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-2Linkage 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.