438 2011 633 MOESM1 ESM
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49 J 50 J 51 J 52 J 55 I 54 I 56 I 57 I 58 I 59 I 60 I 61 I 62 J 63 J 53 U M 33 A 34 A 35 A 36 A 39 A 38 A 40 A 41 J 42 A 43 J 44 J 45 J 46 J 47 J 48 J 37 A M 17 I 18 I 19 I 20 A 22 I 23 A 24 A 25 A 26 A 27 A 28 A 29 A 30 A 31 A 32 A 21 I M 1 J 2 A 3 I 4 A 5 I 6 I 7 I 8 I 9 I 10 I 11 I 12 I 13 I 14 I 15 I 16 I M Fig. S1 nDart distribution among cultivated rice varieties, a total of 63 accessions of the rice core collection. Genomic DNA was digested with DraI. After electrophoresis in 0.6% agarose gels, DNA was blotted on to a filter and hybridized with a probe comprised of the 309-bp EaeI fragment of nDart. M indicates size marker of HindIII-digested lamda DNA. Numbers indicate the lane numbers listed in Table S1. J (japonica), A (aus), and I (indica) indicate the
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Transcript of 438 2011 633 MOESM1 ESM
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Fig. S1 nDart distribution among cultivated rice varieties, a total of 63 accessions of the rice core collection. Genomic DNA was digested with DraI. After electrophoresis in 0.6% agarose gels, DNA was blotted on to a filter and hybridized with a probe comprised of the 309-bp EaeI fragment of nDart. M indicates size marker of HindIII-digested lamda DNA. Numbers indicate the lane numbers listed in Table S1. J (japonica), A (aus), and I (indica) indicate the subspecies classification of cultivated rice.
M 33343536 38371 2 3 4 5 6 7 8 9 10111213141516M 17181920 222324252627282930313221M
Fig. S2 nDart distribution among cultivated rice varieties, a total of 38 accessions of the Japanese rice core collection. Genomic DNA was digested with DraI. After electrophoresis in 0.6% agarose gels, DNA was blotted on to a filter and hybridized with a probe comprised of the 309-bp EaeI fragment of nDart. M indicates size marker of HindIII-digested lamda DNA. Numbers indicate the lane numbers listed in Table S2.
Table S1 Distribution of nDart at 14 loci among cultivated riceLocus
Lanea Code No. Variety Typeb Originb SubspeciesbnDart1-4(3-2)
nDart1-1
nDart1-3(6)
nDart1-12
nDart1-3(8)
nDart1-2
nDart1-4(3-1)
nDart1-7
nDart101
nDart102
nDart103
nDart105
nDart106
nDart108
1 WRC1 NIPPONBARE Breeding Japan Japonica P P P P P P P P A A A a A A
2 WRC2 KASALATH Landrace India Aus A a a a a NA a P P A A a A P
3 WRC3 BEI KHE Landrace Cambodia Indica A A NA a a NA a NA A P P P P P
4 WRC4 JENA 035 Landrace Nepal Aus P P a a a a a NA P a A P A P
5 WRC5 NABA Landrace India Indica A P a a a NA a NA P P P P P P
6 WRC6 PULUIK ARANG Landrace Indonesia Indica A P a a a NA a NA P P P a P P
7 WRC7 DAVAO 1 Landrace Philippines Indica A P NA a a NA a NA P P A P P P
8 WRC9 RYOU SUISAN KOUMAI Landrace China Indica A A NA a a NA a NA P P P P P P
9 WRC10 SHUUSOUSHU Landrace China Indica A NA NA a a NA a NA P A P P A P
10 WRC11 JINGUOYIN Landrace China Indica A P a a a a a NA A A P P P P
11 WRC13 ASU Landrace Bhutan Indica A A a a a a a NA a P P P P P
12 WRC14 IR 58 Breeding Philippines Indica P P a a a NA a NA A P P P P P
13 WRC15 CO 13 Unknown India Indica P A NA a a a a NA P P P a P P
14 WRC16 VARY FUTSI Landrace Madagascar Indica A A NA a a NA a NA A A A P A P
15 WRC17 KEIBOBA Landrace China Indica A NA NA a a NA a NA P P P P P P
16 WRC18 QINGYU(SEIYU) Landrace Taiwan Indica A NA NA a a NA a P P P A P P P
17 WRC19 DENG PAO ZHAI Breeding China Indica A P NA a a NA a NA P P P a P P
18 WRC20 TADUKAN Landrace Philippines Indica A A NA a a NA a NA P a A P P P
19 WRC21 SHWE NANG GYI Landrace Myanmar Indica A P NA P a a a NA A P P a P P
20 WRC22 CALOTOC Landrace Philippines Aus A P NA P a a a NA A A A P P P
21 WRC23 LEBED Landrace Philippines Indica A P NA a a NA a NA A P P P A P
22 WRC24 PINULUPOT 1 Landrace Philippines Indica A P NA a a NA a P P A A a P P
23 WRC25 MUHA Unknown India Aus P P a a a a a P P A A a A P
24 WRC26 JHONA 2 Unknown India Aus A A a a a a a NA P A A a a P
25 WRC27 NEPAL 8 Landrace Nepal Aus P NA a a a NA a NA A P A P A P
26 WRC28 JARJAN Landrace Bhutan Aus P NA a a a NA a NA P P A P A P
27 WRC29 KALO DHAN Landrace Nepal Aus P P a a a NA a NA P A A a A P
28 WRC30 ANJANA DHAN Landrace Nepal Aus P A a a a NA a NA P P A a A P
29 WRC31 SHONI Landrace Bangladesh Aus A A a a a a a P A A A a A P
30 WRC32 TUPA 121-3 Landrace Bangladesh Aus P A a a a NA a P A A A a A P
31 WRC33 SURJAMUKHI Breeding India Aus P A a a a NA a NA P P A a A P
32 WRC34 ARC 7291 Landrace India Aus P P a a a NA NA NA P a A P A P
33 WRC35 ARC 5955 Landrace India Aus A A a a a NA a P P A A a A P
34 WRC36 RATUL Landrace India Aus A A a a a NA a P A A A a A P
35 WRC37 ARC 7047 Landrace India Aus A A NA a a NA a NA P A A a A P
36 WRC38 ARC 11094 Landrace India Aus A A a a a NA a P P P A a A P
37 WRC39 BADARI DHAN Landrace Nepal Aus A A a a a a a P A A A a A P
38 WRC40 NEPAL 555 Unknown India Aus A A NA a a NA a P A A A a A P
39 WRC41 KALUHEENATI Landrace Sri Lanka Aus A A a a a P a P A A A a A P
40 WRC42 LOCAL BASMATI Landrace India Aus A P a P a NA a P A A A a A P
41 WRC43 DIANYU 1 Breeding China Japonica P P a P a a a P A P P a A A
42 WRC44 BASILANON Landrace Philippines Aus A A a a a a a NA P A A P P P
43 WRC45 MA SHO Landrace Myanmar Japonica P A a P a P a P A A A a A P
44 WRC46 KHAO NOK Landrace Laos Japonica P P a P a P a NA A A P a A P
45 WRC47 JAGUARY Unknown Brazil Japonica P P a P a a a NA A A A a A P
46 WRC48 KHAU MAC KHO Landrace Vietnam Japonica P P a a a a a NA A A A a A P
47 WRC49 PADI PERAK Landrace Indonesia Japonica P P NA P a a a NA A A A a a P
48 WRC50 REXMONT Breeding America Japonica P P a a a NA a NA A A A a A P
49 WRC51 URASAN 1 Landrace Japan Japonica P A NA P a a a NA A P P a A A
50 WRC52 KHAU TAN CHIEM Landrace Vietnam Japonica P P a P a P a P A A A a A P
51 WRC53 TIMA Landrace Bhutan Japonica P P a a a a a P A A A a A P
52 WRC55 TUPA 729 Landrace Bangladesh Japonica P P a P a NA a P A A A a A P
53 WRC57 MILYANG 23 Breeding Korea Unknown A NA NA a a a a P A P P a P P
54 WRC58 NEANG MENH Landrace Cambodia Indica A A a a a NA a NA A A A P A P
55 WRC59 NEANG PHTONG Landrace Cambodia Indica A A a a a NA a NA P P P P A P
56 WRC61 RADIN GOI SESAT Landrace Malaysia Indica A A a a a NA a NA A A A P A P
57 WRC62 KEMASIN Landrace Malaysia Indica A A a a a NA a NA P A A P P P
58 WRC63 BLEIYO Landrace Thailand Indica A A a a a NA a NA A A A P P P
59 WRC64 PADI KUNING Landrace Indonesia Indica A P a a a NA a NA A A P P P P
60 WRC65 RAMBHONG Landrace Indonesia Indica A P a a a NA a NA P A P P A P
61 WRC66 BINGALA Landrace Myanmar Indica A A a a a NA a NA A P P a P P
62 WRC67 PHULBA Landrace India Japonica A A a P a a a P A A A a A P
63 WRC68 KHAO NAM JEN Landrace Laos Japonica P P a P NA NA a P A A A a A AaLane shows the lane number in the DNA blot analysis of nDart in Figs. 1 and S1.
bKojima et al. 2005
A/a and P indicate absence and presence of nDart , respectively. A of absence shows no sequence alternation confirmed by sequencing and a was determined only by a PCR experiment. NA indicates no amplification.
Table S2 Distribution of nDart at 8 loci among Japanese landracesLocus
Lanea
Code No. Variety Typeb
Habitb
nDart1-4(3-1)
nDart1-3(8)
nDart1-3(6)
nDart1-4(3-2)
nDart1-1
nDart1-2
nDart1-7
nDart1-12
1 JRC1 GAISENMOCHI-7 Landrace Upland A A NA NA a a NA P2 JRC4 SENSHOU-2 Landrace Upland A A NA NA a a NA P3 JRC5 YAMADA BAKE Landrace Upland A A NA NA P NA P P4 JRC6 KANEKO-4 Landrace Upland A A NA NA a a NA P5 JRC7 IRIMA NISHIKI Landrace Upland A A NA P a a P P6 JRC8 OKKA MODOSHI Landrace Upland A A NA NA a a P P7 JRC12 OIRAN Landrace Upland A A NA NA a a NA P8 JRC13 BOUZU MOCHI Landrace Upland A A NA NA a a P P9 JRC14 MEGURO MOCHI Landrace Upland P A P NA P a P P
10 JRC17 AKAGE-7 Landrace Lowland P A A P P P P P11 JRC18 HASSOKUHO Landrace Upland A A P NA P a P P12 JRC19 WATARIBUNE Landrace Lowland P A A P P P NA P13 JRC20 SAIKAN Landrace Lowland E1 A P P P a P P14 JRC21 AKAMAI-2 Landrace Lowland A NA NA A NA NA NA a15 JRC22 MANSAKU Landrace Lowland P A A E3 P a P P16 JRC23 ISHIJIRO Landrace Lowland P A P P P a P P17 JRC26 AIKOKU-3 Landrace Lowland P A P P P a P P18 JRC28 SHINRIKI MOCHI-8 Landrace Lowland P P P P P a P P19 JRC29 SHICHIMENTYOU MOCHI Landrace Upland E1 A P P P P P P20 JRC31 KAMEJI-9 Landrace Lowland P A A P P P P P21 JRC32 OMACHI-1 Landrace Lowland P A A P P P P P22 JRC33 SHINRIKI-6 Landrace Lowland P P A P P a P P23 JRC34 ASAHI-9 Landrace Lowland P P P P P a P P24 JRC35 KABASHIKO-4 Landrace Lowland E1 A A P P a P P25 JRC36 SEKIYAMA-9 Landrace Lowland E1 A A P P a P P26 JRC37 SHIN YAMADAHO 2 Landrace Lowland A A P P P a P P27 JRC38 NAGOYA SHIRO Landrace Lowland E2 A P P P a P P28 JRC39 SHIROINE (KEMOMI) Landrace Lowland P A A P P a P P29 JRC40 AKAMAI-3 Landrace Upland E1 A A P P a P P30 JRC41 AKAMAI-5 Landrace Lowland A A A P P a NA a31 JRC42 TOUBOSHI Landrace Lowland A A NA A NA NA NA a32 JRC43 AKAMAI-1 Landrace Upland A A NA A NA NA NA a33 JRC44 KARAHOUSHI Landrace Lowland A A NA A NA NA NA a34 JRC45 HIYADACHITOU Landrace Lowland E1 A A P P a P P35 JRC46 FUKOKU Breeding Lowland E2 A P P P a P P36 JRC51 SHINSHUU Landrace Lowland A P P P a P P P37 JRC52 AICHI ASAHI Breeding Lowland P P P P P a P P38 JRC53 RAIDEN Landrace Upland P A A P P P P P
aLane shows the lane number in the DNA blot analysis of nDart in Figs. 1 and S2.
bEbana et al. 2008
A/a and P indicate absence and presence of nDart , respectively. A of absence shows no sequence alternation confirmed by sequencing and a was determined onlyby a PCR experiment. NA indicates no amplification. E1-E3 indicate indipendent excision events at each locus. E1, type 4; E2, type 2; E3 type 2.
Table S3 Variation of footprints in somatic excision at the nDart1-4(3-2) locus in 10 different varietiesVariety
Type Sequence Aya Hoshitaro Tannemochi Kamedasoutou Honoka 224 Shinriki Kitaibuki Yukihikari Hanabusa Hoshinoyume Total Frequency (%)Original TACCTGCC
1 TACCTGC- --CCTGCC +5 2 5 1 8 9.22 TACCTGC- GG -ACCTGCC +8 2 5 5 4 2 1 2 1 22 25.33 TACCTG-- ---CTGCC +3 4 1 5 5.74 TACCTGC- GG --CCTGCC +7 3 1 4 4.65 TACCT--- A -ACCTGCC +5 1 1 2 2.36 TACCTGC- ----TGCC +3 1 2 5 2 10 11.57 TACCTGC- GTA -ACCTGCC +9 6 6 6.98 TACCTGC- G -----GCC +3 3 1 4 4.69 TACCTGC- ---CTGCC +4 1 1 1.110 TACCTGC- TGA -ACCTGCC +9 1 1 1.111 TACCTGC- -----GCC +2 5 5 5.712 TACCTGC- GGT ------CC +4 7 7 8.013 TACCTGC- TA -ACCTGCC +8 1 1 1.114 TACCTGCC ----TGCC +4 2 2 2.315 TACCTGCC -----GCC +3 1 1 1.116 TACCTGCC ---CTGCC +5 1 1 1.117 TACCTGC- G --CCTGCC +6 1 1 1.118 TACCTGC- GGCA ----TGCC +7 1 1 1.119 TACCTGC- GG ---CTGCC +6 1 1 1.120 TACCTG-- -ACCTGCC +5 2 2 2.321 TACCTG-- G ---CTGCC +4 1 1 1.122 TACCTGCC -------- 0 1 1 1.1
Total 12 12 12 17 4 6 5 7 6 6 87
Insertion(bp)
Table S4 Variation of footprints in the somatic excision at three nDart loci in different varieties
VarietyLocus Type Sequence Aya Hanabusa Honoka 224 Total Frequency (%)nDart1-3(6) Original CCCACCCC
1 CCCACCC- -CCACCCC 11 11 28.22 CCCACCC- GG -CCACCCC 9 6 7 22 56.43 CCCACCCC -------- 5 5 12.84 CCCACC-- -CCACCCC 1 1 2.6
Total 20 11 8 39
VarietyLocus Type Sequence Aya Kitamiakage Hayayuki Total Frequency (%)nDart1-4(3-1) Original CTCACTCG
1 CTCAC--- AG -TCACTCG 12 12 42.92 CTCACTC- AG -TCACTCG 8 4 12 42.93 CTCACT-- TCG -TCACTCG 1 1 3.64 CTCACTC- CG -TCACTCG 3 3 10.7
Total 12 8 8 28
VarietyLocus Type Sequence Hoshitaro Kamedasoutou Tannemochi Hoshinoyume Total Frequency (%)nDart1-12 Original CTCTCTCG
1 CTCTCTC- ----CTCG 6 6 14.32 CTCTCTC- AG -TCTCTCG 5 1 10 1 17 40.53 CTCTCT-- AG -TCTCTCG 1 11 12 28.64 CTCTCTC- CG -TCTCTCG 1 5 6 14.35 CTCTCTC- -TCTCTCG 1 1 2.4
Total 12 12 11 7 42
Table S5 Variation of footprints in somatic excision at the nDart1-A locus in backcrossed progeniesLine
Type Sequence #20 #38 #19 #8 #46 #10 #7 #9 Total Frequency(%)Original CATGGCGC
1 CATGGCG- -ATGGCGC +6 4 3 7 12.32 CATGGCG- G -ATGGCGC +7 1 1 2 3.53 CATGGCG- G CATGGCGC +8 3 1 6 6 8 6 6 2 38 66.74 CATGGCG- GCG -ATGGCGC +9 1 1 1.85 CATGGCG- GC ----GCGC +5 1 1 1.86 CATGGCG- GC ---GGCGC +6 1 1 1.87 CATGGCG- GC --TGGCGC +7 1 1 1.88 CATGGCG- G --TGGCGC +6 1 2 3 6 10.5
Total 8 5 8 7 8 8 7 6 57
Insertion(bp)
Table S6 Footprints derived from germinal excision in two nDart loci
Population Generation Locus Typea Sequence No. of lines
Hoshinoyume/Italica Livorno/4/Hoshinoyume BC4F2 nDart1-A 7 CATGGCG- GC --TGGCGC 4
3 CATGGCG- G CATGGCGC 1
Hoshinoyume/Italica Livorno//Hoshinoyume BC1F6 nDart1-4(3-2) 2 TACCTGC- GG -ACCTGCC 5
6 TACCTGC- ----TGCC 123 TACCTGC- GGC -ACCTGCC 1
aType is referred from that of somatic excision in Tables S3 and S5.
