IV. Current linkage maps
Genes assigned to the linkage groups
Group I P Group VI+IX ga-3
al-1 Pin-1 An-2 Gb*
al-9(t) rk-1 bd-1 Lk-f
bc-4 rl-2 er Mi
chl-7 s-c-2 eui pgi-1
d-21 s-e-2 Ga* rl-5
dw-1 Sc-1 gl-1 s-e-1
fc-2(t) spr-1 Glh-6 st-3
drp-6(t) ssk I-Pl-1 v-5
ga-4 Wh xa-5 v-7
ga-5 ylm ylb
Hl-a z-5 fgl group
I-Pl-2 Group VII Bph-3
mp-2 Group III Bp bph-4
rcn-1 al-4 d-57 d-20
S-1 al-8 Pi-ta du-1
s-a-1 chl-6 sl Ef-1
s-b-1 d-18 Glh-3
s-c-1 d-26(t) Group VIII rk-2
s-d-1 d-54 Adh-1 ygl*
S-A-1 d-55 M-Pi-z
S-B-2 fs-2 nal-2 d-33 group
spl-4 ga-9 Pgd-1 d-33
Stv-a I-Ps-b Pi-f nal-3
Un-a lgt Pi-se-1 Sdh-1
v-1 mp-1 Pi-is-1
zn Prp-a esp-2 sug group
ts-a S-3 Amp-2
Group II v-6 Xa-3 An-4(t)
al-5 Xa-4 d-51
al-7 Group IV Xa-10 shr-2
An-1 d-7 stv-b
aul Est-9 Group X ur-2
Bph-1 ge Pi-b z-4
bph-2 lp-1
drp-1 m-Ef-1 Group XI
drp-8(t) rl* An-3
ga-10(t) esp-1 bl-4
nal-1 se-2 d-14
nal-5 Un-b ga-2
Linkage maps of rice newly constructed gathering latest information are
presented, since the maps were not presented in RGN 2 and 3. The new maps
include all the information reported in papers listed in Literature on Genic
Analysis, which is presented at the end of this Committee Report. However,
the old numbering systems for the linkage groups, chromosomes and trisomics
are used as the adoption of a unified numbering system of chromosomes is not
agreed yet.
List of marker genes belonging to respective linkage groups
______________________________________________________________
Gene Name Gene Institution Reference
locus (Gene stock)
______________________________________________________________
Group I (wx group), chromosome 6, triplo 3
d-4 bunketsu-waito tillering
dwarf 0 HK 59,99
I-Pl-4 Inhibitor for purple
pericarp-4 9 HK 59
wx(am) glutinous endosperm 22 HK,KY 99,132
dp-1 depressed palea-1 24 HK,KY 96
ms-1 male sterile-1 27 _ 12
v-3 virescent-3 30 KY 122
ga-1 gametophyte gene-1 36 KY 36,108
C Chromogen for
anthocyanin 44 HK 59,92,99
S-5 Hybrid sterility-5 48 NA 25,26
Amp-3
(Amp-1) Aminopeptidase-3 52 GI 134
Est-2 Esterase isozyme-2 53 NA 105
bl-3 brown leaf spot-3 54 HK 164
alk alkali degeneration 55 KY,NA 72
st-l(ws) stripe-1 64 KY,HK 96
Pgi-2 Phosphoglucose
isomerase-2 66 GI 134
Se-1(Lf,
Lm,Rs) Photosensitivity-1 66 NA 4,72,199
Pi-z Pyricularia oryzae
resistance-z 68 NA 11,68,70
d-9 chinese dwarf 75 HK 59
gf gold furrows of hull 79 HK 50
chl-4 chlorina-4 81 KY 35,122
bl-2
(bl-m) brown leaf spot-2 82 HK 49,103
fs-l(fs) fine stripe-1 94 HK 65,99
cl Clustered spikelets 95 HK 49,99
Pi-i Pyricularia oryzae
resistance-i 99 NA 11,68,70
Ur-l(Ur) Undulated rachis-1 122 HK 59,99
Unlocated genes
al-1 albino-1 7.1%-wx KY 34
al-9(t) albino-9 trisomic B KY 43
bc-4 brittle culm-4 triplo-3 IR 79
chl-7(t) chlorina-7 27%-Pi-z NA 79,121
d-21 aomorimochi-14
dwarf 8.3%-wx HK 66
dw-l(fh) deep water
tolerance 30%-Se-1 NA 48,125
fc-2(t) fine culm-2 18%-C KY 144,146
drp-6(t) dripping-wet leaf-6 15%-fc-2 KY 144,146
ga-4
(ga-A) gametophyte gene-4 34%-wx HK,KY 94,108
ga-5
(ga-B) gametophyte gene-5 27%-wx HK 94
Hl-a Hairy leaf 21%-fs-1 HK 99,100
I-Pl-2 Inhibitor for
purple leaf-2 10%-I-Pl-4 HK 59,101
mp-2 multiple pistil-2 triplo-3 IR 79
rcn-1 reduced culm
number-I 32%-C HK 167
S-1 Hybrid sterility-1
(one locus sporo-
gametophytic lethal) close to C GI 133
s-a-1
(s/1,x/1) hybrid sterility-a
(duplicate
gametic lethal) 21%-wx GI 116,118
s-b-1 hybrid sterility-b 18%-wx GI 116,118
s-c-1 hybrid sterility-c 8.6%-C GI 117
s-d-1 hybrid sterility-d 33%-wx GI 118
S-A-1
(A-1) Hybrid sterility-A
(duplicate
fertility genes) 9.5%-C GI 119,120
S-B-2
(B-2) Hybrid sterility-B 28%-wx GI 119,120
spl-4
(bl-15) spotted leaf-4 2.5%-dp-1 KY 35,38
Stv-a(St) Stripe virus
resistance-a 38%-wx NA 189,190,191
Un-a Uneven grain 22%-Cl-a - 175
v-1 virescent-1 25%-C HK 47,99
zn zebra necrosis 20%-C HK 62
Group II (Pl group), chromosome 11, triplo-12
d-2 ebisu dwarf 0 HK,KY 59,99
d-3 bunketsu-waito
tillering dwarf 25 HK 59,99
Pl Purple leaf 61 HK,KY 60,101,102
Prp-b(Pb) Purple pericarp 61 _ 19
Pi(t) Pyricularia oryzae
resistance 66 _ 18
flo-3(t) floury endosperm-3 82 HK 82
lg liguleless 92 HK,KY 99
ga-6 gametophyte gene-6 96 HK 81,87
st-4
(ws-2) stripe-4 97 HK 81
d-42 liguleless dwarf 102 HK 20,61
Ph=,Bh-
c(Po) Phenol staining 113 HK,KY 76,81,99,127
Xa-1(Xe) Xanthomonas
campestris pv.
oryzae resistance-1 119 NA 111,130,193
Xa-12 Xanthomonas camp-
(Xa-kg) estris pv. oryzae
resistance-12 121 NA 192,193
Xa-2 Xanthomonas camp-
estris pv. oryzae
resistance-2 123 NA 5,130
nal-4
(nal) narrow leaf-4 124 _ 198
d-31 taichung-155
irradiated dwarf 131 _ 198
Pr Purple hull 137 HK,KY 59,99
Ps-3 Purple stigma-3 141 _ 16,17
drp-5(t) dripping-wet leaf-5 160 KY 144,146
d-11(d-8) shinkane-aikoku or
norin-28 dwarf 160 KY,HK 32,99
Ps-2 Purple stigma-2 163 _ 16,17
Unlocated genes
al-5 albino-5 34%-lg KY 34
al-7 albino-7 31%-lg KY 34
An-1 Awn-1 5.4%-d-11 HK 99
aul auricleless triplo-12 IR 79
Bph-1 Brown planthopper
resistance-1 trisomic E NA,IR 22,24,155
bph-2 brown planthopper
resistance-2 39%-d-2 NA,IR 22,24,155
close to Bph-1
drp-1 dripping-wet leaf-1 39%-d-2 HK 103
drp-8(t) dripping-wet leaf-8 28%-lg KY 146
ga-10(t) gametophyte gene-10 27%-Ig HK 62
nal-1 narrow leaf-1 25%-d-2 NA,HK 93
nal-5
(nal-1) narrow leaf-S 9.5%-lg KY 35
P Purple apiculus 2.7%-PI HK 92,99,147
Pin-1 Purple internode-1 31%-PI HK 95
rk-1 round kernel-1 35%-lg KY,HK 33,35
rl-2 rolled leaf-2 35%-d-2 HK 93
s-c-2 hybrid sterility-c 31%-Ph GI 117
s-e-2 hybrid sterility-e 15%-lg GI 118
Sc-1 Sclerotium oryzae
resistance 26%-lg NA 13
spr-1 spreading panicle-1 27%-Pl HK 63
ssk(sk) malformed semi-
sterile 6.8%-Pl _ 12
Wh White hull 8.0%-lg HK 49,99
ylm yellow leaf margin 10%-lg KY 35
z-5 zebra-5 ll%-lg HK 62
Group III (A group), chromosome-3, triplo-1
eg extra glume 0 KY 31,35,38
ga-8 gametophyte gene-8 0 HK 106
spl-6 spotted leaf-6 8 KY 35,38
lax(lx) lax panicle 13 HK,KY 38,99
chl-5 chlorina-5 22 KY 41
rl-1 rolled leaf-1 26 HK 51,103
d-10(d- kikeibanshinriki or
15,d-16) toyohikari-bunwai
tillering dwarf 28 KY,HK 31,163
ga-7 gametophyte gene-7 39 HK 81,86
sd-l
(d-47) dee-geo-woo-gen dwarf 43 NA,HK 2,57,160
A Anthocyanin activator 50 HK,KY 92,99
Rd Red pericarp and
seed coat 51 HK,KY 59,99,165
shr-1 shrunken endosperm-1 52 KY 88,143,195
Shp-1 Sheathed panicle-1 53 HK 51,83
rl-4
(rl-2) rolled leaf-4 70 HK 35,37,88
Pn Purple node 70 HK,KY 59,99
Unlocated genes
al-4 albino-4 13%-lax KY 34
al-8 albino-8 11%-d-18 KY 34,41
chl-6 chlorina-6 31%-lax KY 41
d-18 hosetsu dwarf(d-
(d-25) 18h) or kotake-
tamanishiki dwTrf
(d-18k) 0.6%-TR3-8b KY,HK 35,66,150
d-26(t) 7237 dwarf 37%-A _ 16,18
d-54
(d-K-5) dwarf-Kyushu-5 30%-rl-4 KY 41
d-55
(d-K-6) dwarf-Kyushu-6 12%-eg KY 41
fs-2 fine stripe-2 13%-d-18 HK,KY 35,164
ga-9 gametophyte
gene-9 1.3%-d-18h HK 86
I-Ps-b Inhibitor for
purple stigma linked with A - 17
lgt long twisted
grain 16%-d-26(t) - 16
mp-1 multiple pistil-1 triplo-1 IR 79
Prp-a(Pp) Purple pericarp 7.3%-A HK 19
ts-a twisted stem 23%-A _ 16
v-6 virescent-6 27%-lax KY 41
Group-IV(g-1 group),, chromosome 10, triplo-7
d-6 ebisumochi or tankan-
shirasasa dwarf 0 HK,KY 59,99
g-1 long sterile lemmas-1 6 HK,KY 99
spl-5
(bl-6) spotted leaf-5 29 KY 38
Rc Brown pericarp and
seed coat 42 HK,KY 59,99,165
v-11(t) virescent-11 43 KY 145
z-6 zebra-6 45 HK 84
rfs rolled fine striped
leaf 56 HK,KY 35
Unlocated genes
d-7 heiei-daikoku or
cleistogamous dwarf 39%-d-6 HK 59,99
Est-9
(Est-cl) Esterase-9 triplo-7 GI,IR 126,134
ge giant embryo trisomic-F KY,HK 35,143,196
lP-1 long palea-1 12%-Un-b _ 175
m-Ef-l(t) modifier for Ef-1 23-%-Rc CH 182,183,187
rl(t) rolled leaf 12%-1p-1 _ 174
esp-l endosperm storage
(rsp-1) protein-1 trisomic-F KY 73,74
se-2 photosensitivity-2 23%-g-1 _ 203
Un-b Uneven grain 18%-g-1 _ 175
Group VI+IX (d-1 group), chromosome-2, tripro-5
gh-1 gold hull and
internode-1 0 HK,KY 46,98,99
nl-2 neck leaf-2 6 KY 35,44
d-1 daikoku dwarf 28 HK,KY 59,99
st-2(gw) stripe-2 46 HK 99
al-3 albino-3 48 KY 34
spl-8
(bl-8) spotted leaf-8 48 KY 35,38,44
al-6(t) albino-6 53 KY 34
V-10(t) virescent-1O 54 KY 145
ops open spikelet
(ops-1) sterile 66 KY 33,35,44
bgl bright green leaf 79 KY 35,45
ri verticillate rachis 82 HK,KY 31,45,99
spl-7 spotted leaf-7 97 KY 38,45
nl-1 neck leaf-1 107 HK,KY 45,49,99,140
al-2 albino-2 108 KY 34,38,45
Unlocated genes
An-2 Awn-2 33%-gl-1 HK 99,136
bd-1 beaked lemma 22%-gl-1 - 136
er(o) erect growth
habit 38%-gh-1 HK 164
eui elongated upp-
ermost internode 27%-nl-1 HK 79,85,128 129
Ga* Gamadiness 37%-nl-1 _ 14
gl-1 glabrous leaf
blade-1 12%-TR2-3d HK,KY 43,99,140
Glh-6 Green leafhopper
resistance-6 tri-pro-5 _ 173
I-Pl-1 Inhibitor for
purple leaf-1 31%-gh-1 HK 59,99
xa-5 Xanthomonas camp-
estris pv oryzae trisomic L IR 124,157,201
resistance-5 close to gl-1
ylb yellow banded
leaf blade 32%-nl-l _ 17
Group VII (Dn-1 group), chromosome 1, triplo-9
Dn-1 Dense panicle-I 0 HK,KY 99
drp-2 dripping-wet
leaf-2 14 KY 31
dp-2 depressed palea-2 14 HK,KY 31,93
Unlocated genes
Bp Burlush-like
panicle trisomic-H KY 31,33
d-57
(d(x)) dwarf 21%-Dn-1 _ 18,197
Pi-ta Pyricularia oryzae
resistance-ta 4.5%-TRl-4 NA 709,153
sl sekiguchi lesion 10%-Pi-ta NA 69
Group V (I-Bf group), chromosome 1, triplo-9
gm(pd, gall midge
sgm) resistance 0 _ 137,149
I-Bf Inhibitor for brown
furrows of hull 39 HK,KY 98,99,137
lam(t) low amylose
endosperm 39 HK 58
sd semidwarf 73 _ 137
Ps-1 Purple stigma-1 100 HK 59,137,162
Group VIII (la group), chromosome 9, triplo 11
Pi-k Pyricularia oryzae
resistance-k 0 NA 11,70,71,153
d-27(d-t) bunketsuto till-
ering dwarf 28 KY,HK 33,35,39
z-2 zebra-2 33 KY 35,39,44
drp-7(t) drippina-wet
leaf-7 50 KY 146
la ' lazy'growth
habit 55 HK,KY 99
v-4 virescent-4 66 KY 35,39,122
d-28(d-C) chokeidaikoku or
long stemmed
dwarf 81 KY 39
sp short panicle 89 KY,HK 33,35,39
Pi-a Pyricularia oryzae
resistance-a 91 NA 11,70,153
sh shattering 94 HK 99
v-9(t) virescent-9 104 KY 145
z-1 zebra-1 118 KY 33,35,44
D-53
(D-K-3) Dwarf Kyushu-3 127 KY 35,39
Unlocatcd gones
Adh-1 Alcohol dehydro-
genase-1 tripro-11 IR 126
esp-2 endosperm storage
(rsp-2) protein-2 trisomic-G KY 73,74
M-pi-z Modifier for
Pi-z 11%-la YA 9
nal-2 narrow leaf-2 36%-la HK 33,93
Pgd-1 Phosphogluconate
dehydrogenase-1 trisomic-G GI 27
Pi-f Pyricularia oryzae
resistance-f 15%-Pi-k NA 181,205
Pi-se-1 Pyricularia oryzae
(Rb-1) resistance-se 9.5%-la YA 8,10
Pi-is-1 Pyricularia oryzae
(Rb-4) resistance-is 23%-la YA 8
S-3 Hybrid sterility-3
(one locus sporo-
gametophytic lethal) 1%-la IR 131
Xa-3,(Xa
-w,Xa-4 Xanthomonas camp-
b,Xa- estris pv. oryzae
6,Xa-9) resistance-3 22%-d-27 IR 5,110,112,113,
154,158,204
Xa-4 Xanthomonas camp-
estris pv.oryzae close to Xa-3 IR 114,115,124
resistance-4 (tripro-7?) 161
Xa-10 Xanthomonas camp-
estris pv.oryzae
resistance-10 27%-Xa-4 IR 202
Group X (bl-1 group),chromosome-8,tripro-2
d-29 short uppermost
(d-K-1) internode dwarf 0 KY,HK 35,44
tri triangular hull 0 KY,HK 32,97
bl-1 brown leaf spot-1 18 HK,KY 99
bc-3 brittle culm-3 18 KY 35
gh-3 gold hull and
internode-3 36 KY 33,35
d-5 bunketsu-waito
tillering dwarf 43 HK 59,99
spl-2
(bl-3) spotted leaf-2 51 KY 35,38,44
gh-2 gold hull and
internode-2 68 KY,HK 32,38,44
d-30 waisei-shirasasa
(d-W) dwarf 99 KY,HK 32,35,44
d-32(d-
12,d-K
-4) dwarf Kyushu-4 119 KY 30
Unlocated genes
Pi-b Pyricularia oryzae
(Pi-s) resistance-b 5.8%-TR7-8 NA 70,153
Group XI+XII (bc-1 group), chromosome 5, triplo-4
chl-1 chlorina-1 0 KY 32,122
Nal-6(t) Narrow leaf-6 4 KY 46
chl-3 chlorina-3 19 KY 122
fc-1 fine culm-1 40 KY 35,122
V-1(t) virescent-1 58 KY 35,122
bc-1 brittle culm-1 76 HK,KY 99
chl-2 chlorina-2 106 KY 35,40,122
v-2 virescent-2 106 KY 35,42,122
al-10 albino-1O 110 KY 42,43.46
d-56(d-
K-7) dwarf Kyushu-7 125 KY 42,43.46
lhs-1
(lhs-2, leafy hull
op) sterile-1 131.5 KY,IR 21,29,53,64
dl(lop) drooping leaf 132 KY,HK 32,38,93,122
Hg Hairy glume 132 HK 54.56,99,100
drp-4 dripping-wet
leaf-4 139 KY 42.46
spl-3
(bl-14) spotted leaf-3 149 KY 35,38.46
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 40,42.46
Unlocated genes
An-3 Awn-3 38%-bc-1 HK 99,135
bl-4 brown leaf
spot-4 29%-bc-1 HK 164
d-14 kamikawa-bunwai
(d-10) tillering dwarf 32%-dl HK 163
ga-2 gametophyte
gene-2 ll%-dl NA,KY 104,107
ga-3 gametophyte
gene-3 34%-dl NA,KY 104,107
Gb* Gamadiness 27%-bc-1 HK 14
Lk-f 'Fusayoshi' long
grain 19%-bc-1 HK 166,173
Mi Minute grain 24%-Lk-f HK 166,172
Pgi-1 Phosphoglucose
isomerase-1 triplo-4 IR 126
rl-5
(rl-3) rolled leaf-5 13%-chl-1 KY 42,43
s-e-1 hybrid steril-
ity-e 16%-bc-1 GI 118
st-3
(stl) stripe-3 1.1%-bc-1 KY 42,43
v-5 virescent-5 2.0%-chl-1 KY 43,122
v-7 virescent-7 1.7%-bc-1 KY 42,43
fgl group, chromosome-7, triplo-10
pg1 pale green leaf 0 KY 33,37,44,152
Rf-1 Pollen fertility
restoration-1 12 RY,HK,NA 141,151,152
fgl(fl) faded green leaf 12.5 KY 33,37,44,152
Ef-1
(=Ef-2) Earliness-1 28 RY,CH 138,141,182,
185,186
Unlocated genes
Bph-3 Brown plant-
hopper-3 trisomic C NA,IR 22,23,77
bph-4 brown plant-
hopper-4 30%-rk-2 NA,IR 22,23,77,
close to Bph-3
d-20 hayayuki dwarf triplo-10 HK 56,66
du-1 dull endosperm-1 trisomic C KY 35,44,143,196
Glh-3 Green leafhopper
resistance-3 34%-bph-4 IR 3,156,159
rk-2 round kernel-2 2.5%-TR7-9 KY 35,44,200
ygl* yellow green
leaf triplo-10 IR 79
d-33 group, chromosome 4, triplo-6
spl-1
(bl-12) spotted leaf-1 0 KY 33,44,200
rl-3
(-rl-1) rolled leaf-3 28 KY 37,44,200
Unlocated genes
d-33
(d-B) bonsaito dwarf trisomic A KY 33,37,44
du-4 dull endosperm-4 trisomic A KY 194
nal-3
(nal-2) narrow leaf-3 19%-TR3-4b KY,HK 33,200
Sdh-1 Shikimate dehyd-
rogenase-1 triplo-6, IR 27,126
trisomic A
sug group, chromosome-12, triplo-8
sug(su) sugary endosperm 0 KY 28,35,44,56
143,196
v-8 virescent-8 49 KY 35,44,56
Unlocated genes
Amp-2 Aminopeptidase-2 trisomic-D GI 27
An-4(t) Awn-4 5.0%-TR10-12b RY 139
d-51(d-
K-8) dwarf Kyushu-8 trisomic D KY 35
shr-2 shrunken
endosperm-2 trisomic-D KY 89,142,195
Stv-b Stripe virus
(St-2) resistance linked with NA 189,190,191
TR3-12
ur-2 undulate
rachis-2 trisomic D KY 35
z-4 zebra-4 trisomic D KY 35
___________________________________________________________
*Gene symbols unauthorized by the Committee.