Transcript Sakigake Akage Bouzu Kuroge Hokkaiwase Minakuchiine Koumochi Riku132 Kyowa Shiokari Kuiku No.12 Kotikaze Nipponbare Nourin No.9 Nourin No.19 Hokkai No.112 Joiku No.349 Matsumae Joiku No.272 Kitahikari Yukihikari Nihonmasari Sasahonami Dohoku No.14 Douhoku No.5 Tannemochi Kuiku No.100 Joiku No.323 NM391 Eikei73301 Ishikari Eikei 84271 Kukei 56241 Hokuiku No.74 Hayamasari Tomohikari Kuiku No.118 Aya Kitaibuki Kuiku No.151 Oborozuki Daichinohoshi Hoshimaru Yumepirika Joiku No.428 Hoshitaro Fukkurinko Nanatsuboshi Kuiku No.159 Hoshinoyume Hokkai No.287 Yukimaru Kuiku No.135 Hayakaze Dohoku.

Sakigake
Akage
Bouzu
Kuroge
Hokkaiwase
Minakuchiine
Koumochi
Riku132
Kyowa
Shiokari
Kuiku No.12
Kotikaze
Nipponbare
Nourin No.9
Nourin No.19
Hokkai No.112
Joiku No.349
Matsumae
Joiku No.272
Kitahikari
Yukihikari
Nihonmasari
Sasahonami
Dohoku No.14
Douhoku No.5
Tannemochi
Kuiku No.100
Joiku No.323
NM391
Eikei73301
Ishikari
Eikei 84271
Kukei 56241
Hokuiku No.74
Hayamasari
Tomohikari
Kuiku No.118
Aya
Kitaibuki
Kuiku No.151
Oborozuki
Daichinohoshi
Hoshimaru
Yumepirika
Joiku No.428
Hoshitaro
Fukkurinko
Nanatsuboshi
Kuiku No.159
Hoshinoyume
Hokkai No.287
Yukimaru
Kuiku No.135
Hayakaze
Dohoku No.48
Kukei 90242B
Kukei 90242A
Hitomebore
Akiho
Kuiku No.131
Akitakomachi
Kirara397
Jouiku No.394
Kuiku No.133
Honoka224
Kitaake
Hakutyoumochi
Eikei7361
MIchikogane
Onnemochi
Kitakogane
Tomoyutaka
Fukuyuki
Kuiku No.99
Hayakogane
Joiku No.230
Cody
Sorachi
Koshihomare
Shimahikari
Kukei 61060
Kuiku No.133
Mimasari
Kuiku No.109
Nourin No.34
Toyohikarii
Fujisaka No.5
Waseaikoku
Riku132
Nourin No.15
Yoneshiro
Hokkai No.183
Fukoku
Kanto No.53
Yukara
Eiko
Okuteeiko
Wasefukoku
Tsurukame
Hokuto
Shinsetsu
Joiku No.142
Hayayuki
Hokkai No.190
Kamedawase
Ishikarishirage
Shinei
Nanei
Tomoemasari
Megurosakaemochi
Ounotyuto
Sekiyama
Tomoenishiki
Hokkai No.84
Hokkai No.87
Nourin No.20
Nourin No.11
Kokuhourozu
Supplemental Figure 1The pedigree of 63 rice cultivars from Hokkaido.
The color indicate the different groupings into which cultivars were categorized: red for Group I, orange for
Group II, purple for Group IIIa, yellow for Group IIIb, green for Group IV, blue for Group V, and black for Aya and
Nipponbare. The gray colors indicate the exotic cultivars which are the parents of key cultivars.
Wasechinko
Ginbouzu
Futahushi
Hashiribouzu
Bouzu No.6
Nakateaikoku
Kinaiwase No.22
Nouin No.1
Iburiwase
Wasebouzu
Tohoku No.14
-8000.0
λnPr(k)
-7000.0
-6000.0
-5000.0
-4000.0
-3000.0
K2
K3
K4
K5
K6
K7
K8
K9 K10
K2
K3
K4
K5 K6 K7 K8
K9 K10
Supplemental figure 2 The line graph shows the λn(k) values obtained using STRUCTURE program
from K=2 to K=10. No decrease in λn(k) implies that positive structures existed in the rice
population.
Supplemental table 1 Summary of used SSR marker in this study
All
No. of
Marker
Chromosome
IRGSP1.0
alleles
PIC
RM1282
1
549,641
3
0.526
RM1320
1
2,177,733
6
0.57
RM1195
1
6,154,019
4
0.509
RM1032
1
9,318,464
4
0.642
RM6740
1
17,281,795
7
0.644
RM3241
1
27,073,689
7
0.755
RM1297
1
28,613,212
3
0.536
RM5501
1
34,548,947
4
0.626
RM6407
1
42,377,077
2
0.455
Group I
No. of
alleles
3
3
4
3
3
4
3
2
2
PIC
0.595
0.512
0.678
0.512
0.562
0.694
0.595
0.165
0.463
Group II
No. of
alleles
3
1
3
2
2
1
1
2
2
PIC
0.406
0
0.594
0.469
0.469
0
0
0.375
0.5
Group IIIa
No. of
alleles
2
4
3
4
4
6
2
3
2
PIC
0.497
0.675
0.272
0.604
0.556
0.757
0.497
0.462
0.473
Group IIIb
No. of
alleles
2
2
2
2
2
2
2
3
1
PIC
0.278
0.278
0.278
0.278
0.278
0.278
0.5
0.5
0
Group IV
No. of
alleles
2
3
3
2
3
3
3
2
1
PIC
0.463
0.645
0.579
0.298
0.661
0.562
0.43
0.165
0
Group V
No. of
alleles
1
1
2
1
2
2
2
2
2
PIC
0
0
0.142
0
0.142
0.426
0.497
0.142
0.497
RM6911
RM1358
RM6374
RM1379
RM3874
RM1920
RM1385
RM3774
2
2
2
2
2
2
2
2
9,009,029
10,185,526
15,187,984
20,056,672
23,842,982
25,467,312
26,646,465
34,444,317
6
8
4
8
7
6
9
3
0.771
0.767
0.584
0.803
0.674
0.655
0.59
0.293
6
7
3
5
4
5
7
2
0.81
0.826
0.43
0.694
0.545
0.562
0.793
0.165
4
3
1
2
2
3
3
1
0.656
0.594
0
0.5
0.469
0.594
0.531
0
5
3
2
5
3
2
4
2
0.769
0.592
0.142
0.651
0.521
0.473
0.485
0.142
3
4
2
3
2
3
3
2
0.611
0.722
0.444
0.5
0.444
0.611
0.5
0.444
3
2
2
3
2
3
2
2
0.43
0.496
0.165
0.579
0.165
0.645
0.463
0.397
1
2
1
3
5
3
3
2
0
0.142
0
0.272
0.698
0.556
0.272
0.355
RM4108
RM3372
RM3802
RM3807
RM5442
RM3766
RM3461
RM1334
RM5626
RM3601
RM1038
3
3
3
3
3
3
3
3
3
3
3
536,517
1,457,491
1,959,825
3,531,267
5,529,248
6,934,586
8,350,099
17,422,644
24,866,271
25,959,692
33,660,363
9
4
5
4
4
4
3
3
2
3
7
0.686
0.564
0.544
0.601
0.566
0.706
0.485
0.386
0.061
0.334
0.64
7
3
4
4
3
2
2
3
2
2
4
0.843
0.595
0.694
0.694
0.314
0.463
0.165
0.512
0.298
0.165
0.645
3
3
5
3
3
3
1
1
1
1
3
0.406
0.406
0.688
0.594
0.625
0.531
0
0
0
0
0.594
2
1
1
3
1
2
2
2
1
1
3
0.142
0
0
0.604
0
0.26
0.142
0.142
0
0
0.615
2
1
1
2
2
2
1
1
1
2
1
0.278
0
0
0.444
0.444
0.444
0
0
0
0.278
0
2
2
4
2
2
3
2
2
1
2
3
0.298
0.165
0.694
0.165
0.496
0.562
0.496
0.463
0
0.496
0.314
3
3
1
2
3
3
3
2
1
2
2
0.651
0.568
0
0.26
0.639
0.568
0.556
0.355
0
0.473
0.142
RM7200
RM3524
RM1018
RM3648
4
4
4
4
4,042,524
22,893,791
26,967,205
33,306,479
5
7
2
3
0.608
0.74
0.49
0.647
2
4
1
3
0.298
0.645
0
0.562
3
2
2
2
0.406
0.219
0.469
0.375
2
3
2
3
0.355
0.473
0.473
0.592
3
2
2
3
0.611
0.278
0.5
0.611
2
4
2
2
0.397
0.694
0.165
0.463
2
3
2
2
0.26
0.521
0.142
0.426
RM1248
RM1127
RM1386
RM1271
5
5
5
5
93,969
16,015,462
20,057,139
22,478,305
3
2
7
5
0.648
0.328
0.517
0.688
2
2
6
2
0.496
0.165
0.661
0.397
2
1
2
2
0.5
0
0.375
0.219
3
1
3
3
0.272
0
0.379
0.592
2
2
3
2
0.444
0.278
0.611
0.278
3
2
1
1
0.628
0.165
0
0
2
2
2
3
0.142
0.426
0.426
0.544
RM1369
RM5754
RM1169
6
6
6
1,563,617
5,234,113
7,661,599
6
5
2
0.66
0.644
0.455
3
3
1
0.314
0.645
0
3
2
1
0.594
0.469
0
2
2
2
0.142
0.26
0.142
2
4
1
0.444
0.722
0
4
3
2
0.727
0.661
0.463
2
2
1
0.142
0.142
0
RM5752
RM1243
RM1253
RM1048
RM1306
7
7
7
7
7
2,567,818
3,555,641
6,968,820
20,165,312
28,947,956
4
9
3
3
9
0.573
0.722
0.562
0.524
0.643
2
5
2
3
5
0.298
0.645
0.496
0.628
0.694
2
4
2
1
3
0.469
0.719
0.5
0
0.594
2
4
3
2
5
0.26
0.556
0.604
0.355
0.722
2
2
2
2
1
0.278
0.5
0.444
0.444
0
2
3
2
2
3
0.298
0.512
0.165
0.165
0.562
3
3
2
1
1
0.379
0.379
0.26
0
0
RM3181
RM3481
RM5485
8
8
8
7,553,778
9,136,135
24,072,904
2
3
6
0.225
0.503
0.765
2
3
3
0.165
0.512
0.645
1
1
2
0
0
0.375
1
2
3
0
0.26
0.462
2
2
3
0.278
0.5
0.611
1
2
4
0
0.397
0.562
2
2
4
0.5
0.142
0.391
RM3609
RM5526
RM1328
RM1553
9
9
9
9
1,157,791
7,314,035
9,206,385
21,003,925
5
2
3
4
0.591
0.146
0.485
0.683
3
1
1
2
0.314
0
0
0.165
2
1
1
3
0.219
0
0
0.625
3
1
3
4
0.379
0
0.473
0.627
1
2
2
1
0
0.444
0.278
0
3
2
2
3
0.512
0.165
0.397
0.512
3
1
2
4
0.615
0
0.142
0.627
RM3283
RM6704
RM1374
10
10
10
12,383,411
18,005,491
21,644,592
2
3
9
0.408
0.656
0.703
2
1
4
0.463
0
0.645
2
2
3
0.375
0.469
0.594
2
3
4
0.355
0.592
0.627
1
2
1
0
0.444
0
2
2
3
0.298
0.496
0.314
2
2
3
0.426
0.444
0.521
RM1124
RM3137
RM6091
RM1355
RM5354
RM7654
11
11
11
11
11
11
3,855,192
6,188,794
13,869,005
19,816,431
21,796,072
27,666,335
3
3
2
2
2
5
0.43
0.451
0.49
0.27
0.09
0.617
3
1
2
1
1
3
0.43
0
0.165
0
0
0.314
2
3
1
1
1
2
0.469
0.594
0
0
0
0.469
2
2
2
1
1
2
0.26
0.497
0.473
0
0
0.497
1
3
2
2
1
2
0
0.5
0.278
0.44
0
0.444
2
2
2
2
1
2
0.397
0.298
0.298
0.46
0
0.397
2
2
2
2
2
3
0.355
0.497
0.142
0.26
0.35
0.462
RM7619
RM1036
RM1264
12
12
12
4,829,808
8,797,117
26,173,358
Average
4
5
2
4.46
0.459
0.742
0.472
0.56
2
3
2
2.98
0.165
0.314
0.397
0.42
1
2
2
2.06
0
0.5
0.5
0.33
1
2
2
2.51
0
0.473
0.142
0.36
3
3
2
2.02
0.611
0.611
0.444
0.34
2
2
2
2.3
0.496
0.397
0.298
0.38
3
2
2
2.19
0.556
0.355
0.26
0.31
Supplemental table 2 Seven traits of 62 rice cultivars from Hokkaido
Group
Cultivar
HD
CTB (%)
TGW (g)
NP
NS
AC (%)
I
Akage
88
19.5
18.3
28
70.3
22
Bouzu
89
14.9
19.4
14.7
60.8
21
Hashiribouzu
80
11.9
17.9
21.7
65.5
21.2
Nourin No.9
68
7.5
20.9
25
54.5
22
Wasebouzu
64
47.8
20.1
18.3
64
23.1
Nourin No.11
63
10.2
19.5
16.7
78.1
22.4
Nourin No.19
72
44.2
19
21.7
79.7
22.5
Minakuchiine
96
40.9
18.6
16.3
110.7
21.3
Iburiwase
84
4.5
23
16
126.5
20.9
Hokkaiwase
80
40.9
22
15.3
95.1
18.7
Kuroge
84
15.4
22.6
13.3
67.3
22.1
Min
63
4.5
17.9
14.7
54.5
18.7
Max
96
47.8
23
28
126.5
23.1
Meas±SD
78.9±10.8
23.4±16.4
20.1±1.8
18.8±4.7
79.3±22.5
21.5±1.2
II
Bouzu No.6
83
10.8
20
21
104.5
22.8
Nourin No.20
78
3.4
20.2
24.3
78.1
21
Hayayuki
67
61
21.2
19.7
61.6
22.2
Tomoenishiki
94
7.3
18.6
31
64.6
18.5
Tomoemasari
96
26.8
19.2
29.7
68.9
20.6
Nanei
95
27.2
22.1
24
61.2
21.5
Shinei
92
28.3
20.1
23.3
79.7
21.4
Toyohikari
91
1.9
19.9
25
72.9
22.1
Min
67
1.9
18.6
19.7
61.2
18.5
Max
96
61
22.1
31
104.5
22.8
Meas±SD
87.0±10.2
20.8±19.6
20.1±1.1
24.7±3.8
73.9±14.2
21.3±1.3
IIIa Fukoku
89
18.2
23.6
20
58.8
20.9
Wasefukoku
86
7.8
21.7
23.3
84.6
20.9
Eiko
92
18.6
19.7
23.3
79.6
20.3
Kyowa
77
41.1
18
26
83.6
19.6
Hokuto
89
5.2
19.2
21.7
85.4
21.7
Shiokari
92
15
18.7
30.3
75.7
21.4
Hayakogane
73
61.2
19.9
27.1
70
20.6
Mimasari
89
47.4
22
33.3
60.9
22.7
Sorachi
91
47.8
20.5
31
62.5
21.2
Ounotyuto
97
27.4
19.2
23
85
21.3
Ishikarishirage
86
16.5
21.1
22.7
87.6
21.1
Nourin No.34
85
11
23.1
26.7
61.6
22.8
Shinsetu
94
38.6
20.1
25
59.8
21.1
Min
73
5.2
18
20
58.8
19.6
Max
97
61.2
23.6
33.3
87.6
22.7
Meas±SD
87.6±6.6
27.3±17.9
20.5±1.7
25.6±3.9
73.4±11.4
21.2±0.9
IIIb Yukara
94
18
20.3
30
63.7
22.9
Kitahikari
91
36.9
21.4
25.7
65.2
21.8
Matsumae
93
29
21.6
29
68.9
22.5
Shimahikari
84
24.3
19.7
26
68.8
20.6
Kitakogane
79
22.6
21.6
31.7
61.7
23.1
Hakuchoumochi
86
51.5
19.5
28
69
(1.3)*
Min
79
18
19.5
26
61.7
20.6
Max
94
51.5
21.6
31.7
69
23.1
Meas±SD
87.8±8.3
30.4±12.2
20.7±1.0
28.4±2.3
66.2±3.1
22.2±1.0
IV Nourin No.15
65
5.5
20.4
23.7
64.4
21.2
Fukuyuki
80
32.5
19.1
30
78.2
21
Sasahonami
78
41.5
19.4
22.7
78.1
21.3
Hokkai No.112
80
3.5
19.2
29.7
77.2
21.2
Ishikari
78
52
22.5
23.7
64.4
23.9
Tomoyutaka
80
55.5
21.4
34
55.7
23
Hayamasari
67
54.4
20.2
26
52.3
20.9
Michikogane
89
31.7
20.7
22.7
80.4
19.8
Tomohikari
84
17.7
19.9
26.3
74.1
21.2
Yukihikari
88
44.9
20.1
23.3
69.2
20.3
Honoka224
93
15.7
21.5
21.3
65.5
17.4
Min
65
3.5
19.1
21.3
52.3
17.4
Max
93
55.5
22.5
30
80.4
23.9
Meas±SD
80.1±8.5
32.2.±19.2
20.4±1.0
25.7±3.9
69.0±9.4
21.0±1.7
V
Kitakae
81
65.1
22.2
34
53
21
Hayakaze
69
57.3
20.3
35.7
47.1
20.5
Kitaibuki
79
19.9
20.1
27.7
49.9
19.3
Kirara397
85
41.2
21.9
27.3
56.8
19.8
Hokkai No.287
83
29.4
20.8
30.3
55.2
14.9
Akiho
77
65.5
21.6
28.7
54.7
20.2
Oborozuki
86
66.4
21.3
27.3
65.3
14.3
Yumepirika
80
45.8
20.9
32.3
51.6
16.2
Nanatuboshi
84
56.7
21.2
23.7
57.5
18.9
Hoshinoyume
81
74.5
21.3
26.7
51.3
18.9
Fukkurinko
87
73.1
22
25.3
54.9
18.9
Daichinohoshi
79
67.4
23.7
26
50.2
18.4
Hoshimaru
75
49.3
23.8
34.7
43.5
19.1
Min
69
19.9
20.3
23.7
43.5
14.3
Max
87
74.5
23.8
35.7
65.3
21
Meas±SD
80.5±4.9
54.7±16.8
21.6±1.1
29.2±3.8
53.2±5.4
18.5±2.0
all
Min
63
1.9
17.9
14.7
43.5
14.3
Max
97
74.5
23.8
35.7
126.5
23.1
Meas±SD
83.2±8.6
32.7±20.6
20.6±1.4
25.3±5.1
68.8±15.3
20.4±3.1
HD; Heading date, CTB; Cold Tolerance at Booting stage, TGW; 1,000 grain weight, NP; Number of Panicles per a plant, NS; Number of Seed per a panicle
AC; Amylose Contents, GA; Grain Appearance
*Hakuchoumochi is Data was execpt in calctusis of average of AC and GA
GA (%)
0.6
6
13
4.6
2.2
3.4
3.6
0
1.2
7.2
31.4
0
31.4
6.7±9.0
6.2
40.6
10.8
19
52.4
33.4
27.6
39
6.2
52.4
28.6±15.8
4.8
22.8
56.2
34
7.4
30.8
69.4
30
43
26.6
37.4
48
35.2
4.8
69.4
34.2±17.7
66.2
71
77.4
58.6
59.8
(-)*
58.6
77.4
66.6±7.8
8.8
36.2
35.8
37
60
63.8
68.8
53.4
58
61
80.4
8.8
80.4
51.2±20.0
58.8
50
66.6
65.4
68.4
71.8
66
57.8
64.8
70.6
61.8
66.2
64.2
57.8
68.4
64.0±5.8
0
80.4
40.5±24.9
11
10
12
6
10
13
I
II
IIIa
IIIb
IV
V
80.5±4.9
80.1±8.5
87.8±8.3
87.6±6.6
87.0±10.2
78.9±10.8
HD
a
a
a
a
a
a
54.7±16.8
32.2.±19.2
30.4±12.2
27.3±17.9
20.8±19.6
23.4±16.4
CTB (%)
b
a
ab
a
a
a
*
a(ab)
b(b)
18.5±2.0(19.5±0.8)
a(a)
a(a)
a(a)
a(a)
21.0±1.7
22.2±1.0
21.2±0.9
21.3±1.3
21.5±1.2
AC (%)a
TGW
21.6±1.1
20.4±1.0
20.7±1.0
20.5±1.7
20.1±1.1
20.1±1.8
a
a
a
a
a
a
NP
29.2±3.8
25.7±3.9
28.4±2.3
25.6±3.9
24.7±3.8
18.8±4.7
a
a
a
a
a
b
NS
53.2±5.4
69.0±9.4
66.2±3.1
73.4±11.4
73.9±14.2
79.3±22.5
b
a
ab
a
a
a
*Different letters in parentheses indicate significant difference at 5% using Tukey-Kraker HSD test between groupV except for three cultivars possesing Wx1-1 and other groups
a The mean value of AC of groupV except for three cultivars possesing Wx1-1 is shown in parentheses.
Different letters indicate significant difference at 5% using Tukey-Kraker HSD test
cultivar
Group
No. of
Supplemental Table 3 Average of HD, CTB, AC, TGW, NP, NS and GA
GA
64.0±5.8
51.2±20.0
66.6±7.8
34.2±17.7
28.6±15.8
6.7±9.0
a
c
bc
c
b
b