Rice Genetics IV - IRRI books - International Rice Research Institute

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Chan M-T, Chang H-H, Ho S-L, Tang W-F, Yu S-M. 1993. Agrobacterium-mediated productionof transgenic rice plants expressing a chimeric alpha-amylase promoter/beta-glucuronidasegene. Plant Mol. Biol. 22:491-506.Cheng Z, Targolli J, Su J, Wu R. 2000. The importance of plant biotechnology in the twentyfirstcentury. In: Wu W-S, Chang S-T, Guan BT, editors. Proceedings Agriculture of theNew Century: Managing Bio-resources and Bio-diversity, National Taiwan University Press,Taiwan. p 1-9.Christou P, Ford TL, Kofron M. 1991. Production of transgenic rice (Oryza sativa L.) plantsfrom agronomically important indica and japonica varieties via electric discharge particleacceleration of exogenous DNA into immature zygotic embryos. Bio/Technology 9:957-962.Cushman JC, Bohnert HJ. 2000. Genomic approaches to plant stress tolerance. Curr. Opin.Plant Biol. 3:117-124.Delauney AJ, Verma DPS. 1993. Proline biosynthesis and osmoregulation in plants. Plant J.4:215-223.Duan X, Li X, Xue Q, Abo-El-Saad M, Xu D, Wu R. 1996. Transgenic rice plants harboring anintroduced proteinase inhibitor II gene are insect resistant. Nat. Biotechnol. 14:494-498.Dure III L. 1981. Developmental biochemistry of cottonseed embryogenesis and germination:changing mRNA populations as shown in in vitro and in vivo protein synthesis. Biochemistry20:4162-4168.Dure III L. 1992. The LEA proteins of higher plants. In: Verma DPS, editor. Control of plantgene expression. Boca Raton, Fla. (USA): CRC Press. p 325-335.Dure III L. 1993. A repeating 11-mer amino acid motif and plant desiccation. Plant J. 3:363-369.Dure III L, Crouch M, Harada J, Ho T-HD, Mundy J, Quatrano RS, Thomas T, Sung ZR. 1989.Common amino acid sequence domains among the LEA proteins of higher plants. PlantMol. Biol. 12:475-486.Hiei Y, Ohta S, Khomari T, Kumashiro T. 1994. Efficient transformation of rice (Oryza sativaL.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA.Plant J. 6:271-282.Holmes-Davis R, Comai L. 1998. Nuclear matrix attachment regions and plant gene expression.Trends Plant Sci. 3:91-96.Hong B, Barg R, Ho T-HD. 1992. Developmental and organ-specific expression of an ABAandstress-induced protein in barley. Plant Mol. Biol. 18:663-674.Hong B, Uknes SJ, Ho T-HD. 1988. Cloning and characterization of a cDNA encoding a mRNArapidly induced by ABA in barley aleurone layers. Plant Mol. Biol. 11:495-506.Ingram J, Bartels D. 1996. The molecular basis of dehydration tolerance in plants. Annu. Rev.Plant Physiol. Plant Mol. Biol. 47:377-403.Iyer LM, Kumpatla SP, Chandrasekharan MB, Hall TC. 2000. Transgene silencing in monocots.Plant Mol. Biol. 43:323-346.Jaglo-Ottosen KR, Gilmour S, Zarka DG, Schabenberger O, Thomashow MF. 1998. ArabidopsisCBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280:104-106.Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K. 1999. Improving plantdrought, salt and freezing tolerance by gene transfer of a single stress-inducible transcriptionfactor. Nat. Biotechnol. 17:287-291.436 Cheng et al
Kavi Kishor PB, Hong Z, Miao GH, Hu CAA, Verma DPS. 1995. Overexpression of delta 1-pyrroline-5-carboxylase synthetase increases proline production and confers osmotolerancein transgenic plants. Plant Physiol. 108:1387-1394.Khush GS. 1999. Green revolution: preparing for the 21st century. Genome 42:646-655.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.Mlynarova L, Loonen A, Heldens J, Jansen RC, Keizer P, Stiekema WJ, Nap JP. 1994. Reducedposition effect in mature transgenic plants conferred by the chicken lysozyme matrix-associatedregion. Plant Cell 6:417-426.Moons A, Bauw G, Prinsen E, van Montagu M, Straeten DVD. 1995. Molecular and physiologicalresponses to abscisic acid and salts in roots of salt-sensitive and salt-tolerant indicarice varieties. Plant Physiol. 107:177-186.Morris CF, Anderenberg RJ, Goldmark PJ, Walker-Simmons MK. 1995. Molecular cloningand expression of abscisic acid responsive genes in embryos of dormant wheat seeds. PlantPhysiol. 95:814-821.Reddy AR, Ramanathan V, Seetharama N, Bajaj S, Wu R. 1999. Genetic improvement of ricefor drought and salt tolerance: molecular breeding and transgenic strategies. In: Ito O,O’Toole J, Hardy B, editors. Genetic improvement of rice for water-limited environments.Manila (Philippines): International Rice Research Institute. p 135-155.Ried JL, Walker-Simmons MK. 1993. Group 3 late embryogenesis abundant proteins in desiccation-tolerantseedlings of wheat (Triticum aestivum L.). Plant Physiol. 102:125-131.Shinozaki K, Yamaguchi-Shinozaki K. 1997. Gene expression and signal transduction in water-stressresponse. Plant Physiol. 115:327-334.Spiker S, Thompson WF. 1996. Nuclear matrix attachment regions and transgene expression inplants. Plant Physiol. 110:15-21.Stacey RAP, Espelund M, Saeboe LS, Hollum K, Jakobsen KS. 1995. Evolution of the group 1late embryogenesis abundant (LEA) genes: analysis of the LEA B19 gene family in barley.Plant Mol. Biol. 28:1039-1054.Stam M, Mol JNM, Kooter JM. 1997. The silence of genes in transgenic plants. Ann. Bot. 79:3-12.Su J, Shen Q, Ho T-HD, Wu R. 1998. Dehydration-stress-regulated transgene expression instably transformed rice plants. Plant Physiol. 117:913-922.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.Xu D, Duan X, Wang B, Ho T-HD, Wu R. 1996. Expression of a late embryogenesis abundantprotein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenicrice. Plant Physiol. 110:249-257.Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN. 1982. Living with water stress:evolution of osmolyte system. Science 217:1214-1222.Zhang JX, Nguyen HT, Blum A. 1999. Genetic analysis of osmotic adjustment in crop plants. J.Exp. Bot. 50:291-302.Zhang WG, Wu R. 1988. Efficient regeneration of transgenic plants from rice protoplasts andcorrectly regulated expression of the foreign gene in the plants. Theor. Appl. Genet. 76:835-840.Zhu B, Su J, Chang M, Verma DPS, Fan Y-L, Wu R. 1998. Overexpression of a delta 1-pyrroline-5-carboxylate synthetase gene and analysis of tolerance to water- and salt-stress in transgenicrice. Plant Sci. 139:41-48.Transgenic approaches for generating rice . . . 437
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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
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.
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 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 and 492: Garrick D, Fiering S, Martin DI, Wh
Page 493: 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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