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
0
40
80
120
160N
OK
-3H
OD
SF
-1S
AN
-2O
mo
2-3
RE
V-1
KZ
-1K
AS
-1K
ON
DA
RA
ED
I-0
KA
-0W
S-0
BR
-0
VIM
ME
RB
YL
Z-0
UO
D-7
LO
V-1
LO
V-5
HO
V4-
1V
AR
2-1
ULL
2-5
DR
A3
-1S
TU
1-1
LIS
-2B
a3-3
LIL
Lo-1
DR
AII
-1K
UL
TU
RE
N-1
Kav
ling
e-1
Ba
4-1
Bro
1-6
Or-
1S
pr1
-2
Var
2-6
FA
B-2
ED
EN
-1S
AN
NA
-2N
YL
-2B
OO
2-1
BIL
-5B
IL-7
OS
T-0
TA
MM
-27
FA
B-4
0
4
8
12
16 NVT10T30
FLC
exp
ress
ion
(To
UB
C)
FLC haplotypes:
NO
K-3
HO
DS
F-1
SA
N-2
Om
o2-
3R
EV
-1K
Z-1
KA
S-1
KO
ND
AR
AE
DI-0
KA
-0W
S-0
BR
-0
Col
sf2
VIM
ME
RB
YLZ
-0U
OD
-7
LOV
-1LO
V-5
HO
V4-
1A
G-0
VA
R2-
1U
LL2-
5D
RA
3-1
ST
U1-
1LI
S-2
Ba3
-3LI
LLo-
1D
RA
II-1
KU
LTU
RE
N-1
Kav
ling
e-1
PLA
-0
Ba
4-1
Bro
1-6
Or-
1S
pr1-
2
Var
2-6
FA
B-2
ED
EN
-1S
AN
NA
-2N
YL-
2B
OO
2-1
BIL
-5B
IL-7
OS
T-0
TA
MM
-27
FA
B-4
RV1 RV2 SV1 SV2 SV3 SV4
FLC Haplotypes: SV2RV1 SV3SV1 SV4RV2
40
80
120
160
Bol
ting
time
(day
s)
B
0
40
80
120
160
0 2 4 6 8 10
Bol
ting
time
afte
r 4 w
eeks
V
FLC expression 30 days after 4 weeks V (To UBC)
C
R2 = 0.5582
D
A
RV1
RV2
SV2SV1
SV3
SV4A
SVRV
24
11
136
4
9
13
FLC
exp
ress
ion
at d
ay 3
0 (T
30)
FLC expression at day 10 (T10)
8
4
2
10
6
1 2 3 4 50 6 7
SVRV
B
4 weeks V
12 weeks V
Rev-1 Kulturen-1 HetsFLC alleles:
Bol
ting
time
(day
s)
C
D
20
40
60
80
100
10
20
30
40
50
Rev-1 Kulturen-1 Hets
Bol
ting
time
(day
s)
Li_Supplemental Fig. S2
(3)
(13)
(9) (1)
(5)
(11)
RV1RV2
SV1
SV2
SV4SV3
T30/(T30+T10)
270 2200 3800 5700 7000
4
8
12
16
Nucleotide to FLC TSS (bp)
R2FLC
-1700
F C
oeffi
cien
t
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
05
10152025
LOD
A
Hod x Kavlinge-1 (RV1 x SV2)
Chromosomes
0
0.005
0.01
0.015
0.02
0.025
0.03
See
d w
eigh
t of o
ne s
eed
(mg)
Rev-1 Kulturen-1 Hets
FLC alleles:
See
d yi
eld
of o
ne p
lant
(g)
Bolting time (days)
XX Kulturen-1X Hets
20 40 60 80 100
0.2
0.4
0.6
0.5
0.3
0.1
0
FLC alleles:Rev-1
B C
Li_Supplemental Fig. S4
D
1 2 3 4 50
5
10
15
LOD