Document

Report
Toward the Ecological Genomics
Underlying Plant Adaptation
Justin Borevitz
Ecology & Evolution
University of Chicago
http://naturalvariation.org/
Birds/insects in a cotton wood
Fresh water and marine invasives
Deer mouse burrow
Aquilegia, Arabidopsis, Mimulus?
Indiana Dunes National Lakeshore
Talk Outline
•• Genetic
Genetic Diversity
Diversity ~~ biodiverisity
biodiverisity
–– Population
Population structure,
structure, migration,
migration, admixture
admixture
•• Phenotyping
Phenotyping in
in Natural
Natural environments
environments
–– Seasonal
Seasonal Variation
Variation in
in the
the Lab
Lab
• Next Species/ Ecological plant communities
–– Aquilegia
Aquilegia
•• SNP/Tiling
SNP/Tiling microarrays
microarrays
–– Methylation
Methylation
–– Deletions
Deletions
Global and Local Population Structure
Olivier Loudet
Local
adaptation
under
strong
selection
Seasonal Variation
Matt Horton
Megan Dunning
Local Population Structure
common haplotypes
149 Non singleton SNPs >6000 accessions
Megan Dunning, Yan Li
Global, Midwest, and UK
Diversity within and
between populations
80 Major Haplotypes
Google Earth
Fly By
Diversity within and between populations
17 Major Haplotypes
80 Major Haplotypes
Variation within a field http://naturalvariation.org/hapmap
Migration of Clonal Lines
Cluster 20 Cluster 26
PopName: CS
NumLines: 14
LAK
13
Cluster 2
Cluster 10
LR
1
MAP
15
MDN
12
MNFPIN
19
MNFPOT MNFRIV MSGA
9
13
26
MUSKSP
14
PAW
26
Cluster2: 128 lines from diff pops; Cluster10: 16/17 lines are MNFPIN;
Cluster20: all 13 lines from MNFRIV; Cl`uster 26: all 18 lines from PENT
PENT
29
RIV YNG
33
2
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
Seasons in the Growth Chamber
•
•
•
•
Changing Day length
Cycle Light Intensity
Cycle Light Colors
Cycle Temperature
Day Length
Light Intensity
Temperature
1400
Sw eden
Spain
20:00
1200
30
Spain
standard
18:00
25
standard
standard
1000
16:00
600
8:00
Geneva
Scientific/
Percival
15
10
Spain High
5
400
6:00
Spain Low
0
200
0
Spain
standard
month
month
jun
may
apr
mar
feb
jan
dec
nov
oct
aug
jul
jun
may
apr
mar
jan
feb
dec
oct
nov
-10
sep
aug
jul
jun
may
apr
mar
jan
feb
dec
oct
nov
sep
Sweden
month
Sw eden Low
-5
2:00
0:00
Sw eden High
sep
4:00
aug
10:00
800
jul
W/m2
12:00
degrees C
20
14:00
hours
35
Sw eden
22:00
Kurt Spokas
Version 2.0a June 2006
USDA-ARS Website Midwest Area (Morris,MN)
http://www.ars.usda.gov/mwa/ncscrl
Seasonal Flowering Time Response
* Kas/Col RILs
* Van/Col RILs
384 diverse Accessions
* Spain/Sweden
* Spring (early late)
Fall (early late)
10
10 Days
Days 1000X
1000X
FLM
FRI
Kas/Col
flowering
time
QTL
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.
Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
Genetics of Speciation
along 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)
Transcriptome Atlas
The Genomic Response
Mediating the Environment
ORFa
ORFb
start
conservation
MMMM M M
AAAAA
SFP
SFP
SFP
SNP
Chromosome (bp)
deletion
MMMM M M
SNP
Which arrays should be used?
BAC array
cDNA array
Long oligo array
Which arrays should be used?
Gene array
Exon array
35bp tile, 25mers 10bp gaps
Tiling array
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
Universal Whole Genome Array
RNA
Gene/Exon Discovery
Gene model correction
Non-coding/ micro-RNA
DNA
Chromatin
Immunoprecipitation
ChIP chip
Alternative Splicing
Methylation
Antisense transcription
Transcriptome Atlas
Expression levels
Tissues specificity
RNA Immunoprecipitation
RIP chip
Allele Specific Expression
Polymorphism SFPs
Discovery/Genotyping
Comparative Genome
Hybridization (CGH)
Insertion/Deletions
Copy Number Polymorphisms
Control for hybridization/genetic polymorphisms
to understand TRUE expression variation
Potential Deletions
Hpa msp
*
*
*
*
Genomic DNA
Van
HpaII digestion
Van
Col
Col
Col
Hpa msp
Random labeling
Col
*
*
*
mSFP
*
Genomic DNA
MspI digestion
Hpa msp
SFP *
Random labeling
*
*
Van
Van
Col
Col
Van
Genomic DNA
HpaII digestion
Hpa msp
Van
SFP *
Random labeling
*
*
Genomic DNA
MspI digestion
Hpa msp
Van
Van
Col
Random labeling
Col
Intensity
SFPs and CC*GG Methylome
Full model:
Hpa msp Intensity ~ genotype + enzyme + genotype x enzyme
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
0.95
3298
92027
3.4%
Methylation polymorphisms are extensive
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
a
Features of constitutive CG methylation
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
bc Features
Natural Copy Variation on Tiling Arrays
Segregating self seed from wild ME isolate (Early – Late)
Potential Deletions Suggest Candidate Genes
FLM natural deletion
FLOWERING1 QTL
Chr1 (bp)
MAF1
Flowering Time QTL caused by a natural deletion in FLM
(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
Chip genotyping of a Recombinant Inbred Line
Van x Col RIL 23
logLK
50
AA
7472
AB
14
BB
4787
NaturalVariation.org
USC
Magnus Nordborg
Paul Marjoram
Max Planck
Detlef Weigel
Scripps
Sam Hazen
University of Michigan
Sebastian Zoellner
University
University of
of Chicago
Chicago
Xu Zhang
Yan Li
Peter Roycewicz
Evadne Smith
Megan Dunning
Joy Bergelson
Michigan
Michigan State
State
Shinhan Shiu
Purdue
Ivan Baxter
http://www.plosone.org/

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