Rice Genetics IV - IRRI books - International Rice Research Institute

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enging activities at the level of transcription and that this function may be independentof its role in the activation of NADPH oxidase.Model of the signaling pathways for R gene–mediateddisease resistance of riceFigure 3 shows a model for the signaling pathway for R gene–mediated disease resistanceof rice. All the defense reactions are initiated by recognition of the AVR geneproduct or some signals derived from the pathogens. Very recently, direct interactionof the products of the blast resistance gene, Pi-ta, and the corresponding AVR gene,AVR-Pi-ta, was demonstrated (Jia et al 2000); however, whether the observed directinteraction between products of the R gene and AVR gene is a general phenomenon inrice-pathogen interactions remains to be studied. After perception of the signal fromthe pathogen, a cascade of protein phosphorylation occurs and it leads to activation ofNADPH oxidase through the small GTPase Rac. The biochemical nature of the hypotheticalNADPH oxidase is not known. Rac amplifies the signal from the pathogen toactivate ROS production and cell death. These two cellular events initiate activationof defense genes and production of phytoalexin and eventually lead to disease resistance.The second function of Rac in disease resistance may be to transiently suppressexpression of scavengers at the transcriptional level to strengthen the ROS signal.Since this suppression is quickly released after oxidative burst ceases, cells will notbe damaged for a long time after the perception of signals from pathogens. It is alsopossible that R gene products activate some of the defense genes independent of Racaction.Apart from the Rac signaling pathway, our recent studies indicate that heterotrimericG protein appears to function downstream of the R gene. It may directly activatevarious defense genes or it may contribute to resistance by other unknown pathways.Lesion-mimic mutants of riceMutants that show spontaneous cell death in the absence of pathogens are called diseaselesion mimics and have been known to occur in several cereals including maize(Johal et al 1995), rice (Kiyosawa, 1970), and barley (Wolter et al 1993). They arerecessive or dominant, and almost all mutants show a unique lesion phenotype withrespect to the size of the lesion, timing of lesion formation, and color of the lesion(Johal et al 1995). Mutant phenotypes are often influenced by environmental conditionssuch as light and temperature (Johal et al 1995).cdr lesion-mimic mutants of riceWe screened 93 rice mutants that exhibited spontaneous lesions for resistance to blastfungus infection and found eight mutants with increased resistance to blast infection.We called these mutants cdr (cell death and resistance). Characteristics of three suchmutants, cdr1–3, are summarized in Table 1. The three mutants showed many smallbrownish lesions that were uniformly spread over the entire leaf surface (Fig. 4). Incdr1, lesions became visible around 20 d after sowing. In the cdr2 mutant, many328 Shimamoto et al
Table 1. Characteristics of lesion-mimic mutants analyzed.Response to blast bTiming cLine Genetic data (d)Lesion a Race 007WT – S – –cdr1 – S+ RRecessive
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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
Page 289: NotesAuthors’ addresses: R. Greco
Page 292 and 293: These include T-DNA (Azpiroz-Leehan
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Page 302 and 303: Grandbastien M-A, Spielman A, Caboc
Page 304 and 305: NotesAuthors’ addresses: H. Hiroc
Page 306 and 307: human endeavor, greatly contributed
Page 308 and 309: Equally important as the genomic in
Page 310 and 311: Oryzabase is one of the most recent
Page 312 and 313: Database structureA characteristic
Page 314 and 315: types of users. An annotation datab
Page 316 and 317: ReferencesAntonio BA, Fang Z, Sanch
Page 319 and 320: Gene isolation and functionEnhancin
Page 321 and 322: Enhancing deployment of genes forbl
Page 323 and 324: mochi and Tsuyuake (Wu et al 1996).
Page 325 and 326: tive indica rice varieties supports
Page 327 and 328: transcription factor, resulting in
Page 329 and 330: facilitate breeding durable resista
Page 331 and 332: (Inukai et al 1994, Yu et al 1996,
Page 333 and 334: 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: Japonica rice variety Kinmaze, whic
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 386 and 387: Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389: 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
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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
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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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