Transcript Document

Genetics and Genomics of Light Response
adaptation in Arabidopsis thaliana
Justin Borevitz
Ecology & Evolution
University of Chicago
http://naturalvariation.org/
Widely Distributed
Olivier Loudet
http://www.inra.fr/qtlat/NaturalVar/NewCollection.htm
Talk Outline
•• Light
Light Response
Response
•• Wild
Wild Collections
Collections
–– Local
Local Population
Population Sampling/
Sampling/ structure
structure
•• Seasonal
Seasonal Growth
Growth Chambers
Chambers
–– KasC/
KasC/ VanC
VanC RILs
RILs
•• Whole
Whole Genome
Genome SNP/Tiling
SNP/Tiling Arrays
Arrays
–– Single
Single Feature
Feature Polymorphisms
Polymorphisms (SFPs)
(SFPs)
–– Potential
Potential deletions/
deletions/ Copy
Copy Number
Number Variants
Variants
•• Aquilegia
Aquilegia
Light Affects the Entire Plant Life Cycle
de-etiolation
}
hypocotyl
Quantitative Trait Loci
Local Population Variation
Local
adaptation
under
strong
selection
Seasonal Variation
Matt Horton
Megan Dunning
Collections
• 807 Lines from 25 Midwest Populations
– (Diane Byers IL state) – growing!
• 1101 Lines from UK, 51 populations
– (Eric Holub Warwick, UK) – growing!
•
•
•
•
> 500 lines N and S Sweden (Nordborg)
> 400 Lines France and Midwest (Bergelson)
400 lines Midwest (Borevitz)
857 Accessions stock center (Randy Scholl)
– Others welcome…
Will be genotyped with Sequenom 149 SNPs $0.03 per
Variation within a field (web link)
Within and Between Variation
•
BAKKER, E. G., STAHL, E. A., TOOMAJIAN, C., NORDBORG, M., KREITMAN,
M. & BERGELSON, J.
Distribution of genetic variation within and among local populations of Arabidopsis
thaliana over its species range.
Molecular Ecology 15 (5), 1405-1418.
48 Non singleton SNPs of 87 tested
hclust (*, "complete")
P2 44
2
ME 24
ME 28
KN 15
KN 20
4
PNA 34
RMX 53
PNA 41
RMX 54
P2 48
ME 21
ME 31
ME 32
RMX 59
RMX 61
ME 25
ME 23
PNA 40
P2 43
KN 13
KN 14
KN 11
KN 19
RMX 55
ME 22
RMX 62
RMX 52
RMX 60
DM2 6
DM2 10
PNA 42
PNA 39
PNA 38
PNA 35
PNA 36
KN 12
DM2 3
DM2 5
RMX 58
RMX 57
RMX 56
P2 51
P2 50
P2 49
P2 47
P2 46
P2 45
ME 30
ME 29
KN 18
KN 17
KN 16
DM2 9
DM2 8
DM2 7
DM2 4
DM2 1
DM2 2
PNA 33
PNA 37
ME 26
ME 27
0
6
8
Local Population Structure
in the Midwest
Megan Dunning, poster #268
En-1_E04
KZ10_B09
Ler-1_C10
Uk-3_H03
4-1a_A11
Go-2_E02
Ei-6_D11
Tsu-1_D05
Bor-4_C12
Dra-1_D10
Cvi-0_E09
Esc-0_H08
Sae-0_G11
Ll-2_E05
Ts-1_D04
Bla-1_B07
Se-0_B11
SF1_G10
Hh-0_B08
NIL_H04
Kend-L_H07
RRS-10_E12
Bay-0_D01
Kly-3_E08
Koz-1_F02
Kly-1_E07
Koz-3_F03
Rak-1_F09
Nov_3_F07
Rak-3_F10
Bas-3_F12
SER_G01
Noz_F08
Cha-2_G03
Mas_G05
Cha-1_G02
Leb-3_F05
Pan_G04
Bij-1_G06
Leb-1_F04
Nov_1_F06
2-2a_A06
6-7a_B04
Wc-1_E01
8-1a_B06
2-1a_A05
Fe-1_C02
C24_D07
Br-0_C06
Mir-0_B12
Lov-5_F01
Hau-0_G12
Mrk-0_B10
Ang-1_D08
Nfa-8_D02
7-1a_B05
1-3a_A04
1-1a_A02
1-2a_A03
Fei-0_C11
Uk-1_H02
5-3a_B02
5-3a_C04
5-4a_B03
5-2a_B01
5-1a_A12
3-3a_A10
3-1a_A08
3-2a_A09
Nc-1_C01
Van-0_D06
Shakdara1_C03
Shakdara2_C05
Sij-3_G08
Bas-1_F11
Sij-1_G07
Est-1_D03
Est-1_H05
Col-0_H06
Col-0_D12
Col-0_E11
EC48_42_H12
EC48_29_H11
EC48_24_H09
EC48_26_H10
GOT-7_C09
Ler_D09
Cal-0_G09
Bur-0_C07
Bur-0_E03
2-3a_A07
Pf-0_E06
Jet-0_H01
RRS-7_E10
Global Population Structure
120 SNPs of 149 tested including
inbred lines
hclust (*, "complete")
Norman Warthmann`
Regional/Seasonal Variation
• What is Local Adaptation?
• Predictable Seasonal changes unique to
each location.
Tossa Del Mar
Spain
Lund
Sweden
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
15
10
Spain High
5
400
Spain Low
Geneva Scientific/ Percival
0
200
0
standard
month
Developmental
Developmental Plasticity
Plasticity ==
== Behavior
Behavior
month
jun
apr
may
mar
feb
Spain
jan
dec
oct
aug
jul
jun
may
apr
feb
mar
jan
Sweden
dec
nov
oct
-10
sep
jul
aug
jun
apr
may
mar
jan
dec
nov
oct
sep
feb
month
Sw eden Low
-5
2:00
0:00
Sw eden High
nov
4:00
sep
6:00
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
Genetic map of the Kas-1 x Col-gl1 RIL population
1
2
3
I
II
III
0.0
2.4
6.5
9.7
13.6
NGA59
44606354
T1G11
NGA63
44607315
19.8
23.5
29.0
30.3
33.6
44606476
MSAT1.1
21607615
AthZFPG
NGA248
51.7
55.3
56.1
61.7
65.0
67.9
71.6
74.2
44607963
T27K12-SP6
21607540
21607065
44607152
21607057
NGA280 21606928
21607463
83.4
21607700
89.6
MSAT1.13
96.8
99.3
101.7
NGA692
21607030
44606525
0.0
MSAT2.5
7.9
9.9
13.0
NGA1145
44606322
CIW2
20.5
23.2
44606142 21607038
MSAT2.38
30.4
31.8
36.8
42.7
48.3
50.7
53.2
60.5
62.3
68.3
71.9
75.2
75.8
78.3
80.9
85.9
88.9
91.2
CIW3
21607259
THY-1
PHYB
44607727
44607914
PLS7
NGA1126
MSAT2.41
44607824
21607157
NGA361
MSAT2.7
NGA168
44606810
44607922
44606769
44606533
99.1
90J19T7
0.0
1.9
8.1
9.8
11.6
14.1
19.2
23.0
NGA32
21607479
44606607
44607283
ATCHIB2
21607175
44607087
Z30817
45.5
49.5
54.3
44606721
GL1
21607496
67.2
T04109
79.5
44606387
85.0
21607683
94.6
97.4
101.7
44606330
R30025
NGA6 44606273
4
5
IV
V
0.0
MSAT4.39
6.0
8.4
12.0
CIW5
44608028
44606623
21.7
28.8
33.7
36.8
45.1
48.4
49.8
52.2
54.3
56.3
59.2
63.8
67.5
68.1
70.2
74.0
77.9
79.4
NGA8
44607955
21607606
MSAT4.25
MSAT4.15
21607513
44607545
CD3-69
MSAT4.18
21607394
21607184
44606289
MSAT4.9
nga1139
44606688
MSAT4.33
NGA1107
MSAT4.37
0.0
44607046
7.7
11.6
21.0
22.9
25.3
27.8
29.6
32.2
33.5
35.8
39.7
44.8
49.9
52.6
55.9
67.4
68.8
69.5
70.7
73.0
77.3
80.8
87.3
93.5
94.6
99.7
102.4
111.0
44607234
NGA225
NGA249
21607402
44606159
44607242
44606167
MSAT5.14
44606696
NGA139
21607148
44607668
MSAT5.22
44606338
MI137
44606452
CIW9
MSAT5.9
44606346
44607767
44607808
NGA129
MSAT5.12
44607995
44606509
44607413
LFY3
M555
55 markers from Wolyn et al. (2004) & 64 additional SNP markers.
Distribution of flowering time among
96 Kas-1/Col-gl1 RILs
Number of RILs
Col-gl1
Col-gl1
Kas1
Kas1
Col-gl1
Col-gl1
Spain 1
Number of RILs
Sweden 2
Sweden 1
Spain 2
Kas1
Kas1
Kas/Col flowering time QTL
FRI
Chr3
Chr4
Chr5
Kas/Col flowering time QTL GxE
Marker name
Chr. position
cM
*
21607030
21607175
GL1
MSAT4.39
44607955
44607234
21607030 x MSAT4.39†
EnviSweden‡
chr1.27650179
chr3.5140894
chr3.10361870
chr4.89659
chr4.5591486
chr5.1507224
chr1.27650179 x chr4.89659
-
99.3
14.1
49.5
0
28.8
7.7
-
2a
-3.1
-2.5
2.7
15.7
3.8
2.2
6.6
2.1
QTL
SE p-value
1.4 0.0353
1.3 0.0492
1.3 0.0435
2.0 0.0000
1.3 0.0047
1.4 0.1154
2.9 0.0226
2.3 0.4586
QTL x Environment
2a* SE p-value
0.0 2.0 0.9856
-0.7 1.8 0.6864
-0.7 1.9 0.7145
-6.3 2.8 0.0289
0.9 1.9 0.6497
-1.8 1.9 0.3535
-1.7 4.0 0.6684
-
Chr4 FRI
Chr1 FLM Chr4 FRI
Environment and Epistasis
A
B
C
768 VanC AIL-RILs
149 + 87 SNPs
Stock Center Release
(Evadne Smith)
FLC
Total
Number
Van no Leaf
mitochondrial
insertion
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
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?
Ressequencing array
Tiling/SNP array 2007
250k SNPs, 1.6M tiling probes
Transcriptome Atlas
Improved Genome Annotation
ORFa
ORFb
start
conservation
MMMM M M
AAAAA
SFP
SFP
SFP
SNP
Chromosome (bp)
deletion
MMMM M M
SNP
Potential Deletions
SFP
detection
Genotype
effect
on tiling
arrays
Delta
p0
FALSE
Intergenic
1.00
0.95
SFPs
60770
18865
1.25
0.95
1.50
total
0.95
685575 6545
1.75
0.95
4484
2.00
0.95
3298
%
8.86%
Called
Exon
160145
23519
10477
132390
115042
665524
FDR
intron
11.2%
17216
7.5%
5.4%
301648
102385
4.2%
92027
3.4%
3.53%
SFPs/gene
0
>=1
>=2
>=3
>=4
>=5
genes
16322
9146
4304
2495
1687
1121
5.71%
Chip genotyping of a Recombinant Inbred Line
29kb interval
Copy Number Variation (Potential Deletions)
>500 potential deletions
45 confirmed by Ler sequence
23 (of 114) transposons
Disease Resistance
(R) gene clusters
Single R gene deletions
Genes involved in
Secondary metabolism
Unknown genes
Fast Neutron deletions
FKF1 80kb deletion CHR1
Het
cry2 10kb deletion CHR1
Sam Hazen (Scripps)
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)
FLM
Flowering Time QTL caused by a natural deletion in FLM
(Werner et al PNAS 2005)
Experimental Design of Association Study
• Sample > 3000 wild strains, 149 SNPs
• Select 3*384 less structured reference fine
mapping set for SFP resequencing
• Scan Genome for variation/selection
• Measure phenotype in Seasonal Chambers
• Haplotype map/ LD recombination blocks
• Associate Quantitative phenotypes with
HapMap
Array Haplotyping
Chromosome1 ~500kb
Inbred lines
Low effective
recombination
due to partial
selfing
Extensive LD
blocks
Col Ler Cvi Kas Bay Shah Lz Nd
Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
Species with
> 20k ESTs
11/14/2003
Animal lineage:
good coverage
Plant lineage:
crop plant coverage
Genetics of Speciation
along a Hybrid Zone
NSF Genome Complexity
• Microarray 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?)
Scott Hodges (UCSB)
Elena Kramer (Harvard)
Magnus Nordborg (USC)
Justin Borevitz (U Chicago)
Jeff Tompkins (Clemson)
NaturalVariation.org
USC
Magnus Nordborg
Paul Marjoram
Max Planck
Detlef Weigel
University of Chicago
Chicago
Xu Zhang
Yan Li
Peter Roycewicz
Evadne Smith
Scripps
Sam Hazen
Michigan
Michigan State
Shinhan Shiu
University of Michigan
Sebastian Zoellner
Purdue
Ivan Baxter
http://www.plosone.org/
Aquilegia (Columbines)
Scott Hodges (UCSB)
Elena Kramer (Harvard)
Magnus Nordborg (USC)
Justin Borevitz (U Chicago)
Jeff Tompkins (Clemson)
•
•
•
•
300 F4 RILs growing (Evadne Smith)
TIGR gene index 85,000 ESTs >16,00 SNPs
Complete BAC physical map Clemson
Nimblegen arrays of 5 floral whorls
Whole Genome Shotgun Sequencing 2007 JGI