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Table 4. Copy number of transgenes including rearranged copies.No. of No. of intact No. of GUSPlasmid Line no. Copy no. hybridization expression rearranged expressionbands a cassettes bandspAc1PG-CAM 5 2 1 2 0 +(Agrobacterium 6 4 1 4 0 + bmethod) 7 2 1 2 0 + b8 1 1 0 1 –9 2 1 2 0 +10 4 1 4 0 + b11 1 1 1 0 + b12 3 2 2 1 + bAverage 2.3 1.1 2.1 0.25pAc1PG-CAM 14 5 5 2 4 +(particle 15 1 1 0 1 –bombardment 16 4 4 1 3 +method) 17 5 3 3 2 +18 5 5 1 4 +19 10 6 5 5 +20 6 6 1 5 +21 2 2 1 1 + b22 2 1 1 1 +23 3 2 0 3 –24 2 3 1 2 +26 4 4 1 3 +Average 4.3 3.5 1.4 2.8aThe total number of hybridization bands when a two-cut-site enzyme was used to digest genomic DNA inSouthern blotting. b High expression level of GUS was observed in the anther, including pollen of theselines.plants. The size and number of the expression cassette showed the copy number ofintact and rearranged copies of the transgene. Our results showed that the averagenumber of rearranged copies of the transgenic expression cassette in transgenic plantswith pAc1PG-CAM obtained by Agrobacterium-mediated transformation was only0.25, much lower than the 2.8 obtained by using the particle bombardment method.Transgene expression and DNA rearrangement of expression cassettes. Histochemicalanalysis of GUS expression was carried out on pAc1PG-CAM-transformed R 0plants obtained by both the Agrobacterium-mediated transformation method and particlebombardment method. GUS expression levels were observed in young root tipsof all plant lines transformed with pAc1PG-CAM by the Agrobacterium-mediatedmethod except for line 8. Even though there was one copy of the gus gene integratedinto the chromosome, there was no intact gus gene expression cassette in this linebecause of DNA rearrangement. GUS expression was observed in young root tips ofall transgenic plant lines transformed with pAc1PG-CAM by the particle bombardmentmethod except in lines 15 and 23. Even though there were three copies of thegus gene in line 23 and one copy in line 15, no histochemical GUS expression wasobserved, presumably because of gene silencing related to DNA rearrangement. Inplasmid pAc1PG-CAM, Act1, which is mainly a pollen-specific promoter with low434 Cheng et al
expression levels in young root tips, was isolated from Arabidopsis (An et al 1996)Thus, randomly chosen plant lines 6, 7, 8, 10, 11, 15, 16, 17, 21, 23, and 24 were usedfor GUS histochemical analysis of pollen during the flowering stage. High GUS expressionwas observed in the pollen of plant lines 6, 7, 10, 11, 12, and 21. However,no GUS expression was observed in lines 8, 15, and 23. This further confirms theresults observed in young root tips.Future prospectsOne goal of agricultural scientists is to produce superior transgenic rice plants withhigh levels of tolerance for drought and salinity stress. Based on current knowledge,this goal can be best achieved by using a combination of the following strategies:1. Use suitable dehydration-stress-inducible promoters to drive transgene expression.2. Construct plasmids that contain several stress-tolerance genes, as well as atranscription factor gene, each of which has been shown to increase stress tolerance.3. Use suitable MAR sequences to flank the genes of interest to maximize highlevelexpression.4. Use the Agrobacterium-mediated method to transform cells in 3-wk-old calli,regenerate transgenic rice plants, and choose at least 20 transgenic plants, eachharboring a single copy of the input plasmid(s).5. Choose homozygous transgenic plant lines with stable high-level expressionof the transgene for at least six generations.6. Carry out field tests on at least ten plant lines and measure yield of rice grainsper plant under conditions with or without drought or salinity stress.ReferencesAllen GC, Spiker S, Thompson WF. 2000. Use of matrix attachment regions (MARs) to minimizetransgene silencing. Plant. Mol. Biol. 43:361-376.An Y, Huang S, McDowell M, McKinney EC, Meagher RB. 1996. Conserved expression of theArabidopsis ACT1 and ACT3 actin subclass in organ primordia and mature pollen. PlantCell 8:15-30.Bajaj S, Targolli J, Liu L-F, Ho T-HD, Wu R. 1999. Transgenic approaches to increase dehydration-stresstolerance in plants. Mol. Breed. 5:493-503.Boyer JS. 1982. Plant productivity and environment. Science 218:493-498.Bray EA. 1997. Plant responses to water deficit. Trends Plant Sci. 2:48-54.Cao J, Duan X, McElroy D, Wu R. 1992. Regeneration of herbicide resistant transgenic riceplants following microprojectile-mediated transformation of suspension cells. Plant CellRep. 11:586-591.Cao J, Wang Y-C, Klein TM, Sanford J, Wu R. 1990. Transformation of rice and maize usingthe biolistic process. In: Lamb CJ, Beachy RN, editors. Plant gene transfer. Proceedings ofUCLA Symposium. Park City, Utah (USA): Alan R. Liss Press. p 21-33.Transgenic approaches for generating rice . . . 435
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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
Page 396 and 397: Issues related to achieving synthet
Page 398 and 399: come and may use imprinting to achi
Page 400 and 401: Embryo-inducing geneInactive ablati
Page 402 and 403: M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
Page 404 and 405: embryos, several genes characterist
Page 406 and 407: Our search for a rice homologue of
Page 408 and 409: sequenced the two rice DMC1 genes a
Page 410 and 411: Gustine DL, Sherwood RT, Huff DR. 1
Page 412 and 413: Peel MD, Carman JG, Leblanc O. 1997
Page 415 and 416: TransformationEngineering for virus
Page 417 and 418: Engineering for virusresistance in
Page 419 and 420: proteins, (2) the expression of dys
Page 421 and 422: Antisense and cosuppression RNA. Ex
Page 423 and 424: 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 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,
Page 463 and 464: duced by organogenesis, somatic emb
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
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Page 473 and 474: other cases it was not. We observed
Page 475 and 476: Gorbunova V, Levy AA. 1997. Non-hom
Page 477 and 478: Gene silencing and itsreactivation
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
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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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