Rice Genetics IV - IRRI books - International Rice Research Institute

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Transposon library generation10 starter enhancer trap linesT 12,000 total seeds (200 seeds each)Selection for BAR heterozygotes (1/2)1,000 selfed plants selectedSU1BART 2200,000 total seedsSelection for BAR heterozygotes (1/2)100,000 selfed plants selectedSU1BART 320,000,000 total seedsBAR-SU1 selectionSU1 negative (1/4) = 5,000,000{ }Frequency of independent transpositions (10%) = 500,000Frequency of unlinked transpositions (30%)150,000 stable independent insertionsSU1SU1BARBARFig. 5. Transposon library generation. Using a minimum of 10 active single-locus starter enhancertrap lines, with a multiplication rate of 200 seeds per plant (Nipponbare), a total of200,000 T 2 seeds can be obtained from heterozygous plants that are identified on the basis ofprogeny-test segregation for Basta R . Similarly, from the 200,000 plants, half are heterozygotesand are identified by progeny tests in the T 3 generation, in which 20 million seeds areproduced from the heterozygous parents and can be used for selection of the population ofstable transposants. A sketch of the T-DNA carrying the SU1 and BAR (on transposon) markersis shown alongside. Using Basta R and SU1 selection, only the plants bearing a Basta Rtransposed element (BAR + SU1 – ) are selected, whereas all SU1-bearing plants (withtransposase) are rejected. The frequency of independent transposition was observed to be10% and that of unlinked transposition about 30%, which will generate about 150,000 stableindependent insertions.274 Greco et al
ReferencesBaldwin D, Crane V, <strong>Rice</strong> D. 1999. A comparison of gel-based, nylon filter and microarraytechniques to detect differential RNA expression in plants. Curr. Opin. Plant Biol. 2:96-103.Baker B, Schell J, Lörz H, Fedoroff N. 1986. Transposition of the maize controlling element‘Activator’ in tobacco. Proc. Natl. Acad. Sci. USA 83:4844-4848.Baker B, Coupland G, Fedoroff N, Starlinger P, Schell J. 1987. Phenotypic assay for excisionof the maize controlling element Ac in tobacco. EMBO J. 6:1547-1554.Balcells L, Coupland G. 1994. The presence of enhancers adjacent to the Ac promoter increasesthe abundance of transposase mRNA and alters the timing of Ds excision in Arabidopsis.Plant Mol. Biol. 24:789-798.Burns N, Grimwade R, Macdonald PB, Choi E-Y, Finberg K, Roeder GS, Snyder M. 1994.Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomycescerevisiae. Genes Dev. 8:1087-1105.Chin HG, Choe MS, Lee S-H, Park SH, Koo JC, Kim NY, Lee JJ, Oh BG, Yi GH, Kim SC,Choi HC, Cho MJ, Han CD. 1999. Molecular analysis of rice plants harboring an Ac/Dstransposable element-mediated gene trapping system. Plant J. 19:615-623.Chiu W, Niwa Y, Zeng W, Hirano T, Kobayashi H, Sheen J. 1996. Engineered GFP as a vitalreporter in plants. Curr. Biol. 6:325-330.Christou O, Ford T, Kofron M. 1991. Production of transgenic rice (Oryza sativa L.) fromagronomically important indica and japonica varieties via electric discharge particle accelerationof exogenous DNA into immature zygotic embryos. Bio/Technology 9:957-962.Davis SJ, Vierstra RD. 1998. Soluble, highly fluorescent variants of green fluorescent protein(GFP) for use in higher plants. Plant Mol. Biol. 36:521-528.Dove A. 1999. Proteomics: translating genomics into products. Nat. Biotechnol. 17:233-236.Enoki H, Izawa T, Kawahara M, Komatsu M, Koh S, Kyozuka J, Shimamoto K. 1999. Ac as atool for the functional genomics of rice. Plant J. 19:605-613.Gale MD, Devos KM. 1998. Plant comparative genetics after 10 years. Science 282:656-659.Greenblatt IM. 1984. A chromosome replication pattern deduced from pericarp phenotypesresulting from movements of the transposable element Modulator, in maize. <strong>Genetics</strong>108:471-485.Hiei Y, Ohta S, Komari T, Kumashiro T. 1994. Efficient transformation of rice (Oryza sativaL.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA.Plant J. 6:271-282.Hirochika H. 1997. Retrotransposons of rice: their regulation and use for genome analysis.Plant Mol. Biol. 35:231-240.Izawa T, Miyazaki C, Yamamoto M, Terada R, Iida S, Shimamoto K. 1991. Introduction andtransposition of the maize transposable element Ac in rice (Oryza sativa L.). Mol. Gen.Genet. 227:391-396.Izawa T, Ohnishi T, Nakano T, Ishida N, Enoki H, Hashimoto H, Itoh K, Terada R, Wu C,Miyazaki C, Endo T, Iida S, Shimamoto K. 1997. Transposon tagging in rice. Plant Mol.Biol. 35:219-229.Jones JDG, Carland FM, Lin E, Ralston E, Dooner HK. 1990. Preferential transposition of themaize element Activator to linked chromosomal locations in tobacco. Plant Cell 2:701-707.Koprek T, McElroy D, Louwerse J, Williams-Carrier R, Lemaux PG. 1999. Negative selectionsystems for transgenic barley (Hordeum vulgare L.): comparison of bacterial codA- andcytochrome P450 gene-mediated selection. Plant J. 19:719-726.Transposons and functional genomics in rice 275
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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
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Nagao S. 1951. Genic analysis and l
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Yoshimura S, Yamanouchi U, Katayose
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important traits for which segregat
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trolled by a single recessive gene,
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AromaAromatic rice varieties often
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Submergence tolerance is an interes
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Kinoshita T, Maekawa M. 1986. Genet
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NotesAuthors’ addresses: J.N. Rut
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The Rockefeller Foundation has a lo
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Evolution and implementation of the
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Scientific progress and outputsIn t
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Another salient example is that of
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BOX NO. 1recent international works
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For the purposes of this discussion
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Because of the great diversity (sci
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eeders where final products to enha
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Chen S, Lin XH, Xu CG, Zhang Q. 200
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Toenniessen GH. 1998. Rice biotechn
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Molecular markers,genetic diversity
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Evolution and domestication of rice
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ABCDO. barthiiO. rufipogonO. longis
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Wild(O. rufipogon)Geographical diff
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South Asia (particularly on the wes
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al 1992, Sun et al 1996a,b,c), thou
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wild and cultivated types (Est10, W
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Cai HW, Morishima H. 2000a. Diversi
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Sato YI, Tang SX, Yang LU, Tang LH.
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The solid base laid by classical ri
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The synthesis shown in Figure 1 is
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Arabidopsis, long heralded as a “
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Monocots and eudicots: Is there sti
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Zhang H, Jia J, Gale MD, Devos KM.
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ility of rice productivity (Lu 1999
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Table 1 continuedIntrageneric class
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Molecular markers and evolutionary
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A100100521010078100991009894100O. s
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Two distinct types of sequences wer
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arthii and O. longistaminata, and t
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testing Ka/Ks between the homeologo
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Roschevicz RI. 1931. A contribution
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Miniature inverted repeattransposab
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eau and Wessler 1992, 1994), rice (
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MITEs as a source of allelic divers
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ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
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Le QH, Wright S, Yu Z, Bureau T. 20
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Microsatellite markers in rice:abun
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make the best SSR markers for rice.
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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
Page 235 and 236: Miropeats-OSJNBa0065H03 1.2 cMThres
Page 237: NotesAuthors’ addresses: R.A. Win
Page 240 and 241: Sasaki 1997). Such analysis is ofte
Page 242 and 243: ABNipponbare × KasalathF 2QTL anal
Page 244 and 245: were classified into two groups bas
Page 246 and 247: effective at determining the genoty
Page 248 and 249: addition, some accessions of wild r
Page 250 and 251: Sasaki T, Burr T. 2000. Internation
Page 252 and 253: Mutational analysis has long been t
Page 254 and 255: marked by a deletion/chromosomal re
Page 256 and 257: analysis suggests that the mutation
Page 258 and 259: For drought-response screening, our
Page 260 and 261: Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
Page 262 and 263: Although mutants with discrete gene
Page 265 and 266: Generation of T-DNA insertionaltagg
Page 267 and 268: Aprobe AEEprobe BpGA1633RBgus Tn p3
Page 269 and 270: Number of loci36%224%170%010 20 30F
Page 271 and 272: Table 2. GUS assay in roots of tran
Page 273 and 274: 1999, Krysan et al 1999, Sato et al
Page 275 and 276: Transposons and functionalgenomics
Page 277 and 278: cesses. To study the interactions a
Page 279 and 280: Constructs were made with the aim o
Page 281 and 282: RBcis-effect of the adjacent strong
Page 283 and 284: Ac knockout mutagenesisThe Ac lines
Page 285: Table 2 summarizes the transformati
Page 289: NotesAuthors’ addresses: R. Greco
Page 292 and 293: These include T-DNA (Azpiroz-Leehan
Page 294 and 295: polyproteins and two identical 138-
Page 296 and 297: mutant. The mutation in the ent-kau
Page 298 and 299: primers (G1, G2) and two Tos17-spec
Page 300 and 301: of insertion mutants by sequencing
Page 302 and 303: Grandbastien M-A, Spielman A, Caboc
Page 304 and 305: NotesAuthors’ addresses: H. Hiroc
Page 306 and 307: human endeavor, greatly contributed
Page 308 and 309: Equally important as the genomic in
Page 310 and 311: Oryzabase is one of the most recent
Page 312 and 313: Database structureA characteristic
Page 314 and 315: types of users. An annotation datab
Page 316 and 317: ReferencesAntonio BA, Fang Z, Sanch
Page 319 and 320: Gene isolation and functionEnhancin
Page 321 and 322: Enhancing deployment of genes forbl
Page 323 and 324: mochi and Tsuyuake (Wu et al 1996).
Page 325 and 326: tive indica rice varieties supports
Page 327 and 328: transcription factor, resulting in
Page 329 and 330: facilitate breeding durable resista
Page 331 and 332: (Inukai et al 1994, Yu et al 1996,
Page 333 and 334: Rossman AY, Howard RJ, Valent B. 19
Page 335 and 336: 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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