Rice Genetics IV - IRRI books - International Rice Research Institute

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Drew MC, Jackson MB, Giffard S. 1979. Ethylene-promoted adventitious rooting and developmentof cortical air spaces (aerenchyma) in roots may be adaptive responses to floodingin Zea mays L. Planta 147:83-88.Erwee MG, Goodwin PB. 1983. Characterization of the Egeria densa Planch. leaf symplast.Planta 158:320-328.Fan DF, Maclachlan GA. 1966. Control of cellulase activity by indoleacetic acid. Can. J. Bot.44:1025-1034.Fukuda H, Komamine A. 1982. Lignin synthesis and its related enzymes as markers of tracheary-elementdifferentiation in single cells isolated from the mesophyll of Zinnia elegans.Planta 155:423-430.Gaff DF, Okong’O-Ogola O. 1971. The use of non-permeating pigments for testing the survivalof cells. J. Exp. Bot. 22:756-758.Hashimoto J, Hirabayashi T, Hayano Y, Hata S, Ohashi Y, Suzuka I, Utsugi T, Toh-E A, KikuchiY. 1992. Isolation and characterization of cDNA clones encoding cdc2 homologues fromOryza sativa: a functional homologue and cognate variants. Mol. Gen. Genet. 233:10-16.Hata S. 1991. cDNA cloning of a novel cdc2 + /CDC28-related protein kinase from rice. FEBSLett. 279:149-152.Hoffmann I, Clarke PR, Marcote MJ, Karsenti E, Draetta G. 1993. Phosphorylation and activationof human cdc25-C by cdc2-cyclin B and its involvement in the self-amplification ofMPF at mitosis. EMBO J. 12:53-63.Horton RF, Osborne DJ. 1967. Senescence, abscission and cellulase activity in Phaseolus vulgaris.Nature 214:1086-1088.Jackson MB, Fenning TM, Jenkins W. 1985. Aerenchyma (gas-space) formation in adventitiousroots of rice (Oryza sativa L.) is not controlled by ethylene or small partial pressuresof oxygen. J. Exp. Bot. 36:1566-1572.Jackson MB. 1994. Root-to-shoot communication in flooded plants: involvement of abscisicacid, ethylene, and 1-aminocyclopropane-1-carboxylic acid. Agron. J. 86:775-782.Jeffrey PD, Russo AA, Polyak K, Gibbs E, Hurwitz J, Massagu J, Pavletich NP. 1995. Mechanismof CDK activation revealed by the structure of a cyclin A-CDK2 complex. Nature376:313-320.Justin SHFW, Armstrong W. 1991. Evidence for the involvement of ethylene in aerenchymaformation in adventitious roots of rice (Oryza sativa L.). New Phytol. 118:49-62.Kawai M, Umeda M, Uchimiya H. 1998. Stimulation of adenylate kinase in rice seedlingsunder submergence stress. J. Plant Physiol. 152:533-539.Kawai M, Samarajeewa PK, Berrero RA, Nishiguchi M, Uchimiya H. 1998. Cellular dissectionof the degradation pattern of cortical cell death during aerenchyma formation of riceroots. Planta 204:277-287.Kawai M, Uchimiya H. 2000. Coleoptile senescence in rice (Oryza sativa L.). Ann. Bot. 86:405-414.Kawai M, Pan L, Reed JC, Uchimiya H. 1999. Evolutionally conserved plant homologue of theBax Inhibitor-1(BI-1) gene capable of suppressing Bax-induced cell death in yeast. FEBSLett. 464:143-147.Kawase M. 1974. Aerenchyma development is often associated with a radial enlargement ofcortical cells. Physiol. Plant 31:29-38.Kawase M. 1981. Anatomical and morphological adaptation of plants to waterlogging. Hortic.Sci. 16:30-34.Kidou S, Umeda M, Uchimiya H. 1994. Nucleotide sequence of rice (Oryza sativa L.) cDNAhomologous to cdc2 gene. DNA Sequence 5:125-129.374 Uchimiya et al
Levine A, Tenhaken R, Dixon R, Lamb C. 1994. H 2 O 2 from the oxidative burst orchestrates theplant hypersensitive disease resistance response. Cell 79:583-593.Lorbiecke R, Sauter M. 1998. Induction of cell growth and cell division in the intercalarymeristem of submerged deepwater rice (Oryza sativa L.). Planta 204:140-145.Magyar Z, Mészáros T, Miskolczi P, Deák M, Fehér A, Brown S, Kondorosi É, Athanasiadis A,Pongor S, Bilgin M, Bakó L, Koncz C, Dudits D. 1997. Cell cycle phase specificity ofputative cyclin-dependent kinase variants in synchronized alfalfa cells. Plant Cell 9:223-235.Martinez AM, Afshar M, Martin F, Cavadore JC, Labbé JC, Dorée M. 1997. Dual phosphorylationof the T-loop in cdk7: its role in controlling cyclin H binding and CAK activity.EMBO J. 16:343-354.Mironov V, De Veylder L, Van Montagu M, Inzé D. 1999. Cyclin-dependent kinases and celldivision in plants: the nexus. Plant Cell 11:509-521.Mittler R, Lam E. 1995. In situ detection of nDNA fragmentation during the differentiation oftracheary elements in higher plants. Plant Physiol. 108:489-493.Morgan DO. 1995. Principles of CDK regulation. Nature 374:131-134.Morgan DO. 1996. The dynamics of cyclin-dependent kinase structure. Curr. Opin. Cell Biol.8:767-772.Nakagami H, Sekine M, Murakami H, Shinmyo A. 1999. Tobacco retinoblastoma-related proteinphosphorylated by a distinct cyclin-dependent kinase complex with Cdc2/cyclin D invitro. Plant J. 18:243-252.Nigg EA. 1995. Cyclin-dependent protein kinases: key regulators of the eukaryotic cell cycle.BioEssays 17:471-480.Orzáez D, Granell A. 1997. The plant homologue of the defender against apoptotic death geneis down-regulated during senescence of flower petals. FEBS 404:275-278.Renaudin J-P, Doonan JH, Freeman D, Hashimoto J, Hirt H, Inzé D, Jacobs T, Kouchi H,Rouzé P, Sauter M, Savourá A, Sorrell DA, Sundaresan V, Murray JA. 1996. Plant cyclins:a unified nomenclature for plant A-, B- and D-type cyclins based on sequence organization.Plant Mol. Biol. 32:1003-1018.Saab IN, Sachs MM. 1996. A flooding-induced xyloglucan endo-transglycosylase homolog inmaize is responsive to ethylene and associated with aerenchyma. Plant Physiol. 112:385-391.Samarajeewa PK, Barrero RA, Umeda-Hara C, Kawai M, Uchimiya H. 1999. Cortical celldeath, cell proliferation, macromolecular movements and rTipl expression pattern in rootsof rice (Oryza sativa L.) under NaCl stress. Planta 207:354-361.Schussler E, Longstreth DJ. 1996. Aerenchyma develops by cell lysis in roots and cell separationin leaf petioles in Sagittaria lancifolia (Alismataceae). Am. J. Bot. 83:1266-1273.Smirnoff N, Crawford RMM. 1983. Variation in the structure and response to flooding of rootaerenchyma in some wetland plants. Ann. Bot. 51:237-249.Tanaka Y, Makishima T, Sasabe M, Ichinose Y, Shiraishi T, Nishimoto T, Yamada T. 1997. dad-1, a putative programmed cell death suppressor gene in rice. Plant Cell Physiol. 38:379-383.Umeda M, Bhalerao RP, Schell J, Uchimiya H, Koncz C. 1998. A distinct cyclin-dependentkinase-activating kinase of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 95:5021-5026.Umeda M, Iwamoto N, Umeda-Hara C, Yamaguchi M, Hashimoto J, Uchimiya H. 1999a.Molecular characterization of mitotic cyclins in rice plants. Mol. Gen. Genet. 262:230-238.Molecular dissection of cell death in rice 375
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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
Page 335 and 336: Molecular signaling in diseaseresis
Page 337 and 338: AOsRac1IED II III IV 214aaOsRac1 KC
Page 339 and 340: Japonica rice variety Kinmaze, whic
Page 341 and 342: Table 1. Characteristics of lesion-
Page 343 and 344: an effective inducer of host resist
Page 345: Takahashi A, Kawasaki T, Henmi K, S
Page 348 and 349: et al 2000). Sequence analysis of t
Page 350 and 351: 612-amino acid protein, including t
Page 352 and 353: Genetic dissection of the Xa21-medi
Page 354 and 355: ReferencesAnderson PA, Lawrence GJ,
Page 357 and 358: Isolation of candidate genesfor tol
Page 359 and 360: Materials and methodsPlant material
Page 361 and 362: Microarray hybridization and data a
Page 363 and 364: Table 3. Most abundant transcripts
Page 365 and 366: Microarray technologyThe rapid accu
Page 367 and 368: view of procedures, pitfalls, and n
Page 369 and 370: Log(2) ratio1.51.0OC104E01—WCP1OC
Page 371 and 372: Table 5. Strongly regulated transcr
Page 373 and 374: ReferencesAdams MD, Soares MB, Kerl
Page 375: Acknowledgments: We thank Chris Bor
Page 378 and 379: y cells separating during tissue de
Page 380 and 381: (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 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 and 432: McLean GD, Evans G. 1997. Some pote
Page 433: 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
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We now show the effects of the toba
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Since one major goal of plant scien
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Table 4. Copy number of transgenes
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Chan M-T, Chang H-H, Ho S-L, Tang W
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NotesAuthors’ address: Department
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initially fixed by phosphoenolpyruv
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High-level expression of maize C 4-
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The effect of illumination on PPDK
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ate in 2% O 2 can be limited by Pi
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Transgene integration,organization,
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duced by organogenesis, somatic emb
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ing transgene organization. FISH an
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ments and the integration of exogen
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Level 2: activation of local repair
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strongly suggested that plant facto
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other cases it was not. We observed
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Gorbunova V, Levy AA. 1997. Non-hom
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Gene silencing and itsreactivation
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Carbofuran (trade name, Furadan) is
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Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
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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
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Rice genetics cooperativeA meeting
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