515
Gened 3628 (20) Gened 3498 (20) 3498 (20)
Total genee 17760 Total genee 17760 17760
Promoterf 305 (6) Promoterf 455 (9) 455 (9)
Total promoterg 5041 Total promoterg 5041 5041
Intergenich 1298 (16) Intergenich 782 (9) 782 (9)
Total intergenici 8264 Total intergenici 8264 8264
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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Natural Copy Variation on Tiling Arrays
Segregating self seed from wild ME isolate (Early
Late)
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Potential Deletions Suggest Candidate Genes
FLOWERING1 QTL
Chr1 (bp)
MAF1
Flowering Time QTL caused by a natural deletion
in FLM
(Werner et al PNAS 2005)
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Chip genotyping of a Recombinant Inbred Line
Van x Col RIL 23
  logLK20
AA 20198
AB 587
BB 13064
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Chip genotyping of a Recombinant Inbred Line
Van x Col RIL 23
  logLK50
AA 7472
AB 14
BB 4787
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NaturalVariation.org
NaturalVariation.org
USC Magnus Nordborg Paul Marjoram Max
Planck Detlef Weigel Scripps Sam
Hazen University of Michigan Sebastian Zoellner
USC Magnus Nordborg Paul Marjoram Max
Planck Detlef Weigel Scripps Sam
Hazen University of Michigan Sebastian Zoellner
University of Chicago Xu Zhang Yan Li Peter
Roycewicz Evadne Smith Megan Dunning Joy
Bergelson Michigan State Shinhan
Shiu Purdue Ivan Baxter
University of Chicago Xu Zhang Yan Li Peter
Roycewicz Evadne Smith Megan Dunning Joy
Bergelson Michigan State Shinhan
Shiu Purdue Ivan Baxter
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http//www.plosone.org/