Rice Genetics IV - IRRI books - International Rice Research Institute

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ReferencesAmedeo P, Habu Y, Afsar K, Scheid OM, Paszkowski J. 2000. Disruption of the plant geneMOM releases transcriptional silencing of methylated genes. Nature 405:203-206.Assaad FF, Tucker KL, Signer ER. 1993. Epigenetic repeat-induced gene silencing (RIGS) inArabidopsis. Plant Mol. Biol. 22:1067-1085.Battraw MJ, Hall TC. 1991. Stable transformation of Sorghum bicolor protoplasts with chimericneomycin phosphotransferase II and β-glucuronidase genes. Theor. Appl. Genet.82:161-168.Baulcombe D. 1999. Viruses and gene silencing in plants. Arch. Virol. Suppl. 15:189-201.Bernardi G. 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet.29:445-476.Bestor TH, Tycko B. 1996. Creation of genomic methylation patterns. Nat. Genet. 12:363-367.Bird AP, Wolffe AP. 1999. Methylation-induced repression—belts, braces, and chromatin. Cell99:451-454.Buchholz WG, Teng W, Wallace D, Ambler JR, Hall TC. 1998. Production of transgenic rice(Oryza sativa subspecies japonica cv. Taipei 309). Methods Mol. Biol. 81:383-396.Cogoni C, Macino G. 1999a. Gene silencing in Neurospora crassa requires a protein homologousto RNA-dependent RNA polymerase. Nat. 399:166-169.Cogoni C, Macino G. 1999b. Homology-dependent gene silencing in plants and fungi: a numberof variations on the same theme. Curr. Opin. Microbiol. 2:657-662.Dong JJ, Teng WM, Buchholz WG, Hall TC. 1996. Agrobacterium-mediated transformation ofjavanica rice. Mol. Breed. 2:267-276.Dorer DR, Henikoff S. 1994. Expansions of transgene repeats cause heterochromatin formationand gene silencing in Drosophila. Cell 77:993-1002.Elmayan T, Balzergue S, Beon F, Bourdon V, Daubremet J, Guenet Y, Mourrain P, Palauqui JC,Vernhettes S, Vialle T, Wostrikoff K, Vaucheret H. 1998. Arabidopsis mutants impaired incosuppression. Plant Cell 10:1747-1758.English JJ, Mueller E, Baulcombe DC. 1996. Suppression of virus accumulation in transgenicplants exhibiting silencing of nuclear genes. Plant Cell 8:179-188.Fagard M, Vaucheret H. 2000. (Trans)gene silencing in plants: how many mechanisms? Annu.Rev. Plant Physiol. Plant Mol. Biol. 51:167-194.Fire A. 1999. RNA-triggered gene silencing. Trends Genet. 15:358-363.Flavell RB. 1994. Inactivation of gene expression in plants as a consequence of specific sequenceduplication. Proc. Natl. Acad. Sci. USA 91:3490-3496.Francastel C, Walters MC, Groudine M, Martin DI. 1999. A functional enhancer suppressessilencing of a transgene and prevents its localization close to centrometric heterochromatin.Cell 99:259-269.Fu X, Duc LT, Fontana S, Bong BB, Tinjuangjun P, Sudhakar D, Twyman RM, Christou P,Kohli A. 2000a. Linear transgene constructs lacking vector backbone sequences generatelow-copy-number transgenic plants with simple integration patterns. Transgenic Res. 9:11-19.Fu X, Kohli A, Twyman RM, Christou P. 2000b. Alternative silencing effects involve distincttypes of non-spreading cytosine methylation at a three-gene, single-copy transgenic locusin rice. Mol. Gen. Genet. 263:106-118.Furner IJ, Sheikh MA, Collett CE. 1998. Gene silencing and homology-dependent gene silencingin Arabidopsis: genetic modifiers and DNA methylation. <strong>Genetics</strong> 149:651-662.478 Hall et al
Garrick D, Fiering S, Martin DI, Whitelaw E. 1998. Repeat-induced gene silencing in mammals.Nat. Genet. 18:56-59.Genger RK, Kovac KA, Dennis ES, Peacock WJ, Finnegan EJ. 1999. Multiple DNAmethyltransferase genes in Arabidopsis thaliana. Plant Mol. Biol. 41:269-278.Henikoff S. 1998. Conspiracy of silence among repeated transgenes. Bioessays 20:532-535.Hirochika H, Okamoto H, Kakutani T. 2000. Silencing of retrotransposons in Arabidopsis andreactivation by the ddm1 mutation. Plant Cell 12:357-369.Iyer LM, Kumpatla SP, Chandrasekharan MB, Hall TC. 2000. Transgene silencing in monocots.Plant Mol. Biol. 43:323-346.Jeddeloh JA, Bender J, Richards EJ. 1998. The DNA methylation locus DDM1 is required formaintenance of gene silencing in Arabidopsis. Genes Dev. 12:1714-1725.Jeddeloh JA, Stokes TL, Richards EJ. 1999. Maintenance of genomic methylation requires aSWI2/SNF2-like protein. Nat. Genet. 22:94-97.Jefferson RA, Kavanaugh TA, Bevan MW. 1987. GUS fusions β-glucuronidase as a sensitiveand versatile gene fusion marker in higher plants. EMBO J. 6:3901-3908.Kakutani T, Munakata K, Richards EJ, Hirochika H. 1999. Meiotically and mitotically stableinheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana.<strong>Genetics</strong> 151:831-838.Karlin S, Campbell AM, Mrazek J. 1998. Comparative DNA analysis across diverse genomes.Annu. Rev. Genet. 32:185-225.Kohli A, Griffiths S, Palacios N, Twyman RM, Vain P, Laurie DA, Christou P. 1999. Molecularcharacterization of transforming plasmid rearrangements in transgenic rice reveals a recombinationhotspot in the CaMV 35S promoter and confirms the predominance ofmicrohomology mediated recombination. Plant J. 17:591-601.Kohli A, Leech M, Vain P, Laurie DA, Christou P. 1998. Transgene organization in rice engineeredthrough direct DNA transfer supports a two-phase integration mechanism mediatedby the establishment of integration hot spots. Proc. Natl. Acad. Sci. USA 95:7203-7208.Kumpatla SP, Chandrasekharan MB, Iyer LM, Li G, Hall TC. 1998. Genome intruder scanningand modulation systems and transgene silencing. Trends Plant Sci. 3:97-104.Kumpatla SP, Hall TC. 1998a. Longevity of 5-azacytidine-mediated gene expression and reestablishmentof silencing in transgenic rice. Plant Mol. Biol. 38:1113-1122.Kumpatla SP, Hall TC. 1998b. Recurrent onset of epigenetic silencing in rice harboring a multicopytransgene. Plant J. 14:129-135.Kumpatla SP, Hall TC. 1999. Organizational complexity of a rice transgene locus susceptibleto methylation-based silencing. IUBMB Life 48:459-467.Kumpatla SP, Teng W, Buchholz WG, Hall TC. 1997. Epigenetic transcriptional silencing and5-azacytidine-mediated reactivation of a complex transgene in rice. Plant Physiol. 115:361-373.Lindbo JA, Silva Rosales L, Proebsting WM, Dougherty WG. 1993. Induction of a highlyspecific antiviral state in transgenic plants: implications for regulation of gene expressionand virus resistance. Plant Cell 5:1749-1759.Matzke AJ, Neuhuber F, Park YD, Ambros PF, Matzke MA. 1994. Homology-dependent genesilencing in transgenic plants: epistatic silencing loci contain multiple copies of methylatedtransgenes. Mol. Gen. Genet. 244:219-229.Matzke MA, Matzke AJM, Eggleston WB. 1996. Paramutation and transgene silencing: a commonresponse to invasive DNA. Trends Plant Sci. 1:382-388.Gene silencing and its reactivation in transgenic rice 479
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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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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
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
Page 485 and 486: Fig. 4. X-gluc staining of germinat
Page 487 and 488: eflect different causes for silenci
Page 489: Table 4. Suppressors of silencing f
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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