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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