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


Gene  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 XNpbll3 near CD0251 Saito et al. 1991 Yu et al. 1992, Tanksley et al. 1993
Ald-2  Aldolase-2 1.4cM to XNpbll3 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 0cl 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 CD0548 Tanksley et al. 1993
AmB Alpha-amylase-1B 1.0cM to RG146X and 14.4cM to RG173 Parco et al. 1994
sd-1  dee-geo-woo-gen
dwarf		 near CD0962 2.5cM to XNpb363 0.8cM to RG220 and Estl-2 Yu et al. 1992. Tanksley et al. 1993 Ogi et al. 1993 Cho et al. 1994b Maeda et al. 1995
0.3cM to RG220 and 0.6cM to V10 500
EstI-2 Esterase I-2 0cM to RG220 Cho et al. 1994b
A  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

 
 
 
 
(Continued)
Gene') Name Locus Reference
d-2 ebisu dwarf 15.6cM to XNpb359 and 25.4cM to C955 Ideta et b
d-18 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-l (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
Chromosome 3
chl-1 chlorina-1 17.1cM to
XNpb244-1 
7.1cM toXNpb164		 Saito et al. 1991
Yoshimura et al. 1992a

    Rice Genetics Newsletter Vol. 12
 
(Continued)
Gene  Name Locus' Reference
pgi-1 (Pgi-a) sh-4(t)• Phosphogluconate dehydrogenase-1 shattering-4 bracketed by G232 and C217 near XNpb40 Nozue et Fukuta 1995
fc-1 fine culm-1 10.9cM to XNpb249 Yoshimura et al. 1992a
Actin-1 Actin-1 near CD0337 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 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 XNpbl73 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 XNpbl45 Kishimoto et al. 1994b
Chromosome 4
lg liguleless 3.4cM to XNpbl97 9.2cM to XNpbl20 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 VI 7 and Ky3 within O.lcM 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 cM to 
Y03700		 Yoshimura et al. 1994

 
 
 
 
(Continued)
Gene') Name Locus Reference
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-ll norin 28 dwarf 11cM to XNpb49 and 11.6cM to XNpbll4 near CD0456 Yoshimura et al. 1992a Yu et al. 1992. Tanksley et al. 1993
Chromosome 5
xa-5 Xanthomonas campestris close to RG207 near XNpb396 and XNpb208 McCouch et al. 1991a Yoshimura et al. 1992b
oryzae resistance-5
wgl(t) spikelet width OcM 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-l daikoku dwarf near XNpbl05 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 XNpbl05 and 0.8cM to Ald-1 Saito et al. 1991 Nishizawa et al. 1993
Ald-1 Aldolase-1 0.8cM to cM 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 0c-2  Kishimoto et al. 1994c 
Oc-2* Oryzastatin-2 0.4cM to XNpb255 Kishimoto et al. 1994c

 
 
 
 
(Continued)
Gene Name Locus' Reference
spl-7 spotted leaf-7 near XNpb81 Ideta et al. 1994a
nl-l neck leaf-1 OcM to XNpbl88 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 C425A Tanksley et al. 1993 Ideta et al. 1993a Li et al. 1994a.b
dp-l 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-l 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 XNpbl65-l and 17. lcM 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 l.lcM to C1478 and 3.0cM to R2147 11. lcM to RG213 and 4.6cM to Pgi-2 Lin et al. 1994 Yanagihara et al. 1995
Pgi-2 (Pgi-b) Phosphoglucose isomerase-2 7.9hmg2 7.6cM to RZ144 and 4.6cM to alk Brar et al. 1991 Nozue et al. 1994 Yanagihara et al. 1995
Se-I  Photosensitivity-I 
 
 
 
 

 

 4.7Npb294 near RZ612 4.9cM to XNpb233 0.3cM to C235 and 1.3cM to Pi-z' 
 

 

 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

 
 
 
 
(Continued)
Gene Name Locus' Reference
Pi-z' (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 Satoh et al. 1992 Mew et al. 1994 Hittalmani et al. 1994
Xa-7 Xanthomonas campestris oryzae resistance-7 8.8% to G1091 Kaji & Ogawa 1995
Cat-1 Catalase-1 8.1cM to RG244 Zhu et al. 1933
Amy2A- A 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
Chromosome 7
Mal-l 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-l Ideta et al. 1992b
d-6 ebisumochi dwarf near XNpb50 Ideta et al. 1994a
spl-5 spotted leaf-5 near XNpb85-l 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-ll virescent-ll near XNpb85-l 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 3.0Npb20 Teraishi et al. 1994
rfs rolled fine stripe 1.4cM to XNpb20 and 7.0cM to XNpbl52 Kishimoto et al. 1992

 
 
 
(Continued)
Gene') Name Locus' Reference
Wph-l White-backed planthopper resistance-1 near RG146B McCouch et lb 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 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. lcM to RGI and 25.3cM to RZ66 Parco et al. 1994
sk-2(t) scented kernel-2 2.1cM to RG28 6.7Npbl26 and 15.7XNpb369 Ahn et al. 1993a Yano et al. 199 la
Pi-11 (t)-(Pi-zh) Pyricularia oryzae resistance-zh near RZ617 14.9cM to Bpl27 Tanksley et al. 1993 Zhu et al. 1993
v-8 virescent-8 near XNpb278 Ideta et al. 1994a
Chromosome 9
R45s-l- 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 Npb36 Ideta et al. 1992b. 1993b
Est-3 Esterase-3 16.4Npb257 Nakagahra 1990
Amy3A/B/C' Alpha-amylase-3A/B/C 9.4cH 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 XNpbll2 Kishimoto et al. 1992
Est-12 Esterase-12 29. lcM to RZ12 Cai & Wang 1994b
cyc-1 ' cyclophilin-1 4.6cM to RZ404 Tanksley et al. 1993

 
 
 
Gene 1) Name Locus 2) Reference
Man Mannan in endosperm cell wall 4.3cM to XNpb293  Yano et al. 1991b, 1993
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 
26. OcM to XNpbl27 
near RG134 		 Fukuta et al. 1992 
Yu et al. 1992
fgl faded green leaf OcM 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 OcM to XNpb32 Matsuura et al. 1991a,b
Chromosome 11
Xa-3 Xanthomonas campestris 2.3cM to XNpbl81  Yoshimura et al. 1992e, 1993, 1994.
oryzae resistance-3
Xa-4 Xanthomonas campestris pv. oryzae resistance-4 17cM to RG53 
1.7cMtoXNpbl81 
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-2l Xanthomonas campestris OcM to RAPD818. RG103
 2.2 or 2.7cM to pTA818  and 
3.8 or 2.7cM to RG103		 Ronald et al. 1992, 1994
pv. oryzae resistance-21 Abenes et al. 1994
Pi-7 (t) Pyricularia oryzae resistance -7 bracketed by RG103A 

and RG16

 Wang et al.1994

 
 
 
(Continued)
Gene Name Locus2) Reference
z-2 zebra-2 4.2cM to gmz410 and 13. lcM to XNpb78 OcM to CD0365 Ideta et al. 
 
 

Abenes et al. 1994
Stv-b' Stripe disease resistance 3.0cM to XNpb257 and XNpb254 Hayano-Saito et al. 1993
la lazy growth habit 13. lcM 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 0072000 and 16.2cM to CD0365 Yoshimura et al. 1993
Pgd-1 Phosphogluconate dehydrogenase-1 near RG167 Tanksley et al. 1993
R5s-1 5S ribosomal DNA-I near RG167 Tanksley et al. 1993
sp short panicle 7.7cM to XNpb320 Ando et al. 1993
Adh-l Alcohol dehydrogenase-1 7.3% to RG118 13cM to RG1094 Brar et al. 1991 Abenes et al. 1994
v-9 virescent-9 11. lcM to XNpbl83 and 22.2cM to XNpbl89 Ideta et al. 1993b
Chromosome 12
Lec Lectin near RG190 Tanksley et al. 1993
Acp-l Acid phosphatase-1 29.2cM to RG361 and OcM 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 XNpbl48 and 15.9cM to XNpb248 Kishimoto et al. 1992
rl-3 rolled leaf-3 near XNpb402 Ideta et al. 1994a
Sdh-l Shikimate dehydrogenase-1 6.7% to XNpb860-C 4.9cM to XNpb402 Nakagahra 1990 Saito et al. 1991
spl-l spotted leaf-1 3.6cM to XNpb88 4.3cM to XNpbl54 and 9.2cM to XNpbl24-l Ideta et al. 1992b Kishimoto et al. 1992
Bph-l Brown planthopper resistance-1 10.9cM to XMpb248 Hirabayashi and Ogawa 1995

 
 
 
Gene Name Locus Reference
Pi-ta,Pi-ta^2 Pyricularia oryzae 15.3cM to RG869 Yu et al. 1991
Pi-4'a) resistance-ta OcM to XNpb289. 319 Miyamoto et al. 1994.
and 239 Rybka et al. 1994
3.3cM to RZ397 and Mew et al. 1994
5.2cM to RG241
Pi-6 (t)• Pyricularia oryzae near RG81 Tanksley et al. 1993
resistance-6 McCouch et al. 1994
Pro-1 Prolamin-1 3.2% to XNpb88 and Satoh 1995
14.2% to XNpbl24-l
Ald-r 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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