Rice Genetics IV - IRRI books - International Rice Research Institute

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Tinland B. 1996. The integration of T-DNA into plant genomes. Trends Plant Sci. 1:178-184.Tsukamoto Y, Ikeda H. 1998. Double-strand break repair mediated by DNA end-joining. GenesCells 3:135-144.Twyman RM, Whitelaw CAB. 2000. Animal cell genetic engineering. In: Spier RE, editor.Encyclopedia of cell technology. New York (USA): John Wiley & Sons. p 737-819.Twyman RM, Christou P, Stoger E. n.d. Genetic transformation of plants and their cells. In:Oksman-Caldentey KM, Barz W, editors. Plant biotechnology and transgenic plants. NewYork (USA): Marcel & Dekker. (In press.)NotesAuthors’ address: Molecular Biotechnology Unit, John Innes Center, Colney Lane,Norwich NR4 7UH, U.K.Citation: Khush GS, Brar DS, Hardy B, editors. 2001. Rice genetics IV. Proceedings of theFourth International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines.New Delhi (India): Science Publishers, Inc., and Los Baños (Philippines): InternationalRice Research Institute. 488 p.464 Christou et al
Gene silencing and itsreactivation in transgenic riceT.C. Hall, S.P. Kumpatla, P. Kharb, L. Iyer, M. Cervera, Y. Jiang, T. Wang,G. Yang, P. Teerawanichpan, J. Narangajavana, and J. DongGenome surveillance systems of higher organisms protect not only againstintragenomic parasites such as retroposons and transposons but also againstinvasive DNA introduced via genome transformation, resulting in (trans)genesilencing at both the transcriptional and posttranscriptional levels. Transcriptionalgene silencing of both bialaphos resistance and Btt CryIIIA crystal toxingenes was encountered in experiments targeted to provide resistance to therice water weevil. Extensive methylation of the transgenes, especially of thepromoter elements, was evident. Germination of seedlings from silenced linesin the presence of 5-azacytidine (which prevents cytosine methylation) led tothe reactivation of bialaphos resistance in progeny of silenced plants. TheCaMV 35S promoter has been implicated in many instances of silencing andthe possibility that some promoters are especially prone to silencing is supportedby the finding that RCg2, a rice root-specific promoter, is silenced inmore than 80% of transformants. Genes flanking RCg2/uidA are rarely silenced,showing that silencing can be highly targeted. Multicopy insertionsare very susceptible to silencing and epistatic interactions between multicopyand single-copy inserts are documented. Several strategies to alleviate silencinghave been considered, such as sequence diversification and flankingtransgene inserts with matrix attachment regions.The ability to isolate genes and transfer them among organisms so that they are expressedin an alien genomic background is surely one of the most exciting discoveriesof the 20th century. Such expression has provided great insight into the fundamentalprinciples of biology as well as opening new practical opportunities for the improvementof crops and the development of novel pharmaceutical products. The realizationthat some transgenes do not express as anticipated is a significant challenge for geneticengineering of crops, but is also leading to an unanticipated understanding ofepigenetic phenomena that were previously perplexing (Wolffe and Matzke 1999).Indeed, over the past decade it has become abundantly clear that some genome surveillancesystems complement and may even evolutionarily precede better knownGene silencing and its reactivation in transgenic rice 465
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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
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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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Page 427 and 428: an ambisense coding strategy (Fig.
Page 429 and 430: first produced and shown to have vi
Page 431 and 432: McLean GD, Evans G. 1997. Some pote
Page 433: Waterhouse PM, Upadhyaya NM. 1998.
Page 436 and 437: duction in response to dehydration
Page 438 and 439: (KIKEKLPG) in the carboxyl terminus
Page 440 and 441: These three plasmids were used to t
Page 442 and 443: We now show the effects of the toba
Page 444 and 445: Since one major goal of plant scien
Page 446 and 447: Table 4. Copy number of transgenes
Page 448 and 449: Chan M-T, Chang H-H, Ho S-L, Tang W
Page 450 and 451: NotesAuthors’ address: Department
Page 452 and 453: initially fixed by phosphoenolpyruv
Page 454 and 455: High-level expression of maize C 4-
Page 456 and 457: The effect of illumination on PPDK
Page 458 and 459: ate in 2% O 2 can be limited by Pi
Page 461 and 462: Transgene integration,organization,
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Page 465 and 466: ing transgene organization. FISH an
Page 467 and 468: ments and the integration of exogen
Page 469 and 470: Level 2: activation of local repair
Page 471 and 472: strongly suggested that plant facto
Page 473 and 474: other cases it was not. We observed
Page 475: Gorbunova V, Levy AA. 1997. Non-hom
Page 479 and 480: Carbofuran (trade name, Furadan) is
Page 481 and 482: Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
Page 483 and 484: ABCDhptuidAmUbi1kb10.08.05.04.13.0F
Page 485 and 486: Fig. 4. X-gluc staining of germinat
Page 487 and 488: eflect different causes for silenci
Page 489 and 490: Table 4. Suppressors of silencing f
Page 491 and 492: Garrick D, Fiering S, Martin DI, Wh
Page 493: Xu Y, Buchholz WG, DeRose RT, Hall
Page 496 and 497: Rice molecular breeding workshopThi
Page 498 and 499: the working group can develop a net
Page 500: Rice genetics cooperativeA meeting
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