Genetics of Adaptation: Arabidopsis thaliana as an ecological model

Justin BorevitzEcology & EvolutionUniversity of Chicagonaturalvariation.org

Light Affects the Entire Plant Life Cycle

de-etiolation

hypocotyl

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Light Affects the Entire Plant Life Cycle

Light response variation can be seen under constant conditions in the labNatural Variation != Natural Selection

Widely Distributed

http://www.inra.fr/qtlat/NaturalVar/NewCollection.htm

Olivier Loudet

Quantitative Trait Loci

6+ years ago

Local Population Variation

Local adaptation

under strong

selection

Seasonal Variation

Matt Horton

Megan Dunning

ME

26

ME

27

KN

15

PN

A 3

3P

NA

37

RM

X 5

5P

2 4

4R

MX

58

RM

X 5

7R

MX

56

P2

51

P2

50

P2

49

P2

47

P2

46

P2

45

ME

30

ME

29

KN

18

KN

17

KN

16

DM

2 9

DM

2 8

DM

2 7

DM

2 4

DM

2 1

DM

2 2

ME

24

ME

28

KN

20

KN

13

KN

14

KN

11

KN

19

ME

31

ME

32

RM

X 5

9R

MX

61

ME

25

ME

23

PN

A 4

0P

2 4

3K

N 1

2D

M2

3D

M2

5M

E 2

1P

NA

42

PN

A 3

9P

NA

38

PN

A 3

5P

NA

36

RM

X 5

3P

NA

41

RM

X 5

4 P2

48

DM

2 6

DM

2 1

0P

NA

34

ME

22

RM

X 6

2R

MX

52

RM

X 6

0

02

46

8

hclust (*, "complete")

He

igh

t

48 Non singleton SNPs of 87 tested Megan Dunning, poster #268

Local Population Structure in the Midwest

2-3

a_

A0

7P

f-0

_E

06

Jet-

0_

H0

1R

RS

-7_

E1

0G

OT

-7_

C0

9L

er_

D0

9B

ay-

0_

D0

1C

al-

0_

G0

9B

ur-

0_

C0

7B

ur-

0_

E0

3K

en

d-L

_H

07

RR

S-1

0_

E1

2E

n-1

_E

04

EC

48

_4

2_

H1

2E

C4

8_

29

_H

11

EC

48

_2

4_

H0

9E

C4

8_

26

_H

10

NIL

_H

04

Co

l-0

_H

06

Co

l-0

_D

12

Co

l-0

_E

11

Cvi

-0_

E0

9E

sc-0

_H

08

Sa

e-0

_G

11

Ll-

2_

E0

5T

s-1

_D

04

Bla

-1_

B0

7S

e-0

_B

11

SF

1_

G1

0 Hh

-0_

B0

8E

st-1

_D

03

Est

-1_

H0

5L

er-

1_

C1

0U

k-3

_H

03

4-1

a_

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1G

o-2

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02

Ei-

6_

D1

1T

su-1

_D

05

Bo

r-4

_C

12

Dra

-1_

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ij-3

_G

08

Ba

s-1

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11

Sij-

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ha

kda

ra1

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03

Sh

akd

ara

2_

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5K

ly-3

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08

Ko

z-1

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02

Kly

-1_

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7K

oz-

3_

F0

3R

ak-

1_

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9N

ov_

3_

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7R

ak-

3_

F1

0B

as-

3_

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2S

ER

_G

01

No

z_F

08

Ch

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03

Ma

s_G

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Ch

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02

Le

b-3

_F

05

Pa

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4B

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_G

06

Le

b-1

_F

04

No

v_1

_F

06

2-2

a_

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66

-7a

_B

04

Wc-

1_

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18

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06

2-1

a_

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r-0

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06

Mir

-0_

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2L

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5_

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1H

au

-0_

G1

2M

rk-0

_B

10

An

g-1

_D

08

Nfa

-8_

D0

27

-1a

_B

05

1-3

a_

A0

41

-1a

_A

02

1-2

a_

A0

3F

ei-

0_

C1

1U

k-1

_H

02

5-3

a_

B0

25

-3a

_C

04

5-4

a_

B0

35

-2a

_B

01

5-1

a_

A1

23

-3a

_A

10

3-1

a_

A0

83

-2a

_A

09

Nc-

1_

C0

1V

an

-0_

D0

6

02

46

81

01

21

4

hclust (*, "complete")

He

igh

t

120 SNPs of 149 tested including inbred lines Norman Warthmann`

Global Population Structure

Collections

• > 500 lines N and S Sweden (Nordborg)

• > 400 Lines France and Midwest (Bergelson)

• 800 Lines Midwest (Diane Byers IL state)

• 400 lines Midwest (Borevitz)

• 857 Accessions stock center (Randy Scholl)

• Others welcome…– Will be genotyped with Sequenom 149 SNPs

$0.03 per SNP, 40plex > 400SNPs available

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

Geneva Scientific/ Percival

Day Length

0:00

2:00

4:00

6:00

8:00

10:00

12:00

14:00

16:00

18:00

20:00

22:00

sep

oct

nov

dec

jan

feb

mar

apr

may jun jul

aug

month

hour

s

Sweden

Spain

standard

standard

Light Intensity

0

200

400

600

800

1000

1200

1400se

p

oct

nov

dec

jan

feb

mar

apr

may jun jul

aug

month

W/m

2

Sweden

Spain

standard

Temperature

-10

-5

0

5

10

15

20

25

30

35

sep

oct

nov

dec

jan

feb

mar

apr

may jun jul

aug

month

degr

ees

C

Spain High

Spain Low

Sweden High

Sweden Low

standard

Developmental Plasticity == BehaviorDevelopmental Plasticity == Behavior

Kurt Spokas

Version 2.0a June 2006

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

I II III IV V

NGA590.0446063542.4T1G116.5NGA639.74460731513.6

4460647619.8MSAT1.123.52160761529.0AthZFPG30.3NGA24833.6

4460796351.7T27K12-SP655.32160754056.12160706561.74460715265.02160705767.9NGA280 2160692871.62160746374.2

2160770083.4

MSAT1.1389.6

NGA69296.82160703099.344606525101.7

1

MSAT2.50.0

NGA11457.9446063229.9CIW213.0

44606142 2160703820.5MSAT2.3823.2

CIW330.42160725931.8THY-136.8PHYB42.74460772748.34460791450.7PLS753.2NGA112660.5MSAT2.4162.34460782468.32160715771.9NGA36175.2MSAT2.775.8NGA16878.34460681080.94460792285.94460676988.94460653391.2

90J19T799.1

2

NGA320.0216074791.9446066078.1446072839.8ATCHIB211.62160717514.14460708719.2Z3081723.0

4460672145.5GL149.52160749654.3

T0410967.2

4460638779.5

2160768385.0

4460633094.6R3002597.4NGA6 44606273101.7

3

MSAT4.390.0

CIW56.0446080288.44460662312.0

NGA821.74460795528.82160760633.7MSAT4.2536.8MSAT4.1545.12160751348.44460754549.8CD3-6952.2MSAT4.1854.32160739456.32160718459.24460628963.8MSAT4.967.5nga113968.14460668870.2MSAT4.3374.0NGA110777.9MSAT4.3779.4

4

446070460.0

446072347.7NGA22511.6NGA24921.02160740222.94460615925.34460724227.84460616729.6MSAT5.1432.24460669633.5NGA13935.82160714839.74460766844.8MSAT5.2249.94460633852.6MI13755.94460645267.4CIW968.8MSAT5.969.54460634670.74460776773.04460780877.3NGA12980.8MSAT5.1287.34460799593.54460650994.64460741399.7LFY3102.4M555111.0

5Genetic map of the Kas-1 x Col-gl1 RIL population

55 markers from Wolyn et al. (2004) & 64 additional SNP markers.

Sweden 1

Col-gl1

Kas1

Sweden 2

Col-gl1

Kas1

Spain 1

Col-gl1

Kas1

Spain 2

Col-gl1

Kas1

Distribution of flowering time among 96 Kas-1/Col-gl1 RILs

Num

ber

of R

ILs

Num

ber

of R

ILs

Kas/Col flowering time QTL

Yan Li, poster #362

Chr4 FRI

Marker Chr. Location cM* Gene Environment Gene x Environment

t-value p-value

t-value

p-value

t-value

p-value

21607030 chr1.27650179

99.3 2.68 <0.01 -0.73 0.54 1.30 0.19

21607175 chr3.5140894

14.1 3.19 <0.01 0.85 0.49 -1.16 0.25

GL1 chr3.10361870

49.5 -4.94 <0.01 1.12 0.38 -1.89 0.06

MSAT4.39 chr4.89659 0 -15.94 <0.01 3.66 0.07 -5.82 <0.01

44607955 chr4.5591486

28.8 -7.98 <0.01 1.38 0.30 -2.25 0.02

44607234 chr5.1507224

7.7 -4.11 <0.01 2.03 0.18 -3.66 <0.01

Kas/Col flowering time QTL GxE

Chr4 FRI

768 VanC AIL-RILs149 + 87 SNPsStock Center Release(Evadne Smith)

768 VanC AIL-RILs149 + 87 SNPsStock Center Release(Evadne Smith)

Van no mitochondrial insertion

FLC

Total Leaf Number

• Webcam

• http://growth1-cam.bsd.uchicago.edu

• Record growth

QTL geneConfirmation

MarkerIdentificationGenotyping

Genomics path

Experimental DesignMapping population PhenotypingQTL AnalysisFine Mapping

Candidate genePolymorphismsgene expressionloss of function

QTL gene

Confirmation

Experimental Design

Mapping population

Phenotyping

QTL Analysis

Fine Mapping

With the Aid of Genomics

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

Aquilegia (Columbines)

Recent adaptive radiation, 350Mb genome

> 20k dbEST 11/14/2003

Animal lineage: good coverage

Plant lineage: crop plant coverage

NaturalVariation.orgNaturalVariation.orgUSC

Magnus NordborgPaul Marjoram

Max Planck

Detlef Weigel

Scripps

Sam Hazen

University of Michigan

Sebastian Zollner

USC

Magnus NordborgPaul Marjoram

Max Planck

Detlef Weigel

Scripps

Sam Hazen

University of Michigan

Sebastian Zollner

University of Chicago

Xu ZhangYan Li

Peter RoycewiczEvadne Smith

Michigan State

Shinhan Shui

PurdueIvan Baxter

University of Chicago

Xu ZhangYan Li

Peter RoycewiczEvadne Smith

Michigan State

Shinhan Shui

PurdueIvan Baxter