III. Current linkage maps

Construction of current linkage maps are presented as shown in Fig. 1 and Table 3. In the linkage maps, the Kosambi mapping function was used to correct the recombination values between genes. In the table, recombination values are expressed as cM or percentages. Thus about 463 genes were allotted to the twelve groups and 185 marker genes were positioned on twelve chromosomes.

Molecular linkage maps are already constructed in several groups independently (Ref. 192, 219, 266, 385, 396, 539, 540. 572, 640, 644, 648, 650) and the integration of the different linkage maps has been progressed (Ref. 91-95, 192, 193, 590, 620, 631, 651). Comparative mapping and construction of synteny maps are progressed rapidly among different cereals and grasses (Ref. 3, 5, 147, 220, 338, 575). Depending on the information of the position of centromere, the orientation of the maps and allocation of genes to short and long arms are going to be dissolved.
 
 


 
 


 
 

Fig. 1 1995 linkage maps of rice.

Figures in parentheses show the number of marker genes assigned to the chromosome, but not given in the map.(as the exact location remains undetermined).

 Report of Committee on Gene Symbolization
Genes assigned to the linkage groups
Chromosome 1 z-12 bc-2 S-A-1 z-4 Hbv
al-8 bd-I S-B-2 Lec
Ald-2 Chromosome 3 Cht-2 S-1 Chromosome 9 Pi-ta
Amy1B Actin-I Em S-8 Adh-2 Pi-6(t)
Arf-2 bl-4 er S-10 Amy3A/B/C Pro-1
chl-5 Cat-AI Est-13 sbe-I chs-I(t) S-15
d-2 d-14 eui Se-5 cyc-l
d-26 ga-2 gl-1 spl-4 d-57
d-54 ga-3 Glh-6 Stv-a du-2120(t)
d-55 L glup-4 Un-a Est-3
Dm-l Pms-2 1-Pl-1 Wc Est-12
Est-5 Pox-cA M-Pox-1 Xa-7 Glup-l
Est-10 rl-5 Mdh-3 z-13 glup-2
ga-9 s-e-I ms-14 zn gm-l
g.f-2 sh-4(t) 0c-2 Man
Glu-l Shp-4 Pox-I Chromosome 7 ms-10
Glu-1t st-3 Pro-2 Acp-4 R5s-3
Glu-2t v-5 Pro-3 Beta-amy-1 R45s-l
Glu-3t v-7 Pro-5 d-7
Glu-4t z-9 Rk-3 d-60 Chromosome 10
glu-3(t) sd-7(t) ds-3(t) Bph-3
Got-I Chromosome 4 sdg E-l bph-4
lcd-l al-5 Shp-3 Est-I du-l
I-Ps-b a/-7(t) wgl(t) Est-7 ef(t)
lgt An-I xa-5 Est-9 Glh-3
mp-l aul xa-13 ga-ll glu-2(t)
ms-m77(t) bph-2 ylb lp-i rDNA-2
Oc-l drp-l z-7 Mal-I rk-2
Prp-a drp-8 Mal-2 ygl
Rf-4 flo(t) Choromosome 6 ms-8
S-13 ga-10(t) al-I Pms-I Chromosome 11
S-16 ga-12 a/-9(t) Pox-3 D-2
salT glup-3 Amp-5 Pox-4 esp-3
sh-2 Gm-2 Amy2A Pro-4 Fdp-l
Tos-1 gpd-2 aph R5s-2 gal
tpi hpg-l bc-4 R.f-3 M-Pi-z
ts-a nal-I Cat-1 rl-6(t) nal-2
z-8 nal-5 chl-7 S-7 PBR
Pi-5(t) Cht-l S-9 Pi-f
Chromosome 2 Pin-1 Cht-3 se-2 Pi-is-1
ae-3(t) pl-2W d-21 spl- 9 Pi-kur-2
Amp-l rk-l drp-6 st-8 Pi-se-1
AmyIA/C rl-2 du-2035(t) Un-b Pi-1
bc-5 s-c-2 du-EM47(t) wp-l Pi-7(t)
cyc-2 s-e-2 dw-l Wph-l R5s-1
D-l shp-5(t) Enp-l xa-k S-3
Ef-x spr-l fc-2 z-10 Stv-b
Glu-5t ssk ga-4 Xa-3
Glu-6t st-7 ga-5 Chromosome 8 Xa-4
Glu-7t Wh Got-2 Amp-4 Xa-10
Glu-8t Xa-14 1-PI-2 Amy3D/E Xa-a
Glu-9t ylm Ldh An-4(t) Xa-h
Glu-10t z-5 mp-2 chl-8
glu-I(t) Pox-5 chl-9 Chromosome 12
Got-3 Chromosome 5 PS d-51 Ald-3
gpd-l Ald-1 rcn-5 shr-2 Bph-l
ms-17 An-2 s-a-I sk-2(t) Bph(t)
Pi-b Arf-l s-c-l ur-2 du-4
z-11 ATP s-d-I xa(t) ga-13

Table 3. List of marker genes assigned to the respective linkage group
 

Gene Name Gene locus Institution1 Literature No.
Group 1
v-6 virescent-6 o KY 126,139,146
M extra glume 17 5.3cM to XNpb97 KY 129,137,146,620
ga-8 gametophyte gene-8 17 HK 304
spl-6 spotted leaf-6 24 5.4cM to XNpbl74 KY 136,137,146,620
lax(lx) lax panicle 30 6.6cM to XNpbll3 HK.KY 129,137,146,292, 298,396,631
ms-m67(t)* male sterile (Milyang 67ms) 31 - 491,492
rl-1 rolled leaf-1 42 HK 153,301
al-4 albino-4 43 KY 133,146
d-10(d-15. d-16) kikeibanshinriki or toyohikari-bunwaitillering dwarf 53 KY.HK 129,146,503
chl-6 chlorina-6 65 KY 126,139,146
ga-7 gametophyte gene-7 72 HK 242,249
sd-l(d-47) dee-geo-woo-gen dwarf 76 0.3cM to RG220 NA,HK 10,29,30,49,179, 241,314,337,490, 565,566,631
Est1-2* Esterase 1-2 77 OcM to RG220 - 29,30
A Anthocyanin activator 83 4.4cM to XNpbl21 HK,KY 146,192,281, 298,457
Rd Red pericarp and seed coat 84 fs-2 181,298
shr-1 shrunken endosperm-l 85 KY 262,442,602
Shp-1 Sheathed panicle-1 86 HK 153,244,256
rl-4(rl-2) rolled leaf-4 104 9.4cM to XNpb368 HK.KY 131,132,139,146, 262,620
Pn Purple node 114 HK.KY 146,181,298
Pau Purple auricle 123 - 30,274,480
d-18(d-25)- hosetsu dwarf (d-18h) of kotake-tamanishiki dwarf(d-18k) 131 4.1cM to XNpb96 KY.HK 126,134,139,146, 189,464,489,617, 620
fs-2 fine stripe-2 149 8.7cM to XNpb216 HK.KY 134,139,146,504, 620

 
 
 
(Continued)
Gene Name  Gene Locus  Institution 1)  Literature No.
Unlocated genes
al-8 albino-8  11%-d-18k KY 133,139,146
Ald-2* Aldolase-2  1.4cM-XNpbll3 NA 50,196,396
Amy1B* Alpha-amylase-1B  1.0cM-RG146x IR 365,376,386
Arf-2* ADP-ribosylation factor (ARF)-2 2.1cM-0c-1 NA 196
chl-5 chlorina-5  13.2%-eg KY 139,146
d-2 ebisu dwarf  15.6cM-XNpb359 HK,KY 96,181,298
d-26 7237 dwarf 37%-A - 81,83
d-54(d-K-5) dwarf-Kyushu-5  25%-1ax KY 139,146
d-55(d-K-6) dwarf-Kyushu-6  13%-eg KY 139,146
Dm-l* Short culm showing dm type-1 39%-d-18k NG 393
Est-5 Esterase-5 triplo-1 IR 369,589
Est-10 Esterase-10 12.6CM-RG220 - 18,19,20,640
ga-9 gametophyte gene-9 l.3%-d-18k HK 249
gf-2 gold furrows of hull -2 triplo-1 IR 401
Glu-1(SrP) Rice glutelin-1  17%-sd-1 NA 76,312,313,314, 350,508
Glu-4t.lt.2t.3t* Glutelin subunits (lt,2t,3t,4t) near XNpb343 Glutelin subunits (1t, 2t, 3t, 4t) near XNpb343 441
glu-3(t)* lack of glutelin subunit-3  10.2cM-C250 NA 99
Got-1 Aspartate aminotransferase-1  triplo-1 IR 369,589
Icd-l Isocitrate dehydrogenase-1 triplo-1 IR 369,589
I-Ps-b Inhibitor for purple stigma linked with A - 82
lgt. long twisted grain 16%-d-26 - 81
mp-l multiple pistil -1  triplo-1 IR 228,367
ms-m77(t)* male sterile(Milyang 77ms)  15%-mp-l - 491,492
Oc-1* Oryzacystatin-1  l.lcM-XNpb92 NA 196
Prp-a(Pp) Purple pericarp  7.2%-A HK 84
Rf-4*(Rf-2) Fertility restoration-4 near RG532 - 235,545,637
s-13 Hybrid sterility-13 (Pollen killer)  near A Gl 649
s-16 Hybrid sterility-16  15 20%-Est-5 KT 581
salT* salt tolerance  near CD0548 - 35,540
sh-2 shattering-2  l1%-sd-1 near X Npbl74 NA 314,323,337
Tos-1* Retrotransposon-1 26%-sd-1 NA 49,77
tpi* triophosphate isomerase (cloned gene)  near C146 NA 50
ts-a twisted stem  23%-A - 81

 
 
 
 
(Continued)
Gene Name  Gene Locus Institution 1) Literature No.
z-8 zebra-8 triplo-1 IR 400,401
Group 2
d-29(d-K-l) short uppernost internode dwarf 0 KY.HK 132,134
tri triangular hull 12 16.7cM to XNpb250 KY,HK 130,146,296,620
bc-3 brittle culm-3 25 KY 132,134,145
bl-1 brown leaf spot-1 34 10.3cM to XNpb250 HK.KY 145,298,620
chl-10 chlorina-10 55 KY 145
d-5 bunketsu-waito tillering dwarf 60 HK 181,298
gh-3 gold hull and internode-3 70 KY 145
d-32 (d-12. d-K-4) dwarf Kyushu-4 116 KY 128,145
Rf-2 Pollen fertility restoration-2 132 RY 468,470,587
d-30(d-W) waisei-shirasasa dwarf 135 near XNpb227 KY.HK 91,130,134, 145,631
gh-2 gold hull and internode-2 177 KY.HK 130,134,138,145, 401
spl-2(bl-3) spotted leaf-2 197 9.2cM to XNpb349 KY 92,134,137,145
Unlocated genes
ae-3(t)* amylose extender-3 triplo-2 IR 166
Amp-l Aminopeptidase-1 triplo-2 19.4cM-XNpb223 IR.NA 306,369,396,569
AmylA/C* Alpha-amylase-IA/C 9.2CN-RG95 IR 365,376,386
bc-5 brittle node triplo-2 IR 173,401
cyc2* cyclophilin-2 near RZ957 - 540
D-1* Dominant lethal from Q.longistaminata 39%-Amp-l IR 57
Ef-x* Earliness-x 18%-TR2-9 RY 426,434
Glu-5t* Glutelin subunit-5t 10%-XNpb227 KY 441,574
Glu-6t.7t.8t* Glutelin subunits (6t,7t,8t) 0.7%-Glu-5t 2.2%-XNpb21 KY 441,574
Glu-9t* Glutelin subunit-9t near XNpb227 KY 441
Glu-10t* Glutelin subunit-10t near Glu-9t KY 441
glu-1(t)* lack of glutelin subunit-1 near XNpb243 NA 98,99
Got-3 Asparate aminotransferase-3 triplo-2 IR 369,453
gpd-1* glyceraldehydephosphate dehydrogenase-1 near C1061 NA 50

 
 
(Continued)
Literature No.
Gene Name Gene locus  Institution 1)
ms-17 male sterile-17 35%-gh-2 KT 206,207
Pi-b(Pi-s) Pyricularia oryzae resistance-b 5.8%-TR2-10 OcM-R1792 NA 71,203,277, 451,471
z-11 zebra-ll trlplo-2 IR 400,401
z-12 zebra-12 triplo-2 IR 400,401
Group 3
chl-l chlorina-1 0 7.1cM to XNpbl64 KY 130,134,144,358, 396,620
Gdh-l Glutametedehydrogenase-1 4 Gl 115,120,122, 123,287
Nal-6 Narrow leaf-6 4 KY 144
Pgi-1 (Pgi-a) Phosphoglucose isomerase-1 12 near C217 IR,GI 120,122,123, 322,374.375
chl-3 chlorina-3 20 KY 144,358
fc-1 fine culm-l 42 10.9cM to XNpb249 KY 132,134,138,144, 358,620
Mi Minute grain 60 HK 512,517,524, 527,528
v-1 virescent-1 61 KY,HK 132,134,144,148, 149,358
bc-l brittle culm-1 80 HK.KY 144,298
ms-7 male sterile-7 80 KT 206,207
Lk-f 'Fusayoshi' long grain 101 HK, OK 256,512,516. 517,527,529
chl-2 chlorina-2 III KY 134,136,358
v-2. virescent-2 III KY 134,140,144,358
An-3 Awn-3 112 HK 298,421,517,524
al-10 albino-10 115 KY 140,144
st-6(t) stripe-6 122 HK 254
d-56(d-K-7) dwarf Kyushu-7 131 KY 140,144
lhs (lhs-2,op) leafy hull sterile 137.5 KY,HK,IR 80,127,170,191, 256
dl(lop) drooping leaf 138 16.6cM to XNpb394 KY,HK 130,137,138,144, 192,256,282,358
drp-4 dripping-wet leaf-4 145 KY 140,141,144
scl-3(bl-14) spotted leaf-3 155 15.OcM to XNpbl73 KY 134,137,138,144, 620
drp-3 dripping-wet leaf-3 dl(lop) KY 140,141,144

 
(Continued)
Gene Name Gene locus  Institution 1) Literature No.
z-3 zebra-3 155 KY 136,140,144
d-52(d-K-2) dwarf Kyushu-2 155 KY 136,140,144
Hg Hairy glume 159 near RG348 HK 182,298,299,631
d-20 hayayuki dwarf 188 HK 174,189,517,524
Unlocated genes
Actin-1* Actin-1 near CD0337 - 540
bl-4 brown leaf spot-4 29%-bc-l HK 504
Cat-AI* Catalase-AI (cDNA clone) 1.4cM-XNpb279 NA 195
d-14(d-10) kanikawa-bunwai tlllering dwarf 32%-dl HK 503
ga-2 ganetophyte gene-2 11%-dl NA.KY 302,308
ga-3 gametophyte gene-3 34%-dl NA.KY 302,308
L* Lethal factor 0.2gcM-XNpb23 NA 28
Pms-2* Photoperiod-sensitive male sterility-2 near RG191 - 635
Pox-cA* Peroxidase-cA (cloned gene) l.lcM-XNpb244-2 NA 194
rl-5(rl-3) rolled leaf-5 13%-chl-l KY 140
s-e-1 hybrid sterility-e 16%-bc-l Gl 346
sh-4(t)* shattering-4 near XNpb40 NA 52
Shp-4(Gb) Sheathed panicle-3 27%-bc-l HK 73,474
st-3(stl) stripe-3 1.1%-bc-l KY 140
v-5 virescent-5 2.0%-chl-l KY 141,144,358
v-7 virescent-7 1. 7%-bc-l KY 140
z-9 zebra-9 13cM-Pgi-l IR 382,400,401
Group 4
d-3 bunketsu-waito tillering dwarf 0 HK 181,298
st-5 stripe-5 3 HK 246,256
Pl Purple leaf 41 HK.KY 185,298,300,501
Prp-b(Fb) Purple pericarp 41 19.0cM to RG329 - 84,642
Pi(t) Pyricularia oryzae resistance 46 - 83
flo-2 floury endosperm-2 63 HK.KY 166,243,443
lg 1iguleless 73 3.4cM to XNpbl97 HK.KY 247,256,298, 396,620
ga-6 ganetophyte gene-6 77 HK 242,252
st-4(ws-2) stripe-4 78 HK 242

 
 
 
Gene Name Gene Locus Institution 1) Literature No.
Ps-1 Purple stigma-1 79 Gl 348,500
{•i-Kur-I* Pyricularia oryzae resistance-kur-1 82 YA 61
d-42 liguleless dwarf 83 HK 85,183
Spr-3(t) Spreading panicle-3 86 Gl 39,414
Sh-3 Shattering-3 88 Gl 39,414
Ph=Bh-c(Po) Phenol staining 94 0.lcM to V17 HK,KY,GI 7,221,231,297, 377,396,540,640
Xa-l(Xe) Xanthomonas campestris pv. oryzae resistance-1 100 0cM to Y03700 NA 397,594,623, 624,626.627
Xa-12(Xar-kg) oryzae resistance-12 102 NA 326,593,594
Xa-2 Xanthomonas campestris pv. oryzae resistance-2 104 2.0cM to XNpb264 NA 43,397,626
nal-4(nal) narrow leaf-4 105 611
d-31 tai chung-155 irradiated dwarf 112 - 611
Pr Purple hull 118 16.8cM to RG163 HK.KY 181,298,631 642
Ps-2 Purple stigma-2 122 Gl 81,82,348
P Colored apiculus 131 HK 281,298,348,457
1118-3 malformed spikelet-3 140 HK 511,518,522
rcn-2 reduced culm number-2 154 HK 256,511,522,523
drp-5 dripping-wet leaf-5 158 KY 445,447
d-ll (d-g) shinkane-aikoku or nohrin-28 dwarf 158 11.0cM to XNpb49 KY.HK 130,298,620,631
lk-i -l IRAT 13' long grain 168 HK 187,256,515, 522,530
Unlocated genes
al-5 albino-5 34%-lg KY 133
al-7(t) albino-7 31%-lg KY 133
An-1 Awn-1 5. 4%-d-ll HK 298
aul auricleless triplo-4 IR 228
bph-2 brown planthopper resistance-2 near Bph-l (chr.l2) NA,IR 100,101,476
drp-l dripping-wet leaf-1 39%-d-2(chr.l) HK 301
drp-g dripping-wet leaf-8 28%-lg KY 447
flo(t)* floury endosperm triplo-4 IR 166
ga-10(t) gametophytegene-10 27%-lg HK ga-10(t)

 
 
(Continued)
Gene Name Gene locus Institution 1) Literature No.
ga-12 gametophyte gene-12 2.1%-shp-5(t)
glup-3 (esp-7) glutelin precursor-3  trisomic-4 KY 125,449
Gm-2 Gall midge resistance-2  1.3 cM-RG329 IR 26,178,279,395
gpd-2* glyceraldehydephosphate dehydrogenase-2  near C377 NA 50
hpg-l* high preproglutelin-1  13.3cM-L102 NA 98
nal-l narrow leaf-1  25%-d-2(chr.1) HK 282
nal-5(nal-l) narrow leaf-5  9.5%-lg KY 132,134
Pi-5(t) Pyricularia oryzae resistance-5  near RG788 IH 582
Pin-1 Purple internode-1  31%-Pl HK 284
pl-2(t) purple leaf-2  triplo-4 IR 401
rk-1 round kernel-1  35% -lg KY.HK 131,132,134
rl-2 rolled leaf-2  35%-d-2(chr.1) HK 282
s-c-2 hybrid sterility-c  31%-Ph Gl 344
s-e-2 hybrid sterility-e  15%-lg Gl 346
shp-5(t) sheathed panicle-5 near d-2(chr.1) HK 250
spr-1 spreading panicle-1  27%-Pl HK 186
ssk(sk) malformed semisterile  6.8%-Pl - 66
st-7 stripe-7 triplo-4 IR 401
Wh White hull  8.0%-lg HK 150,298
Xa-14 Xanthomonas campestris pv oryzae resistance-14 NA 541
ylm yellow leaf margin  10%-lg KY 132,134
z-5 zebra-5  11%-lg HK 184
Group 5
gh-1 gold hull and internode-1  0 HK.KY 144,298
nl-2 neck leaf-2  6 KY 132,134,143
d-l daikoku dwarf  30 near XNpb105 HK.KY 95,143,181,276, 298,617
st-2(gw) stripe-2  49 HK 298
al-3 albino-3  51 KY 133,143
spl-8(bl-8) spotted leaf-8  51 KY 134,137,143
al-6(t) albino-6  56 KY 133
flo-l floury endosperm-l  63 KY 166,443,444
ops open hull sterile  69 KY 129,134,143
v-10 virescent-10  77 KY 444,446

 
 
 
(Continued)
Gene Name Gene locus  Institution 1) Literature No.
bg1 bright green leaf 82 KY 134,141,143
ri verticillate rachis 85 HK.KY 129,143,298,617
spl-7 spotted leaf-7 100 near XNpb81 KY 95,134,136,137, 143
nl-1 neck leaf-1 110 0cM to XNpb188 HK.KY 143,192,298, 431,621
al-2 albino-2 111 KY 133,137,143
Unlocated genes
Ald-1* Aldolase-1 0.8cM-Cht-2 7.7cM-C13 NA 50,196,396
An-2 Awn-2 33%-gl-l HK 298,422
Arf-1* ADP-ribosylation factor (ARF)-1 1. 7cM-Oc-2 NA 196
ATP* ATPase near RG697 - 540
bc-2 brittle culm-2 triplo-5 IR 401,504
bd-1 beaked lemma 22%-gI-1 - 274,422
Cht-2* Chitinase-2 2.9cM-XNpbl05  NA 320,396
Em* ABA-regulated gene/expressed in embryogenesis trisomic-5 IR 376
er(o) erect growth habit 38%-gh- 1 HK 504
Est-13 Esterase-13 17.9cM-RG13 - 19
eui elongated uppermost internode 27%-nl-l  HK 248,253,390, 391,643
gl-1 glabrous leaf and hull 12%-TRI-5d 10.5cM-XNpb396 HK.KY 298,431,621,631
Glh-6 Green leafhopperresistance-6 tripro-5 IR 383,550
glup-4 glutelin precursor-4 trisomic-4 KY 125
l-Pl-1 Inhibitor for purple leaf-1 31%-gh-1 HK 181,298,300
M-Pox-1 Modifier for Pox-1 near gl-l CH 360,362
Mdh-3* Malate dehydrogenase-3 MAAL 5  IR 177
ms-14 male sterile-l4 11%-nl-1 KT 205,206
Oc-2* Oryzacystatin-2 0.4cM-XNpb255  NA 196
Pox-1 Peroxidase-1 38%-nl-1 CH.GI 288,362,363
Pro-2* Prolamin-2 6.8%-XNpb251 KY 441
Pro-3* Prolamin-3 2.2%-Pro-2 KY 441
Pro-5* Prolamin-5 3.0%-Pro-3 KY 441
Rk-3 Round Kernel-3 triplo-5 IR 401
sd-7(t) semidwarf-7 O%-d-1 CH 562, 564

 
 
Gene Name Gene locus Institution Literature No.
sdg* semidwarf (BRGPC) 4.3cM-RZ182 227,638
Shp-3(Ga) Sheathed panlcle-3 37%-nl-l - 73,474
wgl(t)* spikelet width OCM-W168A NA 157
xa-5 Xanthomonas campestris pv oryzae resistance-5 trisomic-5 near gl-l. and XNpb396 IR RG207 267,368,478, 484,618,621
xa-13 Xanthomonas campestris pv oryzae resistance-13 9. 7%-xa-5 IR 331,394
ylb yellow banded leaf blade 32%-nl-l - 82
z-7 zebra-7 triplo-5 IR 400,401
Group 6
d-4 bunketsu-waito tillering dwarf 0 HK 181,298
I-Pl-4 Inhibitor for purple pericarp 9 HK 181,187
wx(am) glutinous endosperm 22 l.lcM to C425A HK.KY 74,91,93,225, 298,405,417, 443,540
dp-l depressed palea-1 24 10.8cM to XNpb209 HK.KY 94,130,294
ms-1 male sterile-1 27 - 66
En-Se-1 Enhancer for photosensitivity (Se-I) 28 Gl 410,412
Pgd-2 Phosphogluconate dehydrogenase-2 29 GI,IR 117,122,123, 177,287,453
v-3 virescent-3 30 KY 134,358
ga-1 gametophyte gene-1 36 KY 135,309
lcr Low crossability 41 Gl 411,412
C Chromogen for anthocyanin 44 16.4cM to XNpbl65-l HK 181,192,298, 317,457
S-5 Hybrid sterility-5 48 4.4cM to RG213 NA.KT 103,104,105, 579,598
Amp-3(Amp-l) Aminopeptidase-3 53 1.7%-RG213 GI.IR 16,122,123,369, 403
Est-2 Esterase-2 54 1.7% to RG213 NA.IR 16,18,303,305, 307.369,579,698
bl-3 brown leaf spot-3 55 HK 604
alK alkali degeneration 56 1.1 cM to C1478  KY.NA 210,231,598
st-l(ws) stripe-1 65 KY.HK 294

 
 
 
Gene Name Gene locus  Institution Literature No.
Pgi-2 (Pgi-b) Phosphoglucose isomerase-2 67 7.9% to RG213 GI,IR 16,122,123,322, 359,369,398, 403,598
Se-l (Lf, Lm, Rs) Photosensitivity-1 67 4.7%. to XNpb294 and 0.3cM to C235 NA 22,48,210,339, 340,341,355,359, 534,540,598,613, 614,615
Pi-z (Pi-2) Pyricularia oryzae
resistance-z		 69 2.9cM to XNpb294 and 2.1cM to RG64 NA 48,64,78,108, 110,201,203, 237.271,451, 452,471,630
S-6 Hybrid sterility-6 74 Cl 407,409
d-9 Chinese dwarf 76 HK 181,187
rcn-1 reduced culm number-1 77 HK 513,522
gf-1 gold furrows of hull-1 80 HK 152
chl-4 chlorina-4 82 KY 134,358
bl-2(bl-m) brown leaf spot-2 83 HK 150,301
fs-1 fine stripe-1 95 HK 190,298
Cl Clustered spikelets 96 HK 150,298,367
ms-9 male sterile-9 100 KT 206,425,429
HI-a Hairly leaf 118 HK 182,298,299.522
Ur-1 Undulate rachis-1 125 HK 181,298
d-58 small grained dwarf 139 HK 514,517,522
Unlocated genes
al-l albino-1 7.1%-wx KY 133
al-9(t) albino-9 trisomic-6 KY 141
Amp-5 Aninopeptidase-5 15.OcM-Est-2 - 17
Amy2A* Alpha-amylase-2A 6.3cM-HG433 - 365,376,386
aph apiculus hairs linked with Est-2 and Pgi-2 GI 436,438
bc-4 brittle culm-4 triplo-6 IR 228
Cat-1 Catalase-1 22%-Pox-5 8.1cM-BG244 IR,GI 118,120,589,640
chl-7 chlorina-7 27%-Pi-z 13%-Pgi-2 NA 228,357,399
Cht-I* Chitinase-1 0.4cM-XNpb342 NA 320,396
Cht-3* Chitinase-3 0.4cM-XNpb342 NA 320,396
d-21 aomorimochi-14 dwarf 8.3%-wx HK 189
drp-6 dripping-wet leaf-6 15%-fc-2 KY 445,447
du-2035* dull endosperm (2035) triplo-6 IR 15%-fc-2

 
 
 
 
(Continued)
Gene Name Gene locus  Institution 1) Literature No.
du-EM47* dull endospern (EM47) tri plo-6 IR 166
dw-l(fh) deep water tolerance-1 30%-Se-l - 149,373
Enp-l* Endopeptidase-1 2.2%-Cat-l IR 369
fc-2 fine culm-2 18%-C KY 445,447
ga-4(ga-A) gametophyte gene-4 34%-wx HK.KY 283,309,310
ga-5(ga-B) gametophytegene-5 27%-wx HK 283
Got-2 Aspartateam inotranspherase-2 31%- Pgi-2 GI,IR 369,453
1-Pl-2 Inhibitor for purple leaf-2 10%-1-Pl-4 HK 181,187,300
Ldh* Lactate dehydrogenase 0.9cM-C1003B NA 22B.226
mp-2 multiple pistil-2 triplo-6 IR 228.366
Pox-5 Peroxidase-5 39%-Pgi-2 IR 589
PS* Photoperiod sensitivity 23%-Pgi-2 0cM-RG64 IR 239,398
rcn-5 reduced culm number-5 22%-C HK 520
s-a-1 (s1, x1 hybrid sterility-a 21%-wx Gl 343,346
s-c-l hybrid sterility-c 8.6%-C Gl 344
s-d-l hybrid sterility-d 33%-wx GI 346
S-A-I(A-I) Hybrid sterillty-A 9.5%-C Gl 347,349
S-B-2(B-2) Hybrid sterility-B 28%-wx Gl 347,349.
S-1 Hybrid sterility-1 near C Gl 408,416
S-8 Hybrid sterility-8 ll%-Cat-1 KT 579,596,597
S-10 Hybrid sterility-10/gamete eliminator 0.16%-wx Gl 418,420
sbe-1* starch branching enzyme-1 0.3cM-G342 NA 168,316
Se-5 Photosensitivity-5 27%-Pi-zt 23cM-Pgi-2 NA 616
spl-4(bl-15) spotted leaf-4 2.5%-dp-l 5.0cM-XNpb209 KY 94,134,137
Stv-a(St) Stripe disease resistance-a 38%-wx NA 584,585,586
Un-a Uneven grain 22%-Cl-a - 548
Wc* Wide compatibility 5.9cM-Est-2 IR 216,234
Xa-7 Xanthomonas campestris pv oryzae resistance-7 8.8X-Q1091 NA 156,324,478,484
z-13 zebra-13 triplo-6 IR 400,401
zn zebra necrosis 20%-C HK 184,256
Group 7
d-6 ebisumochi or tankanshirasasa dwarf 0 near XNpb50 HK.KY 0 near XNpb50

 
 
Gene Name  Gene locus Institution 1) Literature No.
g-1 long sterile lemmas-1 6 24.9cM to XNpb85-l HK.KY 92,95,141,298, 518
spl-5(bl-6) spotted leaf-5 31 near XNpb85-l KY 95,132,137,141
Rc Brown pericarp and seed coat 44 OcM to C67A HK.KY 141,181,231,298, 505,631
v-11 virescent-11 45 near XNpb85-l KY 95,444,446
z-6 zebra-6 47 HK 245,256
rfs rolled fine striped leaf 58 1.4cM to XNpb20 HK.KY 134,141,192,256
slg slender glume/mutator 64 3.0% to XNpb33 KT 209,546
ge giant embryo 79 KY.HK 79,134,442,444
esp-l(rsp-1) endosperm storage protein-1 88 KY 211,212,213,215, 440
Unlocated genes
Acp-4 Acid phosphatase-4 near R2387 IR 65,540
Beta-Amy-1 Beta-amylaseisozyme-1 trsomic-7 KY 472,473
d-7 heiei-daikoku or cleistogamous dwarf 39%-d-6 HK 181,298
d-60 dwarf (Hokuriku 100) trisomic-7 KT 537,553
ds-3(t) desynapsis-3 tripro-7 KY 197,609
E-1=m-Ef-1* Earliness-1 trisomic-7 23%-Rc KT,CH 351,352,354,355 498,558,559
Est-1 Esterase-1 triplo-7 NA,IH 16,65,303,306, 369
Est-7 Esterase-7 24%-Acp-4 IR 65,453
Est-9 (Est-cl) Esterase-9 triplo-7 0.4%-Rc GI,IR 229,369,374, 375,403
ga-ll gametophytegene-ll 23%-Est-9 KT 229,230
lp-1 long palea-1 12%-Un-b - 548
Mal-l Malate dehydrogenase (MADP)-1 20.3cM-RGS28 gi.ir 16,114,540,640
Mal-2 Malate dehydrogenase (MADP)-2 1.8cM-Ra511 - 21,640
ms-8 male sterile-8 20%-rfs KT 205,206,207
Pms-1* Photoperiod-sensitive malesterility-1 4.3cM-RG477 - 635
Pox-3 Peroxidase-3 5%-Pox-4 IR 361,369
Pox-4 Peroxidase-4 31%-Est -l IR 369,453
Pro-4* Prolamin-4 1.6%-XNpb338 KY 441

 
Gene Name Gene locus Institution 1) Liiterature No.
R5s-2* 5s ribosomal DNA-2 short arm NA 33
Rf-3*(Rf-l) Fertility restoration-3 near XNpb379 - 235,545,637
rl-6(t) rolled leaf-6 12%-lp-1 - 547
S-7 Hybrid sterility-7 9%-Rc KT 577,579,596,597
S-9 Hybrid sterility-9 19%-Est-l KT 578
se-2 photosensitivity-2 23%-g-1 - 628
spl-9 spotted leaf-9 triplo-7 IR 137,401
st-8 stripe-8 4cM-wp-l IR 401
Un-b Uneven grain 18%-g-1 - 548
wp-1 white panicle-1 triplo-7 IR 401
Wph-l White-backed planthopper resistance-1 near RG146B IR 8,268,479,540
xa-k* Xanthomonas campestris pv. Oryzae resistance triplo-7 - 232
z-10 zebra-10 OcM-wp-l. trlplo-7 IR 400,401
Group 8
Amp-2 Aminopeptidase-2 0 8.3cM to RG136 GI.IR 120,369,589, 640
Pi-11 (t)* (Pi-zh) Pyricularia oryzae resistance-11 30 near RZ617 14.9cM to Bpl27 IR 540,640
sug(su) sugary endosperm 0 near XNpb397 KY 95,134,142,174, 442,602
v-8 virescent-8 115 near XNpb278 KY 95,134,142,174
Unlocated genes
Amp-4 Aminopeptidase-4 triplo-8 IR 257,589
Amy3D/E* Alpha-amylase-3D/E ll.lcM-RGI IR 365,376,386
An-4(t)* Awn-4 5.0%-TR7-8b RY 427
chl-8 chlorina-8 triplo-8 IR 172,401
chl-9 chlorina-9 triplo-6 IR 172
d-51(d-K-8) dwarf Kyushu-8 trisomic-8 KY 134,142
shr-2 shrunken endosperm-2 trisomic-8 KY 263,439
sk-2(t) (scl,fgr) scented kernel-2 6.7%-XNpbl26 2.1cM-RG28 NA,IR 4,540,606
ur-2 undulate rachis-2 trisomic-8 KY 134,142
xa(t)* Xanthomonascampestris pv. Oryzae

resistance

 3.8cM-RG136 - xa(t)*

 
 
 
 
(Continued)
Gene Name Gene locus Institution 1) Literature No.
z-4 zebra-4 trisomic-8 KY 134,142
Group 9
I-Bf Inhibitor for brown furrows 0 11.lcM to XNpb36 HK,KY 92,94,131,134, 297,298,423
lam(t) low amylose endosperm 0 HK 180
Dn-1 Dense panicle-1 45 HK.KY 298
dp-2 depressed palea-2 45 3.3cM to XNpb385 HK.KY 129,131,192,282
drp-2 dripping-wet leaf-2 51 0cM to XNpb385 KY 94,129,134,192
Bp Burlush-like panicle 63 1.4cM to XNpb339 KY 131,134,192
Unlocated genes
Adh-2* Alcohol dehydrogenase-2 trisomic-9 IR 376
Amy3A/B/C* Alpha-amylase-3A/B/C 9.4cM-RZ228 IH 365,376,386
chs-l(t)* chlorosis caused by low temperature (17ºC)-l 27%-dp-2 KY 34
cyc-1* cyclophilin-1 4.6cM-RZ404 - 540
d-57(d(x)) dwarf 21%-Dn-1 - 83,610
du-2120* dull endosperm (2120) triplo-9 IR 166
Est-3 Esterase-3 16.4%-XNpb257 NA.IR 303,369,605
Est-12 Esterase-12 29.1cM-RZ12 - 19
GIUP-I(GUP-I) Glutelinprecursor-I trisomic-9 KY 450
glup-2(gup-2) glutelin precursor-2 trisomic-9 KY 450
gm-1 (pd.sgm) gall midge resistance 35%-I-Bf - 423,424,460
man Mannan in endosperm cell wall 4.3cM-XNpb293 NA 607,608
ms-10 male sterile-10 5%-Dn-l KT 205,206,207
R5s-3* 5S ribosomal DNA-3 short arm NA 33
R45s-l*(rDNA-l) 45s ribosomal DNA-1 1.0cM-XNpb315 NA 51,265,266,540
Group 10
pgl pale green leaf 0 3.5cM to XNpbl27 KY 92,93,131,466, 617
spl-10 spotted leaf-10 8 10.9cM to XNpbl27 KY 92,93

 
 
 
 
(Continued)
Gene Name Gene locus Institution 1) Literary No.
Rf-1 Pollen fertility restoration-1 12 7.5cM to XNpb291 RY.HK.NA 53,432,465,466, 467,631
fgl(fl) faded green leaf 12.5 OcM to XNpb291 KY 131,134,192,466, 605,617
Ef-l.(=Ef-2) Earliness-1 28.5 RY.CH 432.433,435, 558,561,569,571
Unlocated genes
Bph-3 Brown planthopper resistance-3 trisomic-10 NA.IR 100,101,223,476
bph-4 brown planthopper resistance-4 30%-rk-2 near Bph-3 NA.IR 100,101,223, 476,477
du-l dull endosperm-l trisomic-10 KY 134,442,443,604
Ef(t)* Earliness introduced from O. australiensis 10.0cM-CD098 IR 113
Glh-3 Green leaf hopper resistance-3 34%-bph-4 IR 12,477,485
glu-2(t)* lack of glutelin subunit-2 6.8cM-G1082 NA 99
rDNA-2* ribosomal DNA-2 0-llc M-XNpb32 NA 33,51,265
rk-2 round kernel-2 2.5%-TR10-11 7.5cM-pg1 KY 134,617
yg l yellow green leaf trlplo-10 IR 228
Group 11
Pi-k Pyricularia orvzae resistance-k 0 17.8% to G181 NA 64,155,202,203, 204,471
d-27(d-t) bunketsuto tillering dwarf 32 2.6cM to pTA818 KY.HK 1,132,134,138
Xa-21* Xanthomonas campestris pv oryzae resistance-21 37 2.2cM to pTA818 NA.IR 1,102,176,387, 388,389
z-2 drp-7 zebra-2 dripping-wet leaf-7 46 0cM to CD0365 64 KY KY 1,94,132,134, 138 445,447
la lazy growth habit 69 3.0cM to RG1094 HK.KY 1,192,298
v-4 virescent-4 80 KY 136,138,358
Pgd-1 Phosphogluconate dehydrogenase-1 85 near RG167 GI.IR 119,120,122,123 369.540,689
d-28(d-C) chokeldaikoku or long stemroed dwarf 95 KY 134,138
sp short panicle 103 7.7cM to XNpb320 KY.HK 130,134,138

 
 
 
 
Gene Name Gene locus Institution 1) Literature No.
Adh-l Alcohol dehydrogenase-1 104 7. 3% to RG118 IR.GI 1,16,117,122, 123,374,375,402
Pr-a Pyricularia oryzae resistance-a 105 NA 64,203,471
sh-1 shattering-l 108 HK 298
v-9 virescent-9 116 11.lcM to XNpbl83 KY 94,446
esp-2(rsp-2) endosperm storage protein-2 124 KY 211,212,215,440
z-l zebra-1 132 KY 131,132,134
D-53(D-K-3) Dwarf Kyushu-3 141 KY 134,136,138
Unlocated genes
D-2 Dominant lethal from O.sativa 37.3%-Pgd-1. IR 57
esp-3(rsp-3) endosperm storage protein-3 trisomic-11 KY 212,214,215
Fdp-l* Fructose-1, 6-diphosphatase-1 triplo-ll IR 16,381
gal (It) gametic letal 24%-la KT 537,553
M-Pi-z Modifier for Pi-z 11%-la YA 60
nal-2 narrow leaf-2 36%-la HK 282
PBR* Panicle blast resistance 10.8cM-CD0226 NA 46
Pi-f Pyricularia oryzae resistance-f 15%-Pi-k NA 471,555,633,634
Pi-is-l(Rb-4) Pyricularia oryzae resistance-is 23%-la YA 59
Pi-kur-2* Pyricularia oryzae resistance-kur-2 14%-la YA 61
Pi-se-l(Rb-l) Pyricularia oryzae resistance-se 9.5%-la YA 62,63
Pi-1 Pyricularia oryzae resistance-1 4.7%-Pi-k 3.5cM-NpB181 IR 110,237,271, 540
Pi-7(t) Pyricularia oryzae resistance-7 near RG16 IR 582
R5S-1* 5S ribosomal DNA-1 near RG167 NA 33,158,266,540
S-3 Hybrid sterllity-3 1%-la Gl 404
Stv-b Stripe disease resistance 3.0cM-XNpb257 NA 70,584,585.586
Xa-3 (Xa-w. Xa-4°Xa-6 Xa-9) Xanthomonas campestrispv. oryzae resistance-3 22%-d-27 2.3cM-XNpbl81 IR 43,325,326,327, 328,329,330,333 334,335,475,484 622,624
Xa-4(Xa-4a) oryzae resistance-4 near Xa-3 1. 7cM-XNpb78 IR 268,329,330,368 478,484,495,622 624,625,626
Xa-10 Xanthomonaas campestris pv oryzae resistance-10 27%-Xa-4 5.3cM-Oo72000 KY 619,626
28%-la triplo-ll oryzae resistance 28%-la triplo-ll 232,629

 
 
Gene Name Gene locus Institution 1) Literature No.
Xa-h* Xanthomonas campestris pv oryzae resistance 17%-Xa-a - 629
Group 12
acp-1 Acid phosphatase-1 0 IR.GI 42,65.116,117,118,120,122,123 369,589,640
Acp-2 Acid phosphatase-2 0 1.9cM to RG181A IR.GI 65,120,364,369, 589,640
Pox-2 Peroxidase-2 26 GI.IR 65,116,117,120, 121,122,123, 369,589
nal-3(nal-2) narrow leaf-3 29 KY,HK 131,134,192, 287,617
d-33(d-B) bonsai to dwarf 34 7.5cM to XNpbl48 KY 131,134,192,287
rl-3(rl-l) rolled leaf-3 36 near XNpb402 KY.IR 95,116,131,134, 287,617
spl-l(bl-12) spotted leaf-1 45 3.6cM to XNpb88 KY 92,95,116,131, 134,137,192,617
Sdh-l Shikimate dehydrogenase-1 49 4.9cM to XNpb402 IH.GI 65,116,120,122,123,306,369,374 375,396,461
Unlocated genes
Ald-3* Aldolase-3 near C1336 NA 50
Bph-l Brown planthopper resistance-1 10.9cM-X Npb248 NA.IR 100,101,476,647
Bph(t)* Brown planthopper resistance introduced from O. australiensis 3.7cM-RG457 IR 113,178
du-4 dull endosperm-4 trisomic-12 31%-d-33 KY 444,604
ga-13 gametophytegene-13 10%-Acp-l CH 384
Hbv Hojablanca resistance IR 178,554
lec* Lectin near RG190 IR 540
Pi-ta (=Pi-4a) Pyricularia oryzae resistance-ta 5%-spl-1 0cM-XNpb289 NA.IR 110,112,202,203237,271,278,392 452,471,582,630
Pi-6(t)* Pyricularia oryzae resistance-6 near RG81 IH 269,540
Pro-1* Prolamin-1 3.2%-XNpb88 KY 441
S-15 Hybrid Sterility-15 27%-Sdh-l KT 27%-Sdh-l
  1. Name and address of institution are listed in appendix.
 Appendix: Institution code

CH: Food Crops Research Institute, National Chung Hsing University, Taichung, Taiwan
            400, ROC
Gl: Genetic Stock Center, National Institute of Genetics, Mishima, 411 Japan. Fax
             81-559-81-6804
HK: Plant Breedking Institute, Faculty of Agriculture, Hokkaido University, Kita 9, Nishi
              9, Kita-ku, Sapporo, 060 Japan, Fax 81-1 1-706-4934
IR: Rice Germplasm Center, International Rice Research Institute, P. 0. Box 933, Manila,
              Pfilippines, Fax 63-2-817-8470 or 63-2-891-1292
KT: Plant Breeding Laboratory, Faculty of Agriculture, Kyoto University, Kitashirakawa.
              Sakyo-ku, Kyoto, 606 Japan, Fax 81-75-753-6025
KY: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Hakozaki,
              Fukuoka, 305 Japan, Fax 81-92-641-2928
NA:Gremplasm Center, National Institute of Agrobiological Resources, Tsukuba
              lbaraki-ken. 305 Japan, Fax 81-298-38-7408
NG: Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Nagoy
              University, Chikusa-ku, Nagoya, 464-01 Japan, Fax 81-52-781-4447
OK: Institute of Agricultural and Biological Science, Okayama University, Kurashiki.
               710 Japan, Fax 81 -864-21 -0699
RY: Plant Breeding Laboratory, College of Agriculture, University of Ryukyus,
                Nishihara. Okinawa, 903-01 Japan, Fax 81-9889-5-2864
YA: College of Agriculture, Yamagata University, Tsuruoka, 997 Japan, Fax 81-235-28-2853