Rice Genetics IV - IRRI books - International Rice Research Institute

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Stam M, de Bruin R, Kenter S, van der Hourn RAL, van Blokland R, Mol JNM, Kooter JM.1997. Post-transcriptional silencing of chalcone synthase in Petunia by inverted transgenerepeats. Plant J. 12:63-82.Tacke E, Salamini F, Rohde W. 1996. Genetic engineering of potato for broad spectrum protectionagainst virus infection. Nat. Biotechnol. 14:1597-1601.Tavladoraki P, Benvenuto E, Trinca S, DeMartinis D, Cattaneo A, Galeffi P, De Martinis D.1993. Transgenic plants expressing a functional single-chain Fv antibody are specificallyprotected from virus attack. Nature 366:469-472.Tenllado F, Garcia-Luque I, Serra MT, Diaz-Ruiz JR. 1995. Nicotiana benthamiana plantstransformed with the 54-kDa region of the pepper mild mottle tobravirus replicase geneexhibit two types of resistance responses against viral infection. Virology 211:170-183.Tepfer M, Balazs E. 1997. Virus-resistant transgenic plants: potential ecological impact. Heidelberg,Berlin (Germany): Springer-Verlag. 126 p.Tien P, Wu G. 1991. Satellite RNA for the biocontrol of plant disease. Adv. Virus Res. 39:321-339.Truve E, Aaspôllu A, Honkanen J, Puska R, Mehto M, Hassl A, Teeri TH, Kelve M, SeppanenP, Saarma M. 1993. Transgenic potato plants expressing mammalian 2’-5’ oligoadenylatesynthetase are protected from potato virus X infection under field conditions. Bio/Technology11:1048-1052.Upadhyaya NM, Yang M, Kositratana W, Ghosh A, Waterhouse PM. 1995. Molecular analysisof rice ragged stunt oryzavirus segment S9 and sequence conservation among isolates fromThailand and India. Arch. Virol. 140:1945-1956.Upadhyaya NM, Li Z, Yang M, Kositratana W, Waterhouse PM. 1996. Rice ragged stunt virussynthetic resistance genes and japonica rice transformation. In: Khush GS, editor. Ricegenetics III. Proceedings of the Third International Rice Genetics Symposium, 16-20 Oct.1995, Manila (Philippines). Manila (Philippines): International Rice Research Institute.p 773-779.Upadhyaya NM, Ramm K, Li Z, Kositratana M, Waterhouse PM. 1998a. Rice ragged stuntoryzavirus genome segment S4 could encode an RNA dependent RNA polymerase and asecond protein of unknown function. Arch. Virol.143:1815-1822.Upadhyaya NM, Li Z, Ramm K, Gaudron J, Waterhouse PM, Wang M-B, Kositratana W, GongZ-X. 1998b. Production of transgenic rice with rice ragged stunt virus synthetic resistancegenes. In: Drew RA, editor. Proceedings of the International Symposium on Biotechnologyof Tropical and Subtropical Species. Acta Hortic. 461:393-400.van den Elzen PJM, Huisman MJ, Posthumus-L, Willink D, Jongedijk E, Hoekema A,Cornelissen BJ. 1989. Engineering virus resistance in agricultural crops. Plant Mol. Biol.13:337-346.Wang M-B, Waterhouse PM. 2000. High efficient silencing of a β-glucuronidase gene in rice iscorrelated with repetitive transgene structure but is independent of DNA methylation. PlantMol. Biol. 43:67-82.Watanabe Y, Ogawa T, Takahashi H, Ishida I, Takeuchi Y, Yamamoto M, Okada Y. 1995. Resistanceagainst multiple plant viruses in plants mediated by double-stranded RNA-specificribonuclease. FEBS Lett. 372:165-168.Waterhouse PM, Graham MW, Wang M-B. 1998. Virus resistance and gene silencing in plantscan be induced by simultaneous expression of sense and antisense RNA. Proc. Natl. Acad.Sci. USA 95:13959-13964.Waterhouse PM, Smith NA, Wang M-B. 1999. Virus resistance and gene silencing: killing themessenger. Trends Plant Sci. 4:452-457.420 Upadhyaya et al
Waterhouse PM, Upadhyaya NM. 1998. Genetic engineering of virus resistance. In: ShimamotoK, editor. Molecular biology of rice. Tokyo (Japan): Springer-Verlag. p 257-282.Wilson TMA, Watkins PAC. 1986. Influence of exogenous viral coat protein on thecotranslational disassembly of tobacco mosaic virus (TMV) particles in vitro. Virology149:132-135.Wisniewski LA, Powell PA, Nelson RS, Beachy RN. 1990. Local and systemic spread of tobaccomosaic virus in transgenic tobacco. Plant Cell 2:559-567.Yan Y-T, Wang J-F, Qiu B-S, Tien P. 1997. Resistance to rice stripe virus conferred by expressionof coat protein in transgenic indica rice plants regenerated from bombarded suspensioncultures. Virol. Sin. 12:260-269.Yang X-C, Ye Y, Zhu F, Liu Y-L, Kang L-Y, Wang X-F, Tien P. 1997. Ribozyme-mediated highresistance against potato spindle tuber viroid in transgenic potatoes. Proc. Natl. Acad. Sci.USA 94:4861-4865.Yassi MNA, Ritzenthaler C, Brugidou C, Fauquet C, Beachy RN. 1994. Nucleotide sequenceand genome characterization of rice yellow mottle virus RNA. J. Gen. Virol. 75:249-257.Zheng HH, Li Y, Yu ZH, Li W, Chen MY, Ming XT, Casper R, Chen ZL. 1997. Recovery oftransgenic rice plants expressing the rice dwarf virus outer coat protein gene (S8). Theor.Appl. Genet. 94:522-527.NotesAuthors’ addresses: N.M. Upadhyaya, Z. Li, M-B. Wang, P.M. Waterhouse, CSIRO Plant Industry,Canberra, ACT 2601, Australia; S. Chen, Zhejiang Academy of Agricultural Sciences,Hangzhou, China; Z-X. Gong, The Institute of Biochemistry and Cell Biology, ShanghaiInstitute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200030,China, E-mail: N.Upadhyaya@pi.csiro.au.Acknowledgments: We would like to thank research teams from the International Laboratoryfor Tropical Agricultural Biotechnology (ILTAB), Scripps Research Institute, USA (E.Sivamani, P. Shen, C.A. Ong, H. Huet, A. de Kochko, C. Fauquet, and R. Beachy), fromCIAT, Colombia (Z. Lentini, L. Calvert, I. Lozano, E. Tabres, M. Cuervo, and E. Restrepo),and from ITH Jurich, Switzerland (J. Fütterer and I. Potrykus), for allowing access to theirunpublished information. We would also like to thank W. Kositratana, Kasetsart University,Thailand, for collaboration on the RRSV genome organization study, K. Ramm, J.Gaudron, J. Gellately, M. Yang, and E. Zinkowsky for technical support, Andrew Eamensfor technical editing, and Roger Hull for valuable comments on the manuscript. We gratefullyacknowledge financial support from the Rockefeller Foundation for our RRSV research.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.Engineering for virus resistance in rice 421
Page 6:
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
Page 64 and 65:
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
Page 85 and 86:
wild and cultivated types (Est10, W
Page 87 and 88:
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
Page 125 and 126:
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
Page 382 and 383: tion between the abundance of CDK t
Page 384 and 385: in a complex of 105 kDa. These resu
Page 386 and 387: Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389: Umeda M, Umeda-Hara C, Yamaguchi M,
Page 390 and 391: asexual reproduction through apomix
Page 392 and 393: MPManual pollination by breeders×
Page 394 and 395: 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
Page 425 and 426: the disease symptoms. Efforts from
Page 427 and 428: an ambisense coding strategy (Fig.
Page 429 and 430: first produced and shown to have vi
Page 431: McLean GD, Evans G. 1997. Some pote
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,
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
Page 471 and 472: strongly suggested that plant facto
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
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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
Page 496 and 497:
Rice molecular breeding workshopThi
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the working group can develop a net
Page 500:
Rice genetics cooperativeA meeting
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