V. List of marker genes belonging to respective linkage groups
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Gene Name Gene Institution* Reference
locus
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Group 1
v-6 virescent-6 0 KY 29,41
eg extra glume 16 KY 29,31,38
ga-8 gametophyte gene-8 16 HK 110
spl-6 spotted leaf-6 23 KY 29,38,40,220
lax(lx) lax panicle 29 HK,KY 29,31,38,104
rl-1 rolled leaf-1 41 HK 53,107
al-4 albino-4 42 KY 29,35
ms-18 male sterile-18 46 KT 182
d-1O(d-15, kikeibanshinriki or
d-16) toyohikari-bunwai
tillering dwarf 52 KY,HK 29,31,187
chl-6 chlorina-6 64 KY 29,41
ga-7 gametophyte gene-7 71 HK 84,90
sd-1(d-47) dee-geo-woo-gen
dwarf 75 NA,HK 2,59,183
A Anthocyanin activator 82 HK,KY 61,96,104
Rd Red pericarp and seed
coat 83 HK,KY 104,189
shr-1 shrunken endosperm-1 84 KY 93,164,212
Shp-1 Sheathed panicle-1 85 HK 53,86
rl-4(rl-2) rolled leaf-4 102 HK 34,36,93
Pn purple node 112 HK,KY 29,61,104
d-18(d-25) hosetsu dwarf
(d-18h) or kotake-
tamanishiki dwarf
(d-18K) 128 KY,HK 29,36,69,170
fs-2 fine stripe-2 145 HK,KY 29,41,188
Unlocated genes
al-8 albino-8 11%-d-18 KY 29,35,41
chl-5 chlorina-5 13.2%-eg KY 29,41
d-26(t) 7237 dwarf 37%-A - 15,17
d-54(d-K-5) dwarf-Kyushu-5 25%-lax KY 29,41
d-55(d-K-6) dwarf-Kyushu-6 13%-eg KY 29,41
Est-5 Esterase-5 triplo-1 IR 209
ga-9 gametophyte gene-9 1.3%-d-18 HK 90
Got-1 Aspartate aminotrans
ferase-1 triplo-1 IR 209
Icd-1 Isocitrate dehydro
genase-1 triplo-1 IR 209
I-Ps-b Inhibitor for purple
stigma linked with A - 16
lgt long twisted grain 16%-d-26(t) - 15
mp-1 multiple pistil-1 triplo-1 IR 83
Prp-a(Pp) Purple pericarp 7.2%-A HK 18,140
sh-2 shattering-2 11%-sd-1 TS 116
ts-a twisted stem 23%-A - 15
Group 2
d-29(d-K-1) short uppermost
internode dwarf 0 KY,HK 34,36,47,48
tri triangular hull 12 KY,HK 32,36,47
bc-3 brittle culm-3 25 KY 34,47
bl-1 brown leaf spot-1 34 HK,KY 47,48,104
chl-1O chlorina-10 54 KY 47,48
d-5 bunketsu-waito tillering
dwarf 59 HK 104
gh-3 gold hull and internode-3 69 KY 30,34,47
d-32(d-12,
d-K-4) dwarf Kyushu-4 107 KY 30,47,48
d-30(d-W) waisei-shirasasa dwarf 125 KY,HK 32,47,48
gh-2 gold hull and internode-2 159 KY,HK 32,38,47
spl-2(bl-3) spotted leaf-2 178 KY 38,47,48
Unlocated genes
Amp-1 Aminopeptidase-1 triplo-2 IR 209
ms-17 male sterile-17 35%-gh-2 KT 74,75
Pi-b(Pi-s) pyricularia oryzae
resistance-b 5.8%-TR2-10 NA 72,174
Group 3
chl-1 chlorina-1 0 KY 32,34,133
Nal-6(t) Narrow leaf-6 4 KY 46
chl-3 chlorina-3 19 KY 133
Est-1 Esterase-1 23 NA,IR 10,109,112,137
fc-1 fine culm-1 40 KY 30,34,133
v-1(t) virescent-1 58 KY 34,133
bc-1 brittle culm-1 76 HK,KY 104
ms-7 male sterile-7 76 KT 74,75
Lk-f 'Fusayoshi'long grain 96 HK,OK 190,193,196
chl-2 chlorina-2 106 KY 36,40,133
v-2 virescent-2 106 KY 36,42,133
al-10 albino-10 110 KY 42,46
d-56(d-K-7) dwarf Kyushu-7 125 KY 42,46
lhs-1 leafy hull sterile-1 131.5 KY,IR 14,55,56,67
(lhs-2,op)
dl(lop) drooping leaf 132 KY,HK 32,38,97
Hg hairy glume 132 HK 56,104,105
drp-4 dripping-wet leaf-4 139 KY 42,46
spl-3(bl-14) spotted leaf-3 149 KY 34,38,46
drp-3 dripping-wet leaf-3 149 KY 42,43,46
z-3 zebra-3 149 KY 40,42,46
d-52(d-K-2) dwarf Kyushu-2 149 KY 39,40,42,46
Unlocated genes
An-3 Awn-3 38%-bc-1 HK 104,152
bl-4 brown leaf spot-4 29%-bc-1 HK 188
d-14(d-10) kamikawa-bunwai
tillering dwarf32%-dl HK 187
ga-2 gametophyte gene-2 11%-dl NA,KY 108,114
ga-3 gametophyte gene-3 34%-dl NA,KY 108,114
Gdh-1 Glutamete
dehydrogenase-1 8%-Pgi-1 GI 26,100
Mi Minute grain 24%-Lk-f HK 190,195
pgi-1 Phosphoglucose
isomerase-1 27%-chl-1 IR,GI 26,137,139
Pox-3 Peroxidase-3 5%-Pox-4 IR 137
Pox-4 Peroxidase-4 31%-Est-1 IR 137
rl-5(rl-3) rolled leaf-5 13%-chl-1 KY 42
s-e-1 hybrid sterility-e 16%-bc-1 GI 127
Shp-4(Gb) Sheathed panicle-3 27%-bc-1 HK 13
st-3(stl) stripe-3 1.1%-bc-1 KY 42
v-5 virescent-5 2.0%-chl-1 KY 133
v-7 virescent-7 1.7%-bc-1 XY 42
Group 4
d-2 ebisu dwarf 0 HK,KY 104
d-3 bunketsu-waito
tillering dwarf 25 HK 104
st-5 stripe-5 28 HK 88
Pl Purple leaf 61 HK,KY 61,62,104,106
Prp-b(Pb) Purple pericarp 61 - 18,140
Pi(t) Pyricularia oryzae
resistance 66 - 17
flo-3(t) floury endosperm-3 82 HK 85
lg liguleless 92 HK,KY 104
Spr-3(t) Spreading panicle-3 95 GI 149
ga-6 gametophyte gene-6 96 HK 84,91
Sh-3 Shattering-3 97 GI 149
st-4(ws-2) stripe-4 97 HK 84
d-42 liguleless dwarf 102 HK 19,63
Ph=Bh-c(Po) Phenol staining 113 HK,KY,GI 81,84,104
Xa-1(Xe) Xanthomonas campestris pv.
oryzae resistance-1 119 NA 118,145,210,211
Xa-12(Xa-kg) Xanthomonas campestris pv.
oryzae resistance-12 121 NA 118,210,211
Xa-2 Xanthomonas campestris pv.
oryzae resistance-2 123 NA 5,145
nal-4(nal) narrow leaf-4 124 - 216
d-31 taichung-155 irradiated
dwarf 131 - 216
Pr Purple hull 137 HK,KY 61,104
Ps-2 Purple stigma-2 141 GI 15,16,129
rcn-2 reduced culm number-2 156 HK 194
drp-5(t) dripping-wet leaf-5 160 KY 166,168
d-11(d-8) shinkane-aikoku or norin-28
dwarf 160 KY,HK 32,104
lk-i 'IRAT 13' long grain 170 HK 66,192
Unlocated genes
al-5 al.bino-5 34%-lg KY 35
al-7 albino-7 31%-lg KY 35
An-1 Awn-1 5.4%-d-11 HK 104
aul auricleless triplo-4 IR 83
Bph-1 Brown planthopper
resistance-1 trisomic-4 NA,IR 20,21,177
bph-2 brown planthopper
resistance-2 39%-d-2 NA,IR 20,21,177
close to Bph-1
drp-1 dripping-wet leaf-1 39%-d-2 HK 107
drp-8(t) dripping-wet leaf-8 28%-lg KY 168
ga-10(t) gametophyte gene-10 27%-lg HK 64
nal-1 narrow leaf-1 25%-d-2 NA,HK 97
nal-5(nal-1) narrow leaf-5 9.5%-lg KY 30,34
P Purple apiculus 2.7%-Pl HK 61,96,104
Pin-1 Purple internode-1 31%-Pl HK 99
Ps-1 Purple stigma-1 linked to Ph GI 16,129,186
rk-1 round kernel-1 35%-lg KY,HK 33,34,36
rl-2 rolled leaf-2 35%-d-2 HK 97
S-c-2 hybrid sterility-c 31%-Ph GI 126
s-e-2 hybrid sterility-e 15%-lg GI 127
Sc-1 Sclerotium oryzae
resistance 26%-lg NA 12
spr-1 spreading panicle-1 27%-Pl HK 65
Wh White hull 8.0%-lg WK 51,104
Xa-14 Xanthomonas campestris.pv
oryzae resistance-14 NA 198
ylm yellow leaf margin 10%-lg KY 34,36
z-5 zebra-5 11%-lg HK 64
Group 5
gh-1 gold hull and internode-1 O(?) HK,KY 46,103,104
nl-2 neck leaf-2 6 KY 34,45
d-1 daikoku dwarf 28 HK,KY 45,104
st-2(gw) stripe-2 46 HK 104
al-3 albino-3 48 KY 35,45
spl-8(bl-8) spotted leaf-8 48 KY 38,45
al-6(t) albino-6 53 KY 35
v-10(t) virescent-10 54 KY 167
ops open hull sterile 66 KY 31,36,45
bgl bright green leaf 79 KY 36,43,45
ri verticillate rachis 82 HK, KY 31,45,104
spl-7 spotted leaf-7 97 KY 38,40,45,
nl-1 neck leaf-1 107 HK,KY 45,104,157,
al-2 albino-2 108 KY 35,38,45
Unlocated genes
An-2 Awn-2 33%-gl-1 HK 104,153
bd-1 beaked lemma 22%-gl-1 - 95,153
er(o) erect growth habit 38%-gh-1 HK 188
eui elongated uppermost
internode 27%-nl-1 HK 83,89,92,14
gl-1 glabrous leaf
and hull 12%-TRl-5d HK,KY 36,104,157
Glh-6 Green leafhopper
resistance-6 tripro-5 IR 201
I-Pl-1 Inhibitor for
purple leaf-1 31%-gh-1 HK 104
M-Pox-1 Modifier for
Pox-1 close to gl-1 CH 134,135
ms-14 male sterile-14 11%-nl-1 KT 73,74
Pox-1 Peroxidase-1 38%-nl-1 CH 135
Shp-3(Ga) Sheathed
panicle-3 37%-nl-1 - 13
xa-5 Xanthomonas campestris pv trisomic-5 IR 136,179,221
oryzae resistance-5 close to gl-1
xa-13 Xanthomonis campestris pv linked to IR 121,144
oryzae resistance-13 xa-5
Ylb yellow banded leaf blade 32%-nl-1 - 16
Group 6
d-4 bunketsu-waito
tillering dwarf 0 HK 104
I-Pl-4 Inhibiter for
purple pericarp 9 HK 66,106
wx(am) glutinous endosperm 22 HK,KY 104,147,162
dp-1 depressed palea-1 24 HK,KY 32,102
ms-1 male sterile-1 27 - 11
Pgd-2 Phosphogluconate
dehydrogenase-2 29 GI 23,100
v-3 virescent-3 30 KY 133
ga-1 gametophyte gene-1 36 KY 37
C Chromogen for
anthocyanin 44 HK 61,96,104
S-5 Hybrid sterility-5 48 NA 22
Amp-3(Amp-1)
Aminopeptidase-3 52 GI 137,151
Est-2 Esterase-2 53 NA 109,111,113,137
bl-3 brown leaf spot-3 54 HK 188
alk alkali degeneration 55 KY,NA 76
st-1(ws) stripe-1 64 KY,HK 102
Pgi-2 Phosphoglucose
isomerase-2 66 GI 137,151
Se-1(Lf,Lm,Rs)
Photosensitivity-1 66 NA 76,217,218,219
Pi-z Pyricularia oryzae
resistance-z 68 NA 9,70,72,174
S-6 hybrid sterility-6 73 GI 148
d-9 Chinese dwarf 75 HK 66
rcn-1 reduced culm number-1 76 HK 191
gf gold furrows of hull 79 HK 52
chl-4 chlorina-4 81 KY 36,133
bl-2(bl-m) brown leaf
spot-2 82 HK 51,107
fs-l(fs) fine stripe-1 94 HK 68,104
Cl Clustered spikelets 95 HK 51,104
Pi-i Pyricularia oryzae
resistance-i 99 NA 9,72,174
ms-9 male sterile-9 99 KT 74,155
Ur-1(Ur) Undulated rachis-1 122 HK 104
Unlocated genes
al-1 albino-1 7.1%-wx KY 35
al-9(t) albino-9 trisomic-6 KY 43
aph apiculus hairs linked to GI 160,161
Est-2 and Pgi-2
bc-4 brittle culm-4 triplo-6 IR 83
Cat-1 Catalase-1 22%-Pox-5 IR,GL 26,209
chl-7(t) chlorina-7 27%-Pi-z NA 83,131
d-21 aomorimochi-14 dwarf 8.3%-wx HK 69
drp-6(t) dripping-wet
leaf-6 15%-fc-2(t) KY 166,168
dw-1(fh) deep water
tolerance 30%-Se-1 NY 50,138
Enp-1 Endopeptidase-1 2.2%-Cat-1 IR 137
fc-2(t) fine culm-2 18%-C KY 166,168
ga-4(ga-A) gametophyte
gene-4 34%-wx HK,KY 98,115
ga-5(ga-B) gametophyte
gene-5 27%-wx HK 98
Got-2 Aspartate aminotrans-
pherase-2 31%-Pgi-2 GI,IR 137
Hl-a Hairy leaf 21%-fs-1 HK 104,105
I-PI-2 Inhibitor for
purple leaf-2 10%-I-Pl-4 HK 66,106
mp-2 multiple pisiil-2 triplo-6 IR 83
Pox-5 Peroxidase-5 39%-Pgi-2 IR,GI 209
S-1 Hybrid sterility-1 close to C GI 150
s-a-1(s/1,x/1)hybrid
sterility-a 21%-wx GI 125,127
s-c-1 hybrid sterility-c 8.6%-C GI 126
s-d-1 hybrid sterility-d 33%-wx GI 127
S-A-1(A-1) Hybrid
sterility-A 9.5%-C GI 130
S-B-2(B-2) Hybrid sterility-B 28%-wx GI 128,130
spl-4(bl-15) spotted leaf-4 2.5%-dp-1 HY 34,36,38
Stv-a(St) Stripe disease
resistance-a 38%-wx NA 207,208
Un-a Uneven grain 22%-Cl-a - 200
V-1 virescent-1 25%-C HK 49,50,104
zn zebra necrosis 20%-C HK 64
Group 7
d-6 ebisumochi or tankan- 0 HK,KY 104
shirasasa dwarf
g-1 long sterile lemmas-1 6 HK,KY 104
spl-5(bl-6) spotted leaf-5 29 KY 34,38
Rc Brown pericarp and seed coat 42 HK,KY 104,189
v-11(t) virescent-11 43 KY 167
z-6 zebra-6 45 HK 87
rfs rolled fine striped leaf 56 HK,KY 36,43
esp-1(rsp-1) endosperm storage
protein-1 83 KY 78,79,80,163
Unlocated genes
beta-Amy-1(t) beta-amylase
isozyme-1 trisomic-7 KY 175
d-7 heiei-daikoku or cleisto- 39%-d-6 HK 104
gamous dwarf
Est-9(Est-cl) Esterase-9 triplo-7 GI,IR 137,139,151
ge giant embryo trisomic-7 KY,HK 36,164,213
lp-1 long palea-1 12%-Un-b - 199,200
m-Ef-1 modifier for Ef-1 23%-Rc CH 203,204
ms-8 male sterile-8 20%-rfs KT 74,75
rl-6(t) rolled leaf-6 12%-lp-1 - 199
se-2 photosensitivity-2 23%-g-l - 223
Un-b Uneven grain 18%-g-l - 200
Group 8
sug(su) sugary endosperm 0 KY 28,58,164,165
v-8 virescent-8 49 KY 36,44,58
Unlocated genes
Amp-2 Aminopeptidase-2 trisomic-8 GI,IR 24,26,137,209
Amp-4 Aminopeptidase-4 triplo-8 IR 209
An-4(t) Awn-4 5.0%-TR7-8b RY 156
chl-8 chlorina-8 triplo-8 IR 54
ch1-9 chlorina-9 triplo-8 IR 54
d-51(d-K-8) dwarf Kyushu-8 trisomic-8 KY 36,44
shr-2 shrunken endosperm-2 trisomic-8 KY 94,162,212
Stv-b(St-2) Stripe disease
resistance-b linked with NA 207,208
TRl-8
ur-2 undulate rachis-2 trisomic-8 KY 36,44
z-4 zebra-4 trisomic-8 KY 36,44
Group 9
Dn-1 Dense panicle-1 0 HK,KY 31,104
drp-2 dripping-wet leaf-2 14 KY 31,166
dp-2 depressed palea-2 14 HK,KY 31,97
gm(pd,sgm) gall midge resistance 0 - 154,169
I-Bf Inhibitor for brown furrows 39 HK,KY 36,103,104,154
lam(t) low amylose endosperm 39 HK 60
Unlocated genes
Bp Burlush-like panicle trisomic-9 KY 33,36
d-57(d(x)) dwarf 21%-Dn-1 - 17,215
ms-10 male sterile-10 5%-Dn-1 KT 73,74
Pi-ta Pyricularia oryzae
resistance-ta 4.5%-TR9-12 NA 71,72,174
Group 10
pgl pale green leaf 0 KY 33,172,220
Rf-1 Pollen fertility
restoration-1 12 RY,HK,NA 36,171,172,
173
fg1(fl) faded green leaf 12.5 KY 33,172,220
Ef-1(=Ef-2) Earliness-1 28 RY,CH 158,159,203,
205,206
Unlocated genes
Bph-3 Brown planthopper
resistance-3 trisomic-10 NA,IR 20,82,177
bph-4 brown planthopper
resistance-4 30%-rk-2 NA,IR 20,82,177,
close to Bph-3 178
d-20 hayayuki dwarf triplo-10 HK 56,58,69
du-1 dull endosperm-1 trisomic-10 KY 36,132,164,214
Glh-3 Green leafhopper
resistance-3 34%-bph-4 IR 3,178,181
rk-2 round kernel-2 2.5%-TR10-11 KY 36,220
ygl yellow green leaf triplo-10 IR 83
Group 11
Pi-k Pyricularia oryzae
resistance-k 0 NA 9,72,174
d-27(d-t) bunketsuto tillering
dwarf 28 KY,HK 34,39
z-2 zebra-2 33 KY 34,39
drp-7(t) dripping-wet leaf-7 50 KY 166,168
la lazy growth habit 55 HK,KY 39,104
v-4 virescent-4 66 KY 39,40,133
Pgd-1 Phosphogluconate
dehydrogenase-1 71 GI,IR 25,26,137,209
d-28(d-C) chokeidaikoku or
long stemmed dwarf 81 KY 39
sp short panicle 89 KY,HK 32,34,39
Adh-1 Alcohol dehydrogenase-1 90 IR 23,26,139
Pi-a Pyricularia oryzae
resistance-a 91 NA 9,72,174
sh-1 shattering-1 94 HK 104
v-9(t) virescent-9 104 HY 167
esp-2(rsp-2) endosperm storage
protein-2 110 KY 79,80,163
z-1 zebra-1 118 KY 33,34,36
D-53(D-K-3) Dwarf Kyushu-3 127 KY 36,39,40
Unlocated genes
esp-3(rsp-3) endosperm storage
protein-3 trisomic-11 KY 77,78
M-Pi-z Modifier for Pi-z 11%-la YA 7
nal-2 narrow leaf-2 36%-la HK 97
Pi-f Pyricularia oryzae
resistance-f 15%-Pi-k NA 174,202,224
Pi-se-1(Rb-1) Pyricularia oryzae
resistance-se 9.5%-la YA 6,8
Pi-is-1(Rb-4) Pyricularia oryzae
resistance-is 23%-la YA 6
S-3 Hybrid sterility-3 1%-la IR 146
Xa-3(Xa-w,Xanthomonas campestris pv. 22%-d-27 IR 5,119,120,
Xa-4b Xa-6oryzae resistance-3 122,123,176,
Xa-9) 180
Xa-4(Xa-4a) Xanthomonas close to Xa-3 IR 124,136,185
campestris pv.oryzae resistance-4 (tripro-7?)
Xa-10 Xanthomonas campestris pv. 27%-Xa-4 IR 222
oryzae resistance-10
Group 12
Acp-1 Acid phosphatase-1 0 IR,GI 10,23,27,209
Acp-2 Acid phosphatase-2 0 IR,GI 10,26,137,20
Pox-2 Peroxidase-2 24 GI 10,23,26,27,
137,209
nal-3(nal-2) narrow leaf-3 27 KY,HK 33,36,100,22
d-33(d-b) bonsaito dwarf 32 KY 33,36,100
Sdh-1 Shikimate dehydrogenase-1 37 IR 10,26,137,13
spl-1(bl-12) spotted leaf-1 0 HY 33,38,58,220
rl-3(rl-l) rolled leaf-3 28 KY,IR 33,58,100,220
Unlocated genes
du-4 dull endosperm-4 trisomic-12 KY 162,214
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