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gene pool, we performed QTL analysis in the cross O. sativa (indica) × O. rufipogon(perennial type) (Cai and Morishima, n.d.). Based on 125 recombinant inbred lines(RILs), 148 markers were mapped. Because this wild parent carried some japonicaspecificcharacteristics, indica-japonica diagnostic traits segregated in this mappingpopulation in addition to domestication-related traits. Among 34 quantitative traitsexamined, 22 traits revealed 1–29 putative QTLs, respectively. Several QTLs for domestication-relatedtraits were mapped over the whole genome, showing a tendencyto form clusters, each reflecting the domestication syndrome. The same situation wasobserved in QTLs for indica versus japonica diagnostic traits. In addition, some of theclusters joined the domestication syndrome clusters. Figure 4 presents examples ofgene clusters. Several isozyme loci that serve as diagnostic markers to distinguishChr. 1Chr. 8R1613(c)CDO328(c)G165bG270(w)R2635(w)G302CDO470RG345BCD828(c)CDO118(c)RB1(c)G393(cEst10(c)OP(c)gf(c)CDO345(c)Ma13G3709(W)G54(W)C112(C)RZ143(c)C400a(w)C400bG278(c)CharacterDomestication-related Heading Indica/japonica-related SizeSHA DOR AWL ANL P/T DTH BVP KCL APH GMS LTR PTB MSL SWDG104(w)R1394AG2132(c)G187(c)RG181(c)Amp2(c)Fig. 4. Examples of QTL clusters (chromosomes 1 and 8). Genomic regions affecting the respectivetraits (LOD>2.8) are shown by the bars to the right of linkage groups. Character code:SHA = seed shattering, DOR = seed dormancy, AWL = awn length, ANL = anther length, P/T =panicle number/tiller number, DTH = days to heading, BVP = basic vegetative phase, KCL =KClO 3 resistance, APH = apiculus hair length, GMS = germination speed, LTR = low-temperatureresistance, PTB = panicle neck to lowest branch, MSL = mesocotyl length, SWD = spikeletwidth. The small spindle on the chromosome shows the approximate position of the centromere.(Adapted from Cai and Morishima, n.d.)72 Morishima
wild and cultivated types (Est10, Wang XK et al 1992) and indica and japonica types(such as Cat1 and Amp2) were found in or near the QTL clusters. Similar clusterphenomena of domestication-related QTLs were reported by Koinange et al (1996)in common bean and by Xiong et al (1999) in rice.To determine whether QTL clusters are loosely linked loci or a single locus witha pleiotropic effect, more precise analysis is necessary. It is interesting to note thatQTLs for mesocotyl length, which is considered to reflect endogenous hormone level,tended to join those clusters. This might suggest a possibility that the clustering phenomenonis partly due to the pleiotropic effect of an unknown key factor controllingvarious traits through hormonal regulation.In this O. sativa × O. rufipogon cross, character correlations were generally weakamong RILs that represent essentially F 2 variation. This implies that nonrandom characterassociations of the domestication syndrome are mainly due to natural selectionfor coadapted traits. The present analysis revealed several QTL linkages reflectingthe domestication syndrome. Since they were located on different chromosomes, theysegregated into RILs, resulting in decreased correlations. This phenomenon could beunderstood by “multifactorial linkages” advocated by Grant (1975). This phenomenonis inevitably caused by random distribution of multiple factors over the limitednumber of chromosomes that determine the differences in two or more quantitativecharacters.QTL clusters thus identified were mapped on the regions in which cultivar-derivedalleles segregated at higher frequencies than expected. This coincidence couldbe explained by unconscious selection, which worked under cultivation pressure whenestablishing RILs favoring the combination of cultivar-derived gene blocks.Inference for domestication dynamicsThe domestication process is undoubtedly a gradual process directed by humans. Inrice, Oka and Morishima (1971) demonstrated early that “cultivation pressure” broughtabout a rapid change in population genotype toward the cultivated type as suggestedby Harlan (1975). Seed shedding is the critical trait disruptively selected in naturaland cultivated fields. The genetic basis of seed shedding is simpler than other domestication-relatedtraits. Eiguchi and Sano (1990) identified two loci conferring highseed shedding on O. rufipogon, one of which was linked to the spreading paniclelocus on chromosome 4. Our QTL analysis detected five loci for seed shedding andone of them located on chromosome 1 was linked with another spreading paniclelocus (Cai and Morishima 2000b). A spreading panicle is advantageous for wild riceto disperse seeds but disadvantageous for cultivated rice. It may be reasonable toinfer that selection for nonshedding genes with relatively large effects played an importantrole as a trigger for domestication.Our experiments with another cross (O. sativa × O. rufipogon) showed that associationamong seed shedding, seed dormancy, and awn length tended to increase inlater hybrid generations without deliberate selection (Table 3). In the cross propagatedin bulk, the outcrossing rate was higher in the lines with wild characteristicsthan in those with cultivated-rice characters (Table 3). This suggests that flower char-Evolution and domestication of rice 73
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Retrotransposons of rice as a tool
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First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
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Rice genetics from Mendelto functio
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nese cultivar Nipponbare. The chrom
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Gene symbolization in riceIn the ab
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Table 2. Some examples of mapping g
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and YAC libraries, respectively. Th
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gene from wild species is the intro
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ReferencesAbbasi FM, Brar DS, Carpe
Page 35 and 36: Nagao S. 1951. Genic analysis and l
Page 37: Yoshimura S, Yamanouchi U, Katayose
Page 40 and 41: important traits for which segregat
Page 42 and 43: trolled by a single recessive gene,
Page 44 and 45: AromaAromatic rice varieties often
Page 46 and 47: Submergence tolerance is an interes
Page 48 and 49: Kinoshita T, Maekawa M. 1986. Genet
Page 50 and 51: NotesAuthors’ addresses: J.N. Rut
Page 52 and 53: The Rockefeller Foundation has a lo
Page 54 and 55: Evolution and implementation of the
Page 56 and 57: Scientific progress and outputsIn t
Page 58 and 59: Another salient example is that of
Page 60 and 61: BOX NO. 1recent international works
Page 62 and 63: For the purposes of this discussion
Page 64 and 65: Because of the great diversity (sci
Page 66 and 67: eeders where final products to enha
Page 68 and 69: Chen S, Lin XH, Xu CG, Zhang Q. 200
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 73 and 74: Molecular markers,genetic diversity
Page 75 and 76: Evolution and domestication of rice
Page 77 and 78: ABCDO. barthiiO. rufipogonO. longis
Page 79 and 80: Wild(O. rufipogon)Geographical diff
Page 81 and 82: South Asia (particularly on the wes
Page 83: al 1992, Sun et al 1996a,b,c), thou
Page 87 and 88: Cai HW, Morishima H. 2000a. Diversi
Page 89: Sato YI, Tang SX, Yang LU, Tang LH.
Page 92 and 93: The solid base laid by classical ri
Page 94 and 95: The synthesis shown in Figure 1 is
Page 96 and 97: Arabidopsis, long heralded as a “
Page 98 and 99: Monocots and eudicots: Is there sti
Page 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 114 and 115: testing Ka/Ks between the homeologo
Page 116 and 117: Roschevicz RI. 1931. A contribution
Page 119 and 120: Miniature inverted repeattransposab
Page 121 and 122: eau and Wessler 1992, 1994), rice (
Page 123 and 124: MITEs as a source of allelic divers
Page 125 and 126: ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
Page 127 and 128: Le QH, Wright S, Yu Z, Bureau T. 20
Page 129 and 130: Microsatellite markers in rice:abun
Page 131 and 132: make the best SSR markers for rice.
Page 133 and 134: Predicted frequency100,00080,000Cla
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Relationship between SSRs and genes
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are indicated with RM locus designa
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SSRs have been used to define intro
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provide a bridge for moving rapidly
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Ishii T, McCouch SR. 2000. Microsat
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NotesAuthors’ addresses: S.R. McC
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traits of economic importance (Mack
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Table 2. Tagging and mapping of som
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even at the juvenile stage. Several
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Chen et al (2000) transferred the b
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genome sequence of rice, this will
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Kurata N, Nagamura Y, Yamamoto K, H
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Witcombe JR, Hash CT. 2000. Resista
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QTL mapping in rice:a few critical
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M-QTLsM-QTLs are defined as single
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(genetic/statistical models and cor
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Table 5. The percentage of three ty
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Table 7. Some environment-specific
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ferently to the environments. Simil
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(case 3), one may infer that this g
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Simultaneous QTL introgression and
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Doebley J, Stec A, Gustus C. 1995.
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Visscher PM, Haley CS, Thompson R.
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unavailable until recently with the
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Table 1 continued.Trait QTL a Flank
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the remaining parts of the linkage
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Table 3. QTLs detected for yield an
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Table 6. Correlations of various pa
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The functions of these sequences ne
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Structural and functional genomicsT
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The International Rice GenomeSequen
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the RGP, a PAC (P1-derived artifici
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Progress of sequencing in the RGPWe
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ice genome sequencing to organize a
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Strategies and techniquesfor finish
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uses the quality values generated b
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with the advanced techniques requir
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times contain sufficient data to ma
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amplification of regions that previ
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4. Structure problems—subcloning
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estriction maps or optical maps are
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nal assembly may point to areas tha
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McMurray AA, Sulston JE, Quail MA.
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Sequence-tagged connector/DNA finge
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1999). The development of multiple-
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Transposable elements in the rice H
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ers, maps, mapping populations, and
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Miropeats-OSJNBa0065H03 1.2 cMThres
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NotesAuthors’ addresses: R.A. Win
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Sasaki 1997). Such analysis is ofte
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ABNipponbare × KasalathF 2QTL anal
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were classified into two groups bas
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effective at determining the genoty
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addition, some accessions of wild r
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Sasaki T, Burr T. 2000. Internation
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Mutational analysis has long been t
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marked by a deletion/chromosomal re
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analysis suggests that the mutation
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For drought-response screening, our
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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
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Although mutants with discrete gene
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Generation of T-DNA insertionaltagg
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Aprobe AEEprobe BpGA1633RBgus Tn p3
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Number of loci36%224%170%010 20 30F
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Table 2. GUS assay in roots of tran
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1999, Krysan et al 1999, Sato et al
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Transposons and functionalgenomics
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cesses. To study the interactions a
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Constructs were made with the aim o
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RBcis-effect of the adjacent strong
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Ac knockout mutagenesisThe Ac lines
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Table 2 summarizes the transformati
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ReferencesBaldwin D, Crane V, Rice
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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types of users. An annotation datab
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ReferencesAntonio BA, Fang Z, Sanch
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Gene isolation and functionEnhancin
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Enhancing deployment of genes forbl
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mochi and Tsuyuake (Wu et al 1996).
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tive indica rice varieties supports
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transcription factor, resulting in
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facilitate breeding durable resista
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(Inukai et al 1994, Yu et al 1996,
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Rossman AY, Howard RJ, Valent B. 19
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Molecular signaling in diseaseresis
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AOsRac1IED II III IV 214aaOsRac1 KC
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Japonica rice variety Kinmaze, whic
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Table 1. Characteristics of lesion-
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an effective inducer of host resist
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Takahashi A, Kawasaki T, Henmi K, S
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et al 2000). Sequence analysis of t
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612-amino acid protein, including t
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Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
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Isolation of candidate genesfor tol
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Materials and methodsPlant material
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Microarray hybridization and data a
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Table 3. Most abundant transcripts
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Microarray technologyThe rapid accu
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view of procedures, pitfalls, and n
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Log(2) ratio1.51.0OC104E01—WCP1OC
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Table 5. Strongly regulated transcr
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ReferencesAdams MD, Soares MB, Kerl
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Acknowledgments: We thank Chris Bor
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y cells separating during tissue de
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(Erwee and Goodwin 1983). The sympl
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tion between the abundance of CDK t
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in a complex of 105 kDa. These resu
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Drew MC, Jackson MB, Giffard S. 197
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Umeda M, Umeda-Hara C, Yamaguchi M,
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asexual reproduction through apomix
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MPManual pollination by breeders×
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Search for apomixis in riceThere ar
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Issues related to achieving synthet
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come and may use imprinting to achi
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Embryo-inducing geneInactive ablati
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M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
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embryos, several genes characterist
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Our search for a rice homologue of
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sequenced the two rice DMC1 genes a
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Gustine DL, Sherwood RT, Huff DR. 1
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Peel MD, Carman JG, Leblanc O. 1997
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TransformationEngineering for virus
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Engineering for virusresistance in
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proteins, (2) the expression of dys
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Antisense and cosuppression RNA. Ex
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Table 1. Transgenic rice with patho
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the disease symptoms. Efforts from
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an ambisense coding strategy (Fig.
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first produced and shown to have vi
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McLean GD, Evans G. 1997. Some pote
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Waterhouse PM, Upadhyaya NM. 1998.
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duction in response to dehydration
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(KIKEKLPG) in the carboxyl terminus
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These three plasmids were used to t
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We now show the effects of the toba
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Since one major goal of plant scien
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Table 4. Copy number of transgenes
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Chan M-T, Chang H-H, Ho S-L, Tang W
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NotesAuthors’ address: Department
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initially fixed by phosphoenolpyruv
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High-level expression of maize C 4-
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The effect of illumination on PPDK
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ate in 2% O 2 can be limited by Pi
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Transgene integration,organization,
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duced by organogenesis, somatic emb
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ing transgene organization. FISH an
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ments and the integration of exogen
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Level 2: activation of local repair
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strongly suggested that plant facto
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other cases it was not. We observed
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Gorbunova V, Levy AA. 1997. Non-hom
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Gene silencing and itsreactivation
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Carbofuran (trade name, Furadan) is
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Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
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ABCDhptuidAmUbi1kb10.08.05.04.13.0F
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Fig. 4. X-gluc staining of germinat
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eflect different causes for silenci
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Table 4. Suppressors of silencing f
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Garrick D, Fiering S, Martin DI, Wh
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Xu Y, Buchholz WG, DeRose RT, Hall
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Rice molecular breeding workshopThi
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the working group can develop a net
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Rice genetics cooperativeA meeting
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