Rice Genetics IV - IRRI books - International Rice Research Institute

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Antiviral protein–mediated resistanceVirus resistance has also been achieved in transgenic plants by expressing antiviralproteins from other organisms. These include expression of an antiviral protein frompokeweed (Lodge et al 1993), an interferon-associated protein 2’-5’ oligoadenylatesynthetase from rat (Truve et al 1993), a human cysteine-protease inhibitor (Garcia etal 1993), a single-chain antibody against a virus coat protein (Tavladoraki et al 1993),and a double-stranded RNA-specific ribonuclease (Watanabe et al 1995).Progress with engineering virus resistance in riceSome of the approaches proven to work in dicotyledonous plants using transgenics mayalso be useful in engineering virus resistance in rice and other monocotyledonous plants.However, several of the rice viruses differ significantly from the type of viruses shownto be responsive to the approaches described previously. Such differences in the natureof rice viruses may make them intractable to some of these approaches, but at the sametime these differences might provide opportunities for alternative resistance strategies.Here we describe the progress made in understanding the genome organization of economicallyimportant rice viruses, the PDR strategies adopted, and results obtained forvirus resistance (Table 1).Rice tungro virusesRice tungro disease is caused by two viruses, RTSV and RTBV, and genomes of bothviruses have been well characterized. RTSV is a waikavirus and has a single-stranded(plus sense) linear RNA genome (Fig. 1A) with a life cycle strategy similar to that ofthe majority of plant viruses (Shen et al 1993). Its isometric virus particles, however,are composed of three different types of coat protein subunits. RTBV can be vectoredby insects only in the presence of RTSV. Providing rice with RTSV resistance mayprevent tungro epidemics by limiting the spread of the two-virus complex. Researchersat the Scripps Research Institute have recently introduced three coat protein genes(cp1, cp2, and cp3), each under the control of the maize ubiquitin (Ubi1) promoter,individually into rice using the particle bombardment method of transformation(Sivamani et al 1999). The resulting transgenic plants were tested for RTSV resistanceas primary transformants and as T 1 and T 2 progeny. Some of the plants containingthe cp1, cp2, or cp3 genes showed moderate levels of resistance. Interestingly, theplants showing this resistance had detectable levels of mRNA for the transgenes butundetectable levels of the coat proteins (Sivamani et al 1999). Recent results usingthe RTSV replicase transgene seem to be delivering a high level of resistance (Huett,personal communication).RTBV is a Badnavirus and has a circular double-stranded DNA genome (Qu et al1991, Fig. 1B). A large part of its replication cycle occurs in the nucleus with its genesexpressed from a single RNA transcript containing four ORFs. The functions of theproteins encoded by ORFs 1, 2, and 4 remain unknown. ORF3 is by far the largest ofthe four and is predicted to encode a polyprotein containing the coat protein, viralproteinase, reverse transcriptase, and ribonuclease H. RTBV causes the majority of410 Upadhyaya et al
Table 1. Transgenic rice with pathogen-derived resistance genes for virus resistance.Virus a Cultivar Transgene Promoter Transformation Resistance level Laboratory/reference bmethodRTSV Taipei 309, TN1 cp1, cp2, cp3 Ubi1(I) Biolistics Moderate, delayed Sivamani et al (1999);symptoms ILTAB/MARDIRTSV Taipei 309 rep, truncated rep ? Biolistics High to immune ILTAB/MARDIsense or antisenseRTBV Taipei 309 ORFs 1, 2, 3, and 4 sense CaMV 35S(I) Biolistics Low or none ITH Jurich /IRRIORF4 antisense, wild- RTBV(I)type, and mutantsRRSV Taipei 309, C. Boro II S5, S7, S8, S9, S10 Various Biolistics/Agro- Low to moderate, Upadhyaya et al (1998b);sense and antisense bacterium few high CSIRO Plant Industry/SIBS/ZAASRRSV Yokara S9 CaMV 35S Electroporation None Matsumura and Tabayashi(1995)RDV Yokara S8 CaMV 35S Electroporation None Matsumura and Tabayashi(1995)RDV Zhonghua 8, Zhonghua 10 S8 CaMV 35S Biolistics na e Zheng et al (1997)RSV Kinuhikari/Nipponbare N CaMV 35S(I) Electroporation Moderate to high Hayakawa et al (1992)RSV Annong S-1 (indica) N CaMV 35S Biolistics Moderate to high Yan et al (1997)RHBV Circa-8 N CaMV 35S Biolistics High CIATRHBV 2 Costa Rican indica cvs. cp, cp (MAR) c Act1 Biolistics/ na CIBCM/Cornell UniversityAgrobacteriumRYMV Taipei 309 cp Ubi1(I) Biolistics Varied levels Kouassi et al (1997)RYMV Bouaké 189, ITA 212, ORF2 (RDRP) d CaMV 35S Biolistics Medium to high Pinto et al (1999)BG9-2a RTSV = rice tungro spherical virus, RRSV = rice ragged stunt virus, RDV = rice dwarf virus, RSV = rice stripe virus, RHBV = rice hoja blanca virus, RYMV = rice yellowmottle virus. b ILTAB = International Laboratory for Tropical Agricultural Biotechnology, MARDI = Malaysian Agricultural Research and Development Institute, CSIRO= Commonwealth Scientific and Industrial Research Organization, SIB = Shanghai Institute for Biological Sciences, ZAAS = Zhejiang Academy of AgriculturalSciences, CIAT = Centro Internacional de Agricultura Tropical, CIBCM = Centro Internacional de Biología Celular y Molecular. c MAR = matrix attachment region.d RDRP = RNA-dependent RNA polymerase.e na = not available.Engineering for virus resistance in rice 411
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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
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 386 and 387: Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389: Umeda M, Umeda-Hara C, Yamaguchi M,
Page 390 and 391: asexual reproduction through apomix
Page 392 and 393: MPManual pollination by breeders×
Page 394 and 395: Search for apomixis in riceThere ar
Page 396 and 397: Issues related to achieving synthet
Page 398 and 399: come and may use imprinting to achi
Page 400 and 401: Embryo-inducing geneInactive ablati
Page 402 and 403: M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
Page 404 and 405: embryos, several genes characterist
Page 406 and 407: Our search for a rice homologue of
Page 408 and 409: sequenced the two rice DMC1 genes a
Page 410 and 411: Gustine DL, Sherwood RT, Huff DR. 1
Page 412 and 413: Peel MD, Carman JG, Leblanc O. 1997
Page 415 and 416: TransformationEngineering for virus
Page 417 and 418: Engineering for virusresistance in
Page 419 and 420: proteins, (2) the expression of dys
Page 421: Antisense and cosuppression RNA. Ex
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 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
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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
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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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