IV. Gene tagging

A number of molecular markers and agronomically useful genes are located on the RFLP maps as shown in Table 4. These information are important for marker-based gene cloning and marker-aided selection. By using molecular markers flanking the important genes, map-based gene cloning is progressing in bacterial blight disease resistance genes (626. 627), blast disease resistance genes (78, 271, 278) and the gene controlling gall midge resistance (279,645).

Table 4. List of genes tagged to molecular markers


Gene1) Name Locus2) Reference
Chromosome 1
eg  extra glume 5.3cM to XNpb97 and
9.7cM to spl-6
Yoshimura et al. 1992a
spl-6 spotted leaf-6 5.4cM to XNpbl74 Yoshimura et al. 1992a
Est-10  Esterase -10 12.6cM to RG220 and 28.9cM to RG536 Cai Wang 1994b,c
lax  lax panicle 6.6cM to XNpb113
near CD0251
Saito et al. 1991
Yu et al. 1992, Tanksley et al. 1993
Ald-2*  Aldolase-2 1.4cM to XNpb113
near C117
Saito et al. 1991 Fukuda et al. 1994
sh-2 shattering-2 close to XNpbl74 Ogi et al. 1993
Glu-4t, 1t, 2t, 3t*  Glutelin subunits near XNpb343 Satoh 1995
Arf-2* ADP-ribosylation factor(ARF)-2 3.0cM to XNpb370 and 2.1cM to Oc-1 Kishimoto et al. 1994c
Oc-1*  Oryzacystatin -1 Npb92 Kishimoto et al. 1994c
glu-3(t)* lack of glutelin subunit-3 10.2cM to C250 and 14.4cM to XNpb370 Iida et al. 1994
salT* salt tolerance near CDO548 Tanksley et al. 1993
Amy1B* Alpha-amylase-1B 1.0cM to RG146X and 14.4cM to RG173 Parco et al. 1994
sd-1  dee-geo-woo-gen dwarf near CDO962

2.5cM to XNpb363
0.8cM to RG220 and EstI-2
0.3cM to RG220 and
0.6cM to V10500

Yu et al. 1992, Tanksley et al. 1993
Ogi et al. 1993
Cho et al. 1994b
Maeda et al. 1995
EstI-2* Esterase I-2 0cM to RG220 Cho et al. 1994b
Anthocyanin activator 4.4cM to XNpbl21 and 10.5cM to XNpbl36 Kishimoto et al. 1992
rl-4  rolled leaf-4 9.4cM to XNpb368 and 17.4cM to XNpb252 Yoshimura et al. 1992a
Rf-4* Fertility restoration -4 near RG532 Zhang et al. 1994b
d-2 ebisu dwarf 15.6cM to XNpb359 and 25.4cM to C955 Ideta et al.1994b
d-1818 kotaketamanishiki dwarf 4.1cM to XNpb96 Yoshimura et al. 1992a
tpi* triosephosphate isomerase near C146 Fukuda et al. 1994
fs-2 fine stripe-2 8.7cM to XNpb216 Yoshimura et al. 1992a
Chromosome 2
tri triangular hull 16.7cM to XNpb250 Yoshimura et al. 1992a
Pi-b Pyricularia oryzae resistance-b 0.5cM to GN234 0cM to R1792. R2511 and R2821. bracked by C2782B and C379 Miyamoto et al. 1993 Hayasaka et al. 1995
bl-1 brown leaf spot-1 10.3cM to XNpb250 and 17.3cM to XNpb57 Yoshimura et al. 1992a
Glu-6t, 7t, 8t* Glutelin subunits 2.2% to XNpb21 0.7% to Glu-5t Uemura et al. 1994. Satoh 1995
Glu-5t* Glutelin subunit 10.0% to XNpb227 Uemura et al. 1994. Satoh 1995
glu-1(t)* lack of glutelin subunit-1 close to XNpb243 lida et al. 1994
gpd-1* glyceraldehydephosphate dehydrogenase-1 near C1061 Fukuda et al. 1994
Glu-9t* Glutelin subunit-9t near XNpb227 Satoh 1995
Glu-10t* Glutelin subunit-10t near XNpb227 Satoh 1995
d-30 waisei-shirasasa dwarf near XNpb 227 close to RG256 Ideta et al. 1992a Yu et al. 1992
AmylA/C* Alpha-amylase-IA/C 9.2cM to RG95 and 9.5cM to CD0686 Parco et al. 1994
Amp-1 (Lap-1) Aminopeptidase-1 23.2% to XNpb IIINpb223 Nakagahra 1990 Saito et al. 1991
cyc-2* cyclophilin-2 near RZ957 Tanksley et al. 1993
spl-2 spotted leaf-2 9.2cM to XNpb349 Ideta et al. 1992b

 
(Continued)
Gene1) Name Locus2) Reference
Chromosome 3
chl-1 chlorina-1 17.1cM to XNpb244-1
7.1cM toXNpb164
Saito et al. 1991
Yoshimura et al. 1992a
pgi-1
(Pgi-a)
sh-4(t)*
Phosphogluconate dehydrogenase-1
shattering-4
bracketed by G232 and C217
near XNpb40

Nozue et  al. 1994

Fukuta 1995

fc-1 fine culm-1 10.9cM to XNpb249 Yoshimura et al. 1992a
Actin-1* Actin-1 near CDO337 Tanksley et al. 1993
L* Lethal factor 0.29cM to XNpb23 Cheng et al. 1994
dl drooping leaf 16.6cM to XNpb394 Kishimoto et al. 1992
Pox-cA* Peroxidase-cA 1.1cM to Npb244-2 and 1.7cM to XNpb373 Kishimoto et al. 1994a
Pms-2* Photoperiod sensitive male sterility-2 near RG191 Zhang et al. 1993
spl-3 spotted leaf-3 15. 0cM to XNpb173 and 18.7cM to XNpb348 Yoshimura et al. 1992a
Hg Hairly glume near RG348 Yu et al. 1992, Tanksley et al. 1993
Cat-A1* Catalase-A1 1.4cM to XNpb279 and 2.1cM to XNpb145 Kishimoto et al. 1994b
Chromosome 4
lg liguleless 3.4cM to XNpb197
9.2cM to XNpb120
Saito et al. 1991
Yoshimura et al. 1992a
Ph Phenol staining 1.5cM to XNpb261
2.2cM to XNpb267
5.9cM to RG214

bracked by V17 and
Ky3 within 0.1cM

Saito et al. 1991
Ando et al. 1993
Zhu et al. 1993,Tanksley et al.
1993
Lin et al. 1994
hpg-1* high preproglutelin-1 13.3cM to L102 lida et al. 1993
Prp-b
(Pb)
Purple pericarp 19.0cM to RG329 Zhuang et al. 1994
Gm-2 Gall midge resitance-2 1.3cM to RG329 and
3.4cM to RG476
Mohan et al. 1994
Xa-1 Xanthomonas campestris pv. oryzae resistance-1 0cM to Y03700
1.4cM to U08750 and
2 .0cM to XNpb264
Yoshimura et al. 1992d,e.
1994, 1995
Xa-2 Xanthomonas campestris
pv. oryzae resistance-2
2 .0cM to XNpb264
2.5cM to Y03700
Yoshimura et al. 1994
gpd-2* glyceraldehydephosphate dehydrogenase-2 near C377 Fukuda et al. 1994
Pr Purple hull 16.8cM to RG163
18.2cM to RG329 and
3.5cM to Pb
Yu et al. 1992
Zhuang et al. 1994
Pi-5(t) Pyricularia oryzae resistance-5 bracketed by RG498
and RG788
Wang et al. 1994
d-11 sinkane-aikoku or
norin 28 dwarf
11.0cM to XNpb49 and 11.6cM to XNpb114
near CD0456
Yoshimura et al. 1992a

Yu et al. 1992, Tanksley et al. 1993


 
(Continued)
Gene1) Name Locus2) Reference
Chromosome 5
xa-5 Xanthomonas campestris pv. oryzae resistance-5 close to RG207
near XNpb396 and XNpb208
McCouch et al. 1991a
Yoshimura et al. 1992b
wgl(t)* spikelet width 0cM to W168A, Y1060L and Y1060R Kajiya et al. 1995
gl-1 glabrous leaf and hull 10.5cM to XNpb396
14.3cM to RG182 and
20.9cM to RG403
Yoshimura et al. 1992b
Yu et al. 1992
Pro-2* Prolamin-2 6.8% to XNpb251 and
2.2% to Pro-3
Satoh 1995
Pro-3* Prolamin-3 7.8% to XNpb251 and
3.0% to Pro-5
Satoh 1995
Pro-5* Prolamin-5 7.8% to XNpb251 and
18.8% to XNpb387
Satoh 1995
d-1 daikoku dwarf near XNpb105 Ideta et al. 1994a
sdg* semidwarf NJ6 4.3cM to RZ182 Liang et al. 1994
Est-13 Esterase-13 17.9cM to RG13 and 28.5cM to RG474 Cai and Wang 1994b
ATP* ATPase near RG697 Tanksley et al. 1993
Cht-2* Chitinase-2 2.9cM to XNpb105 and 0.8cM to Ald-1 Saito et al. 1991
Nishizawa et al. 1993
Ald-1* Aldolase-1 0.8cM to Cht-2
7.7cM to C13
Saito et al. 1991
Kishimoto et al. 1994c
Arf-1* ADP-ribosylation factor
(ARF)-1
18.2cM to C13 and
1.7cM to Oc-2
Kishimoto et al. 1994c
Oc-2* Oryzastatin-2 0.4cM to XNpb255 Kishimoto et al. 1994c
spl-7 spotted leaf-7 near XNpb81 Ideta et al. 1994a
nl-1 neck leaf-1 0cM to XNpb188 and 11.9cM to XNpb25 Kishimoto et al. 1992
Chromosome 6
Ldh* Lactate dehydrogenase 0.9cM to C1003B and W160 Li et al. 1994a. b
wx glutinous endosperm near RZ1002
near XNpb209
1.1cM to C425A
Tanksley et al. 1993
Ideta et al. 1993a
Li et al. 1994a.b
dp-1 depressed palea-1 10.8cM to XNpb209 Ideta et al. 1993b
spl-4 spotted leaf-4 5.0cM to XNpb209 and 9.6cM to dp-1 Ideta et al. 1993b
Wc* Wide compatibility 12.7cM to RG398 and 5.9cM to Est-2 Liu et al. 1992
C Chromogen for anthocyanin 16.4cM to XNpb165-1 and 17.1cM to XNpb200 Kishimoto et al. 1992
S-5 Hybrid sterility-5 4.4cM to RG213 and
1.6cM to Est-2
Yanagihara et al. 1995
Amp-3 Aminopeptidase-3 1.7% to RG213 Brar et al. 1991
Est-2 Esterase-2 1.7% to RG213 Brar et al. 1991
alk alkali degeneration 1.1cM to C1478 and
3.0cM to R2147
11.1cM to RG213 and
4.6cM to Pgi-2
Lin et al. 1994

Yanagihara et al. 1995

Pgi-2
(Pgi-b)
Phosphoglucose isomerase-2 7.9% to RG213 near hmg2
7.6cM to RZ144 and
4.6cM to alk
Brar et al. 1991
Nozue et al. 1994
Yanagihara et al. 1995
Se-1 Photosensitivity-1 4.7% to Npb294
near RZ612
4.9cM to XNpb233
0.3cM to C235 and
1.3cM to Pi-zt
Ohshima et al. 1993b
Tanksley et al. 1993
Tamura et al. 1994
Tamura et al. 1995
PS* Photosensitivity 0cM to RG64 Mackill et al.1993
Pi-zt
(Pi-2)
Pyricularia oryzae resistance-z 2.8cM to RG64
2.9cM to XNpb294 and
8.8cM to XNpb233
2.1cM to RG64 and
7.2cM to RZ612
2.8cM to RG64 and
5.0cM to RG456
Yu et al. 1991
Satoh et al. 1992

Mew et al. 1994

Hittalmani et al. 1994

Xa-7 Xanthomonas campestris pv. oryzae resistance-7 8.8% to G1091 Kaji & Ogawa 1995
Cat-1 Catalase-1 8.1cM to RG244 Zhu et al. 1933
Amy2A* Alpha-amuylase-2A 6.3cM to RG433 and 10.3cM to RG653 Parco et al. 1994
sbe-1*
(QEI)
starch branching enzyme (Q-enzyme)-1 0.3cM to G342 and
0.5cM to R1167
Nakamura et al. 1994
Cht-1* Chitinase-1 0.4cM to XNpb342 Nishizawa et al. 1993
Cht-3* Chitinase-3 0.4cM to XNpb342 Nishizawa et al. 1993

 
 
(Continued)
Gene1) Name Locus2) Reference
Chromosome 7
Mal-1 Malate dehydrogenase-1 22.7% to RG173
20.3cM to RG528
Brar et al. 1991
Zhu et al. 1993
Acp-4 Acid phosphatase-4 near RZ387 Tanksley et al. 1993
g-1 long sterile lemmas-1 24.9cM to XNpb85-1 Ideta et al. 1992b
d-6 ebisumochi dwarf near XNpb50 Ideta et al. 1994a
spl-5 spotted leaf-5 near XNpb85-1 Ideta et al. 1994a
Rc Brown pericarp and seed coat 12.5cM to RG30
0cM to C67A and R277
Yu et al. 1992 Lin et al. 1994
v-11 virescent-11 near XNpb85-1 Ideta et al. 1994a
Pro-4* Prolamin-4 1.6% to XNpb338 Satoh 1995
Mal-2 Malate dehydrogenase-2 1.8cM to RG511 Zhu et al. 1993
Pms-1* Photoperiod sensitive male sterility-1 4.3cM to RG477 and
16.0cM to RG511
Zhang et al. 1993
slg slender glume (mutator) 3.0% to XNpb33 and
3.0% to Npb20
Teraishi et al. 1994
rfs rolled fine stripe 1.4cM to XNpb20 and
7.0cM to XNpb152
Kishimoto et al. 1992
Wph-1 White-backed planthopper resistance-1 near RG146B

McCouch et al. 1991b
Tanksley et al. 1993

Rf-3* Fertility restoration-3 near XNpb379 Zhang et al. 1994b
Chromosome 8
sug sugary endosperm near XNpb397 Ideta et al. 1994a
xa(t)* Xanthomonas oryzae pv. oryzae resistance 3.8cM to RG136 and
5.1cM to RZ28
Zhang et al. 1994
Amp-2 Aminopeptidase-2 8.3cM to RG136 Zhu et al. 1993
Amy3D/E* Alpha-amylase-3D/E 11. 1cM to RG1 and
25.3cM to RZ66
Parco et al. 1994
sk-2(t) scented kernel-2 2.1cM to RG28
6.7% to XNpb126 and
15.7% to XNpb369
Ahn et al. 1993a
Yano et al. 1991a
Pi-11 (t)*
(Pi-zh)
Pyricularia oryzae resistance-zh near RZ617
14.9cM to Bp127
Tanksley et al. 1993
Zhu et al. 1993
v-8 virescent-8 near XNpb278 Ideta et al. 1994a
Chromosome 9
R45s-1* 45S ribosomal DNA-1 1.0cM to XNpb315 and 2.5cM to XNpb95
2.5cM to RG757
Matsuura et al. 1991a,b

Tanksley et al. 1993

I-Bf Inhibitor for brown furrows 11.1cM to XNpb36 Ideta et al. 1992b, 1993b
Est-3 Esterase-3 16.4% to XNpb257 Nakagahra 1990
Amy3A/B/C* Alpha-amylase-3A/B/C 9.4cM to RZ228
and 11.2cM to RZ422
Parco et al. 1994
dp-2 depressed palea-2 3.3cM to XNpb385
and 15.2cM to XNpb47
Ideta et al. 1993b
drp-2 dripping wet leaf-2 10.6cM to XNpb339
0cM to XNpb385 and
2.9cM to dp-2
Kishimoto et al. 1992 Ideta et al. 1993h
bp Burlush-like panicle 1.4cM to XNpb339 and 14.6cM to XNpb112 Kishimoto et al. 1992
Est-12 Esterase-12 29. 1cM to RZ12 Cai & Wang 1994b
cyc-1* cyclophilin-1 4.6cM to RZ404 Tanksley et al. 1993
Man Mannan in endosperm cell wall 4.3cM to XNpb293  Yano et al. 1991b, 1993


 
(Continued)
Gene1) Name Locus2) Reference
Chromosome 10
pgl pale green leaf 3.5cM to XNpbl27 and
7.5cM to spl-10
Ideta et al. 1992b
spl-10 spotted leaf-10 10.9 cM to XNpb127 and
17.5cM to XNpb291
Ideta et al. 1992b
Rf-1 Fertility restoration-1 7.5cM to XNpb291 and
26.0cM to XNpb127
near RG134
Fukuta et al. 1992

Yu et al. 1992

fgl
faded green leaf 0cM to XNpb291  Kishimoto et al. 1992
Ef(t)* Earliness 9.96cM to CD098 Ishii et al. 1994
glu-2(t)* lack of glutelin subunit-2 6.8cM to G1082 and 
13.7cM to G1084
Iida et al. 1994
rDNA-2 ribosomal DNA-2 0cM to XNpb32 Matsuura et al. 1991a,b
Chromosome 11
Xa-3 Xanthomonas campestris pv. oryzae resistance-3 2.3cM to XNpb181  Yoshimura et al. 1992e, 1993, 1994
Xa-4 Xanthomonas campestris pv. oryzae resistance-4 17cM to RG53 
1.7cM to XNpb181
1.7cM to XNpb78
McCouch et al. 1991b
Yoshimura et al. 1992e, 1993, 1994.
Pi-1 Pyricularia oryzae resistance-1 near RG303
3.5cM to NpB181 and
7.9cM to RZ536
Tanksley et al. 1993
Mew et al. 1994
Pi-k Pyricularia oryzae resistance-k 17.8% to G181  Kaji & Ogawa 1994
PBR* Panicle blast resistance 10.8cM to CD0226  Fujii et al. 1995
d-27 bunketsuto tillering dwarf 2.6cM to pTA818 and 
3.7cM to CD0520
Abenes et al. 1994
Xa-21* Xanthomonas campestrispv. oryzae resistance-21 0cM to RAPD818, RG103,
RAPD248 and TH402
2.2 or 2.7cM to pTA818
and 3.8 or 2.7cM to RG103

Ronald et al. 1992, 1994

Abenes et al. 1994

Pi-7 (t) Pyricularia oryzae
resistance -7
bracketed by RG103A
and RG16
Wang et al.1994
z-2 zebra-2 4.2cM to gmz410 and
13.1cM to XNpb78
0cM to CD0365
Ideta et al.

Abenes et al. 1994

Stv-bi Stripe disease resistance 3.0cM to XNpb257 and XNpb254 Hayano-Saito et al. 1993
la lazy growth habit 13.1cM to XNpb202
3.0cM to RG1094 and
6.2cM to RG247
Kishimoto et al. 1992 Abenes et al. 1994
Xa-10 Xanthomonas campestris pv. oryzae resistance-10 5.3cM to Oo72000 and
16.2cM to CDO365
Yoshimura et al. 1993
Pgd-1 Phosphogluconate dehydrogenase-1 near RG167 Tanksley et al. 1993
R5s-1* 5S ribosomal DNA-1 near RG167 Tanksley et al. 1993
sp short panicle 7.7cM to XNpb320 Ando et al. 1993
Adh-1 Alcohol dehydrogenase-1 7.3% to RG118
13cM to RG1094
Brar et al. 1991
Abenes et al. 1994
v-9 virescent-9 11. 1cM to XNpb183 and
22.2cM to XNpb189
Ideta et al. 1993b
Chromosome 12
Lec* Lectin near RG190 Tanksley et al. 1993
Acp-1 Acid phosphatase-1 29.2cM to RG361 and
0cM to Acp-2
Zhu et al. 1993
Acp-2 Acid phosphatase-2 1.9cM to RG181A Zhu et al. 1993
Bph(t)* Brown planthopper resistance 3.68cM to RG457 Ishii et al. 1994
d-33 bonsaito dwarf 7.5cM to XNpb148 and 15.9cM to XNpb248 Kishimoto et al. 1992
rl-3 rolled leaf-3 near XNpb402 Ideta et al. 1994a
Sdh-1 Shikimate dehydrogenase-1 6.7% to XNpb860-C
4.9cM to XNpb402
Nakagahra 1990
Saito et al. 1991
spl-1 spotted leaf-1 3.6cM to XNpb88
4.3cM to XNpb154 and
9.2cM to XNpb124-1
Ideta et al. 1992b
Kishimoto et al. 1992
Bph-1 Brown planthopper resistance-1 10.9cM to XMpb248 Hirabayashi and Ogawa 1995
Pi-ta, Pi-ta2
(Pi-4a)
Pyricularia oryzae resistance-ta 15.3cM to RG869
0cM to XNpb289, 319
and 239
3.3cM to RZ397 and
5.2cM to RG241
Yu et al. 1991
Miyamoto et al. 1994
Rybka et al. 1994
Mew et al. 1994
Pi-6 (t)* Pyricularia oryzae resistance-6 near RG81 Tanksley et al. 1993
McCouch et al. 1994
Pro-1* Prolamin-1 3.2% to XNpb88 and
14.2% to XNpb124-1
Satoh 1995
Ald-3* Aldolase-3 near C1336 Fukuda et al. 1994
1) Approximate order of genes on the respective chromosome.
2) Distance from flanking DNA markers.
3) As for the molecular maps. refer to Rice Genome 2(1). Saito et al. 1991, Tanksley et al. 1992, 1993,
     Xiao et al. 1992 and Zhu et al. 1993.
4) *  Genes are not registered.

Acknowledgements

The author gratefully acknowledge the assistance of Dr. Itsuro Takamure in preparing the manuscript.

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