B. CURRENT LINKAGE MAPS

In the review of rice genetics by Yamaguchi (1927), only four linkage groups, each consisting of two genes, were reported. Jodon (1948) reported on eight linkage groups involving nearly 50 genes. Since then, information on the location of different genes has accumulated in both the Indica and Japonica rices. In 1963, Nagao and Takahashi first proposed twelve linkage groups corresponding to the haploid number of chromosomes, on the basis of linkage data in Japonica varieties. Misro et al. (1966) also presented twelve linkage groups in the Indica rice. However, because of differences in the genic scheme for organ coloration and scarcity of identical genes involved in the two series of linkage groups at that time, it was difficult to establish twelve groups common to the Indica and Japonica types.

The cytological basis of linkage groups was first reported by Iwata and Omura (1971 a, b) from a study of relationships of gene loci with the points of interchange of reciprocal translocations. Ten linkage groups were then corresponded to different chromosome. Sato et al. (1973) detected the association of the 3rd linkage group with chromosomes 3, thus modifying the relationship established earlier. A series of primary trisomics were established by different workers (Hu 1968; Iwata et al. 1970, 1984; Watanabe and Koga 1975; Kawaguchi et al. 1982; Khush et al. 1984). The extra chromosomes of the trisomics were identified by examining the somatic karyotype of trisomics by Kurata et al. (1981) and at pachytene stage of meiosis by Khush et al. (1984). On the basis of trisomic analysis, the correspondence between linkage groups and chromosomes was partly revised by lwata and Omura (1976b). The 5th and 7th linkage groups were associated with chromosome 1, and the 6th, 9th and 12th groups with chromosome 2. More recently Khush et al. (1984) established associations between twelve linkage groups and cytologically identifiable chromosomes through the trisomic technique.

The linkage map presented in Fig. 1 includes amendments to the Takahashi-Kinoshita's (1977) map made on the basis of recent findings. The 6th and 9th groups have been combined since the points of interchange connecting the two groups were detected by Sato et al. (1982). However, there is no definite map combining the markers of the 5th and 7th groups. The 12th group was retained except that gl-1 and An-2 were shifted to the 6+9th group. Hg and d-20 belonging to the 12th group have not been subjected to trisomic analysis.

Different systems of numbering the chromosomes and linkage groups have been employed by different authors. The relationships among linkage groups, chromosomes and trisomics as determined by different worker are presented in Table 1, Khush et al. (Res. note no. 32) and Table 1, Iwata et al. (no. 34). The chromosome numbering system in the table still follows that of Nishimura (1961).

With the establishment of induced translocation homozygotes, the translocation analysis has also progressed, and chromosome maps have been proposed for ten chromosomes (Sato et al. 1980). The relative positions of breakage points, centromeres and several marker genes in each chromosome are shown in Fig. 2.

1. There is no consistency in the numbering of linkage groups, chromosomes, and the trisomics. We propose to revise the numbering system for chromosomes and the linkage groups on the basis of discussions among rice geneticists during the forthcoming Rice Genetic symposium.

2. The allelism tests between marker genes with similar effects are most important. For this purpose, exchange of gene stocks and information among rice workers must be promoted.

3. Multiple marker stocks, induced mutants and cytogenetic materials are bneing developed bv different workers. Easily identifiable mutants, even though they are of no immediate economic value, are useful in linkage studies.

These useful materials are sometimes lost on account of difficulty of seed maintenance. It is hoped that arrangement will be made to preserve these stocks in certain centers of germplasm conservation.

4. A complete set of primary trisomics has already been established in both the Indica and japonica rices (Khush et al. 1984; Iwata et al. 1984). Rice karyotypes have been described by Hu (1958), Shastry et al. (1960), Kurata and Omura (1978), Kurata et al. (1981), Chen and Wu (1984), Chen et al. (1982), and Khush et al. (1984). The extensive use of cytological mutants such as telo and tertiary trisomics and induced deficiencies should be encouraged to locate the gene loci on the respective arms of chromosomes.

5. The linkage information should be utilized in the breeding programs. Some of the genes for short stature, heading date, disease and insect resistances, and grain chracters have been mapped. Linkage between some marker characters and cold tolerance and germinability at low temperatures has been detected (Futsuhara and Toriyama, 1966; Takahashi, 1977).

I wish to acknowledge the assistance of Drs. N. Iwata and S. Sato in preparing the linkage maps. References used are listed in Publication List, 1. Genic Analysis.

==================================================================== Gene Name Gene locus ==================================================================== Group I (Wx Group), chromosome 6 d-4 bunketsu-waito of tillering dwarf 0 I-Pl-4 Inhibitor for purple pericarp-4 9 wx (am) glutinous endosperm 22 dp-1 depressed palea-1 24 ms-1 (sf) male sterile-1 27 v-3 virescent-3 30 ga-1 gametophyte gene-1 36 C Chromogen for anthocyanin 44 Est-2 Esterase-2 53 bl-3 brown leaf spot-3 54 alk alkali degeneration 55 st-1 (ws) stripe-1 64 Pgi-2 Phosphoglucose isomerase-2 66 Se-1 (Lf,Lm,Rs) Photosensitivity-1 66 Pi-z Pyricularia oryzae resistance-1 68 d-9 chinese dwarf 75 gf gold furrows of glume 79 chl-4 (ch-4) chlorina-4 81 bl-2 brown leaf spot-2 82 fs-1 fine stripe-1 94 Cl Clustered spikelets 95 Pi-i Pyricularia oryzae resistance-i 99 Ur-1 Undulated rachis-1 122 Unlocated genes al-1 (al-K-1) albino-1 7.1%-wx al-9(t)(al-K-9) albino-9 trisomic B chl-7(t) chlorina-7 27%-Pi-z d-21 aomorimochi-14 dwarf 8.3%-wx ga-4 (ga-A) gametophyte gene-4 34%-wx ga-5 (ga-B) gametophyte gene-5 27%-wx Hl-a Hairy leaf 21%-fs-1 I-Pl-2 Inhibitor for purple leaf-2 10%-I-Pl-4 rcn reduced culm number 32%-C S-1 Hybrid sterility (one locus close to C sporogametophytic lethal) s-a-1 (s\1\,x) hybrid sterility-a (duplicate 21%-wx gametophytic lethal) s-b-1 hybrid sterility-b 18%-wx s-c-1 hybrid sterility-c 8.6%-C s-d-1 hybrid sterility-d 33%-wx S-A-1 (A-1) Hybrid sterility-A (duplicate 9.5%-C fertility genes) S-B-2 (B-2) Hybrid sterility-B 28%-wx spl-4 (bl-15) spotted leaf-4 2.5%-dp-1 Stv-a (St-1) Stripe virus resistance 38%-wx Un-a Uneven grain 22%-Cl-a v-1 virescent-1 25%-C zn zebra necrosis 20%-C Group II (Pl group), chromosome 11 d-2 ebisu dwarf 0 d-3 bunketsu-waito of tillering dwarf 25 Pl (Pl-1) Purple leaf 61 Prp-b (Pb) Purple pericarp 61 Pi(t) Pyricularia oryzae resistance 66 lg liguleless 92 ga-6 gametophyte gene-6 96 st-4 (ws-2) stripe-4 97 d-42 liguleless dwarf 102 Ph (Po) Phenol staining 113 Xa-1 (Xe-1) Xanthomonas oryzae resistance-1 119 Xa-2 (Xe-2) Xanthomonas oryzae resistance-2 123 nal-4 (nal) narrow leaf-4 124 d-31 taichung-155 irradiated dwarf 131 Pr Purple hull 137 Ps-3 Purple stigma-3 141 d-11 (d-8) sinkane-aikoku or norin-28 dwarf 160 Ps-2 Purple stigma-2 163 Unlocated genes al-5 (al-K-5) albino-5 34%-lg al-7 (t) (al-K-7) albino-7 31%-lg An-1 Awn-1 5.4%-d-11 Bph-1 Brown planthopper resistance-1 trisomic E bph-2 brown planthopper resistance-2 39%-d-2 drp-1 dripping-wet leaf-1 39%-i-2 drp-5(t) dripping-wet leaf-5 17%-lg ga-10(t) gametophyte gene-10 27%-lg nal-1 narrow leaf-1 25%-d-2 nal-5 (nal-1) narrow leaf-5 9.5%-lg P Purple apiculus 2.7%-Pl Pin-1 Purple internode-1 31%-Pl rk-1 Round kernel-1 35%-lg rl-2 rolled leaf-2 35%-d-2 s-c-2 hybrid sterility-c 31%-Ph s-e-2 hybrid sterility-e 15%-lg Sc-1 Sclerotium oryzae resistance 25%-lg ssk (sk) malformed semi-sterile 6.8%-Pl Wh White hull 8.0%-lg Xa-kg Xanthomas oryzae resistance kg 2.1%-Xa-1 ylm yellow leaf margin 10%-lg z-5 zebra-5 11%-lg Group III (A group), chromosome 3 eg extra glume 0 ga-8 gametophyte gene-8 0 spl-6 spotted leaf-6 8 lax (lx) lax panicle 13 chl-5 (ch-5) chlorina-5 22 rl-1 rolled leaf-1 26 d-10 (d-15,d-16) kikeibanshinriki or toyohikari-bunwai 28 of tillering dwarf sd-1 (d-47) dee-geo-woo-gen dwarf 43 A Anthocyanin activator 68 Rd Red pericarp 69 Pn Purple node 96 Unlocated genes al-4 (al-K-4) albino-4 30%-lax al-8 (al-K-8) albino-8 11%-d-18 bph-4 brown planthopper resistance-4 close to Bph-3 chl-6 (ch-6) chlorina-6 31%-lax d-18 (d-25) hosetsu dwarf and kotaketamanishiki 0.6%-TR3-8b dwarf d-26(t) 7237 dwarf 37%-A d-54 (d-K-5) dwarf-Kyushu-5 30%-rl-4 d-55 (d-K-6) dwarf-Kyushu-6 12%-eg fs-2 fine stripe-2 13%-d-18 ga-7 gametophyte gene-7 29%-A ga-9 gametophyte gene-9 0.6%-d-18 Glh-3 Green leafhopper resistance-3 34%-bph-4 I-Ps-b Inhibitor for purple stigma linked with A lgt long twisted grain 16%-d-26 Prp-a (Pp) Purple pericarp 7.3%-A rl-4 (rl-2) rolled leaf-4 20%-A shr-1 shrunken endosperm 24%-rl-4 ts-a twisted stem 23%-A v-6 virescent-6 27%-lax Group IV (g-1 group), chromosome-10 d-6 ebisumoshi or tankanshirasasa dwarf 0 g-1 (g) long strile lemmas-1 6 spl-5 (bl-6) spotted leaf-5 29 Rc Brown pericarp and seed coat 42 v-11(t) virescent-11 43 rfs rolled fine striped leaf 56 Unlocated genes d-7 heieidaikoku or cleistogamons dwarf 39%-d-6 ge giant embryo trisomic-F lp-1 long palea 12%-Un-b m-Ef-1 modifier for Ef-1 23%-Rc se-2 photosensitivity-2 23%-g-1 Un-b Uneven grain 18%-g-1 Group VI+IX (d-1 group), chromosome-2 gh-1 gold hull and internode-1 0 nl-2 neck leaf-2 6 d-1 daikoku dwarf 28 st-2 (gw) stripe-2 46 al-3 (dl-K-3) albino-3 48 spl-8 (bl-8) spotted leaf-8 48 al-6(t) (al-K-6) albino-6 53 v-10(t) virescent-10 54 ops (ops-1) Open Spikelet sterile 66 bgl bright green leaf 66 ri verticillate rachis 66 spl-7 spotted leaf-7 83 nl-1 neck leaf-1 93 al-2 (al-K-2) albino-2 94 Unlocated genes An-2 Awn-2 33%-gl-1 bd beaked lemma 22%-gl-1 er (0) erect growth habit 38%-gh-1 eui elongated uppermost internode 27%-nl-1 gl-1 glabrous leaf blade-1 12%-RT2-3d I-Pl-1 Inhibitor for purple leaf-1 31%-gh-1 v-10(t) virescent-10 12%-ri xa-5 xanthomonas oryzae resistance -5 trisomic L ylb yellow banded leaf blade 32%-nl-1 Group VII (Dn-1 group), chromosome-1 Dn-1 (Dn) Dense panicle-1 0 drp-2 dripping-wet leaf-2 14 dp-2 depressed palea-2 14 Unlocated genes Bp Burlush-like panicle trisomic H d-57 [d(x)] dwarf 21%-Dn-1 Pi-ta Pyricularia oryzae resistance-ta 4.5%-RTI-4 sl sekiguchi lesion 10%-Pi-ta Group V (I-Bf group), chromosome-1 (I-Bf) gm (pd) gall midge resistance 0 I-Bf Inhibitor for brown furrows of glume 39 sd semidwarf 73 Ps-1 Purple stigma-1 100 Group VII (la group), chromosome 9 Pi-K Pyricularia oryzae resistance-k 0 d-27 (d-t) bunketsuto of tillering dwarf 28 la 'lazy' growth habit 55 v-4 virescent-4 66 d-28 (d-C) chokeidaikoku or long stemmed dwarf 81 sp short panicle 89 Pi-a Pyricularia oryzae resistance-a 91 sh shattering 94 v-9(t) virescent-9 104 z-1 zebra-1 118 D-53 (D-K-3) Dwarf Kyushu-3 127 Unlocated genes drp-7(t) dripping-wet leaf-7 trisomic G Ef-1 (E) Earliness-1 38%-la nal-2 narrow leaf-2 36%-la pi-f Pyricularia oryzae resistance-f 15%-Pi-k Pi-se-1 (Rb-4) Pyricularia oryzae resistance-se 9.5%-la Pi-is-1 (Rb-4) Pyricularia oryzae resistance-is 23%-la S-3 Hybrid serility-3 1%-la z-2 zebra-2 5.9%-d-27 Group X (bl-1 group), chromosome-8 d-29 (d-K-1) short uppermost internode dwarf 0 tri triangular hull 0 bl-1 brown leaf spot-1 18 bc-3 brittle culm-3 18 gh-3 gold hull and internode-3 36 d-5 bunketsu-waito of tillering dwarf 43 spl-2 (bl-13) spotted leaf-2 51 gh-2 gold hull and internode-2 68 d-30 (d-W) waisei-shirasasa dwarf 99 d-32 (d-K-4) dwarf Kyushu-4 119 Unlocated genes d-29 (d-K-1) short uppermost internode dwarf 14%-bl-1 Pi-b (Pi-s) Pyricularia oryzae resistance-b 5.8%-RT7-8 Group XI (bc-1 group), chromosome 5 chl-1 (ch-1) chlorina-1 0 chl-3 (ch-3) chlorina-3 19 fc-1 fine culm-1 40 v-1(t) (v-1) virescent-1 58 bc-1 brittle culm-1 76 chl-2 (ch-2) chlorina-2 106 v-2 virescent-2 106 lhs-1 (op) leafy hull sterile-1 131.5 dl (lop) drooping leaf 132 z-3 zebra-3 146 d-52 (d-K-2) dwarf Kyushu-2 149 spl-3 (bl-14) spotted leaf-3 149 Unlocated genes An-3 Awn-3 38%-bc-1 al-10 (al-K-10) albino-10 22%-dl bl-4 brown leaf spot-4 29%-bc-1 d-14 (d-10) kamikawa bunwai of tillering dwarf 32%-dl d-56 (d-K-7) dwarf Kyushu-7 7.2%-dl drp-3 dripping-wet leaf-3 22%-dl drp-4 dripping-wet leaf-4 6.0%-dl ga-2 gametophyte gene-2 11%-dl ga-3 gametophyte gene-3 34%-dl Lk-f 'Fusayoshi' long grain 19%-bc-1 Mi Minute grain 24%-Lk-f rl-5 (rl-3) rolled leaf-5 13%-chl-1 s-e-1 hybrid sterility-e 16%-bc-1 st-3 (stl) stripe-3 1.1%-bc-1 v-5 virescent-5 2.0%-chl-1 v-7 virescent-7 1.7%-bc-1 Group XII (Hg-group) Hg Hairy glume 0 d-20 hayayuki dwarf 17 Unlocated gene lhs-2 (lhs) leafy hull sterile-2 8.2%-Hg fgl-group, chromosome-7 pgl pale green leaf 0 Rf-1 pollen fertility restoration-1 12 fgl (fl) faded green leaf 12.5 Unlocated genes Bph-3 Brown planthopper resistance-3 trisomic C bph-4 Brown planthopper resistance-4 30%-rk-2 du dull endosperm trisomic C Ef-2 Earliness-2 7.8%-RT3-7 Glh-3 Green planthopper resistance -3 34%-bph-4 rk-2 round kernel-2 2.5%-RT7-9 d-33 group, chromosome 4 (Unlocated genes) d-33 (d-B) bonsaito dwarf trisomic A nal-3 (nal-2) narrow leaf-3 19%-RT3-4b rl-3 (rl-1) rolled leaf 13%-RT4-12 spl-1 (bl-12) spotted leaf-1 1.7%-RT3-4a su-group, chromosome-12 (Unlocated genes) An-4(t) Awn-4 5.0%-RT10-12b d-51 (d-K-8) dwarf Kyushu-8 trisomic D Stv-b (St-2) striped virus resistance linked with RT3-12 su sugary endosperm trisomic D ur-2 undulate rachis-2 trisomic D v-8 virescent-8 trisomic D z-4 zebra-4 trisomic D