Rice Genetics IV - IRRI books - International Rice Research Institute

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Matzke MA, Neuhuber F, Matzke AJ. 1993. A variety of epistatic interactions can occur betweenpartially homologous transgene loci brought together by sexual crossing. Mol. Gen.Genet. 236:379-386.Matzke MA, Primig M, Trnovsky J, Matzke AJM. 1989. Reversible methylation and inactivationof marker genes in sequentially transformed tobacco plants. EMBO J. 8:643-649.Meyer P. 1996. Repeat-induced gene silencing: common mechanisms in plants and fungi. Biol.Chem. Hoppe Seyler 377:87-95.Mittelsten Scheid O, Afsar K, Paszkowski Z. 1998. Release of epigenetic gene silencing bytrans-acting mutations in Arabidopsis. Proc. Natl. Acad. Sci. USA 95:632-637.Mlynárová L, Loonen A, Heldens J, Jansen RC, Keizer P, Stiekama WJ, Nap J-P. 1994. Reducedposition effect in mature transgenic plants conferred by the chicken lysozyme matrix-associatedregion. Plant Cell 6:417-426.Nap JP, Conner AJ, Mlynárová L, Stiekema WJ, Jansen RC. 1997. Dissection of a synthesizedquantitative trait to characterize transgene interactions. Genetics 147:315-320.Napoli C, Lemieux C, Jorgensen R. 1990. Introduction of a chimeric chalcone synthase geneinto petunia results in reversible co-suppression of homologous genes in trans. Plant Cell2:279-289.Neuhuber F, Park YD, Matzke AJM, Matzke MA. 1994. Susceptibility of transgene loci tohomology-dependent gene silencing. Mol. Gen. Genet. 224:230-241.Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL. 1996. Demethylation-induceddevelopmental pleiotropy in Arabidopsis. Science 273:654-657.Schmulling T, Rohrig H. 1995. Gene silencing in transgenic tobacco hybrids: frequency of theevent and visualization of somatic inactivation pattern. Mol. Gen. Genet. 249:375-390.Selker EU. 1999. Gene silencing: repeats that count. Cell 97:157-160.Spiker S, Thompson WF. 1996. Nuclear matrix attachment regions and transgene expression inplants. Plant Physiol. 110:15-21.Steimer A, Amedeo P, Afsar K, Fransz P, Scheid OM, Paszkowski J. 2000. Endogenous targetsof transcriptional gene silencing in Arabidopsis. Plant Cell 12:1165-1178.Sutton DW, Havstad PK, Kemp JD. 1992. Synthetic cryIIIA gene from Bacillus thuringiensisimproved for high expression in plants. Transgenic Res. 1:228-236.Vain P, Worland B, Kohli A, Snape JW, Christou P, Allen GC, Thompson WF. 1999. Matrixattachment regions increase transgene expression levels and stability in transgenic riceplants and their progeny. Plant J. 18:233-242.van der Geest AH, Hall TC. 1997. The β-phaseolin 5’ matrix attachment region acts as anenhancer facilitator. Plant Mol. Biol. 33:553-557.van der Krol AR, Mur LA, Beld M, Mol JNM, Stuitje AR. 1990. Flavonoid genes in Petunia:addition of a limited number of gene copies may lead to a suppression of gene expression.Plant Cell 2:291-299.Vaucheret H. 1993. Identification of a general silencer for 19S and 35S promoters in a transgenictobacco plant: 90 bp of homology in the promoter sequence are sufficient for trans-inactivation.C. R. Acad. Sci. Paris, Sciences de la vie 316:1471-1483.Vaucheret H. 1994. Promoter-dependent trans-inactivation in transgenic tobacco plants:kinetic aspects of gene silencing and gene reactivation. C. R. Acad. Sci. Paris, Sciences dela vie/Life Sciences 317:310-323.Vongs A, Kakutani T, Martienssen RA, Richards EJ. 1993. Arabidopsis thaliana DNA methylationmutants. Science 260:1926-1928.Wolffe AP, Matzke MA. 1999. Epigenetics: regulation through repression. Science 286:481-486.480 Hall et al
Xu Y, Buchholz WG, DeRose RT, Hall TC. 1995. Characterization of a rice gene family encodingroot-specific proteins. Plant Mol. Biol. 27:237-248.Ye F, Signer ER. 1996. RIGS (repeat-induced gene silencing) in Arabidopsis is transcriptionaland alters chromatin configuration. Proc. Natl. Acad. Sci. USA 93:10881-10886.Zamore PD, Tuschl T, Sharp PA, Bartel DP. 2000. RNAi: double-stranded RNA directs theATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25-33.NotesAuthors’ addresses: T.C. Hall, L. Iyer, M. Cervera, Y. Jiang, T. Wang, G. Yang, J. Dong, Instituteof Developmental and Molecular Biology (IDMB) and Department of Biology, TexasA&M University, College Station, TX 77843-3155, USA; S.P. Kumpatla, Dow AgroSciencesLLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA; P. Kharb, Department of Genetics,CCS Haryana Agricultural University, Hisar 125004, India; P. Teerawanichpan, J.Narangajavana, Department of Biotechnology, Faculty of Science, Mahidol University,Bangkok 10400, Thailand.Acknowledgments: Aspects of the work reported here were supported by grants from the TexasAdvanced Technology Program (010366-0092-1999), the National Science Foundation(MCB 99-74706), and Rhône-Poulenc Agro. We thank the Spanish Ministry of Educationand Culture for postdoctoral fellowship support for M. Cervera and the Thailand ResearchFund for partial predoctoral support for P. Teerawanichpan. The FISH analysis of YXBplants was supported in part by an Interdisciplinary Grant from Texas A&M University.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.Gene silencing and its reactivation in transgenic rice 481
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
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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
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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 and 490: Table 4. Suppressors of silencing f
Page 491: Garrick D, Fiering S, Martin DI, Wh
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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