Supplemental Figure Legends: Supplemental Figure S1 ...genesdev.cshlp.org/content/suppl/2014/07/11/gad... · Supplemental Figure Legends: Supplemental Figure S1 Vernalization response

Supplemental Figure Legends:

Supplemental Figure S1 Vernalization response of 47 representative A. thaliana

accessions. (A) Vernalization response of the 47 A. thaliana accessions. The

flowering time value 150 for Lov-1 and Lov-5 indicates the plants had not flowered

when the experiment was finished. Error bars represent standard deviation of 8

individual plants. (B) FLC expression in response to 4 weeks vernalization treatment,

along with non-vernalized plants. Error bars represent standard errors of 3 biological

replicates. (C) Comparison of vernalization response of A. thaliana accessions

carrying different FLC haplotypes. (D) A significant correlation is found between

flowering time and FLC expression in accessions given 4 weeks vernalization. R2

shows the explained amount of variation. The corresponding P-value is <0.001.

Supplemental Figure S2 FLC haplotype analysis and vernalization response of

114 Swedish A. thaliana accessions and association between FLC alleles with

vernalization response. (A) Haplotype analysis of FLC alleles of 114 Swedish

Arabidopsis accessions using FLUXUS network analysis with Median Joining (MJ)

setting. Circle size illustrates the frequency of the corresponding FLC type. Number

along branch shows number of nucleotide differences. Numbers in brackets indicated

the corresponding haplotype numbers. (B) FLC expression (relative to UBC) of

haplotypes containing FLC alleles with a slow (SV, black symbols) and rapid (RV,

white symbols) vernalization response in the Swedish sample. Shown are the means

(±SEM, n=2 to 43) of plants that were given 4 weeks cold followed by 10 days (T10)

or 30 days warm (T30). Significant differences in vernalization response exist

between haplotypes in T10 and T30 (Kruskal-Wallis test: H≥18.42, d.f.=5, p≤0.002 in

all tests). (C) Association of FLC alleles with vernalization response in the F2

population Rev-1 × Kulturen-1 (RV1 × SV2) with 4 weeks vernalization (ANOVA,

R2=0.341, F2,231=61.23, P<0.001). (D) Association of FLC alleles with vernalization

response in the F2 population Rev-1 × Kulturen-1 (RV1 × SV2) with 12 weeks

vernalization (ANOVA, R2=0.078, F2,283=12.98, P<0.001). Crosses indicate statistical

outliers that fall more than 3 Standard Errors away from the mean.

Supplemental Figure S3 R2 region in FLC is associated with FLC silencing

(T30/(T30+T10)). (A) Presentation of natural recombination event R2 in FLC

genomic region. The sequence similarity of three contigs at the FLC region visualized

using the colours of a RBG colour triangle. In areas where two contigs have the same

colour (yellow, purple or turquoise) the accessions share the same polymorphism.

Primary colours (blue, red and green) indicate regions where the accession is

genetically unique. The black square shows the R2 region where recombination was

identified by analysis with the RDP3 software. In the R2 region, the accession Br-0

(Fig. 1A) and Edi-0 (belonging to the RV1 group) share the same polymorphism as is

indicated by the yellow shading. Note however that Br-0 is only distantly related to

the genuine donor (which was not in our dataset). The Br-0 accession shares many

sites in common with Var2-6 (belonging to the SV4 haplotype) between 2400 and

5200 bp. The graphs were made in the R package HybRIDS

(http://www.norwichresearchpark.com/HybRIDS). (B) The polymorphism in R2

region is associated with FLC silencing. The structure of the FLC gene and R2 region

are indicated above the graph. The nucleotide position is relative to the FLC

transcription start site (TSS). The dots indicate the FLC polymorphism of A. thaliana

accessions.

Supplemental Figure S4 Seed yield analysis in F2 populations. (A) QTL analysis

of seed yield in F2 populations between Rev-1 (RV1)× Kulturen-1 (SV2). (B) Seed

weight per seed shows no difference in plants with different FLC alleles in the F2

population of Kulturen-1 × Rev-1 (SV2 × RV1). Error bars represent standard error of

30 individual plants. (C) Rapid vernalization response associates with high seed yield

in the F2 population of a Rev-1 × Kulturen-1 cross. FLC alleles are indicated as × in

black (Rev-1), red (Kulturen-1) and green (heterozygous). (D) QTL analysis of seed

yield in F2 populations (Hod × Kavlinge-1). In (A and D), the FLC region is indicated

with grey vertical lines. The horizontal dashed lines indicate threshold lines.

Bol

ting

time

(Day

s)Li_Supplemental Fig. S1

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40

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RV1 RV2 SV1 SV2 SV3 SV4

FLC Haplotypes: SV2RV1 SV3SV1 SV4RV2

40

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FLC expression 30 days after 4 weeks V (To UBC)

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FLC expression at day 10 (T10)

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1 2 3 4 50 6 7

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12 weeks V

Rev-1 Kulturen-1 HetsFLC alleles:

Bol

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Li_Supplemental Fig. S2

(3)

(13)

(9) (1)

(5)

(11)

RV1RV2

SV1

SV2

SV4SV3

T30/(T30+T10)

270 2200 3800 5700 7000

4

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Nucleotide to FLC TSS (bp)

R2FLC

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Base position relative to FLC transcription start site (TSS)

(bp)

R2 “donor”

R2 insert

-1500 0 1500 3000 4500 6000

RV1Edi-0

SV4Var2-6

Br-0

Sequence similarity between Sequence for triplet Br-0:Edi-0:Var2-6

B

A

Li_Supplemental Fig. S3

Kulturen-1 x Rev-1 (SV2 x RV1)

1 2 3 4 5Chromosomes

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Hod x Kavlinge-1 (RV1 x SV2)

Chromosomes

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Bolting time (days)

XX Kulturen-1X Hets

20 40 60 80 100

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FLC alleles:Rev-1

B C

Li_Supplemental Fig. S4

D

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