Rice Genetics IV - IRRI books - International Rice Research Institute

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ReferencesAtkins JG, Robert AL, Adair CR, Goto K, Kozaka T, Yanagida R, Yamada M, Matsumoto S.1967. An international set of rice varieties for differentiating races of Piricularia oryzae.Phytopathology 57:297-301.Bent AF. 1996. Plant disease resistance genes: function meets structure. Plant Cell 8:1757-1771.Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK,Tarchini R, Valent B. 2000. A single amino acid difference distinguishes resistant and susceptiblealleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033-2045.Chao CT, Moldenhauer KAK, Ellingboe AH. 1999. Genetic analysis of resistance/susceptibilityin individual F 3 families of rice against strains of Magnaporthe grisea containing differentgenes for avirulence. Euphytica 109:183-190.Dong F, Miller JT, Jackson SA, Wang GL, Ronald PC, Jiang J. 1998. Rice (Oryza sativa)centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. USA 95:8135-8140.Flor HH. 1971. Current status of the gene-for-gene concept. Annu. Rev. Phytopathol. 9:275-296.Hammond-Kosack KE, Jones JDG. 1997. Plant disease resistance genes. Annu. Rev. PlantPhysiol. Plant Mol. Biol. 48:575-607.Inukai T, Nelson RJ, Zeigler RS, Sarkarung S, Mackill DJ, Bonman JM, Takamure I, KinoshitaT. 1994. Allelism of blast resistance genes in near-isogenic lines of rice. Phytopathology84:1278-1283.Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B. 2000. Direct interaction of resistancegene and avirulence gene products confers rice blast resistance. EMBO J. 19:4004-4014.Kiyosawa S. 1967. Inheritance of resistance of the rice variety Pi No. 4 to blast. Jpn. J. Breed.17:165-172.Kiyosawa S. 1971. Genetical approach to the biochemical nature of plant disease resistance.Jpn. Agric. Res. Q. 6:73-80.Kiyosawa S. 1984. Establishment of differential varieties for pathogenicity test of rice blastfungus. Rice Genet. Newsl. 1:95-97.Levy M, Correa-Victoria FJ, Zeigler RS, Xu S, Hamer JE. 1993. Genetic diversity of the riceblast fungus in a disease nursery in Colombia. Phytopathology 83:1427-1433.Levy M, Romao J, Marchetti MA, Hamer JE. 1991. DNA fingerprinting with a dispersed repeatedsequence resolves pathotype diversity in the rice blast fungus. Plant Cell 3:95-102.Moldenhauer KAK, Bastawisi AO, Lee FN. 1992. Inheritance of resistance in rice to races IB-49 and IC-17 of Pyricularia grisea rice blast. Crop Sci. 32:584-588.Montenegro-Chamorro MV. 1997. Allelic diversity of an avirulence gene in Colombian fieldisolates of the rice blast fungus. MS thesis. Purdue University, West Lafayette, Ind., USA.Nakamura S, Asakawa S, Ohmido N, Fukui K, Shimizu N, Kawasaki S. 1997. Construction ofan 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta 2using a highly representative rice BAC library. Mol. Gen. Genet. 254:611-620.Nitta N, Farman ML, Leong SA. 1997. Genome organization of Magnaporthe grisea: integrationof genetic maps, clustering of transposable elements and identification of genomeduplications and rearrangements. Theor. Appl. Genet. 95:20-32.Orbach MJ, Farrall L, Sweigard JA, Chumley FG, Valent B. 2000. The fungal avirulence geneAVR-Pita determines efficacy for the rice blast resistance gene Pi-ta. Plant Cell 12:2019-2032.320 Valent et al
Rossman AY, Howard RJ, Valent B. 1990. Pyricularia grisea, the correct name for the riceblast fungus. Mycologia 82:509-512.Rybka K, Miyamoto M, Ando I, Saito A, Kawasaki S. 1997. High resolution mapping of theindica-derived rice blast resistance genes. II. Pi-ta 2 and Pi-ta and a consideration of theirorigin. Mol. Plant-Microbe Interact. 10:517-524.Silué D, Notteghem JL, Tharreau D. 1992. Evidence for a gene-for-gene relationship in theOryza sativa-Magnaporthe grisea pathosystem. Phytopathology 82:577-580.Silué D, Tharreau D, Notteghem JL. 1993. Genetic control of Magnaporthe grisea avirulenceto rice cultivar Pi-No4 and K1. Abstracts, International Congress of Plant Pathology, 6th,Montreal, Canada. p 159.Singh K, Ishii T, Parco A, Huang N, Brar DS, Khush GS. 1996. Centromere mapping andorientation of the molecular linkage map of rice (Oryza sativa L.). Proc. Natl. Acad. Sci.USA 93:6163-6168.Sweigard JA, Valent B, Orbach MJ, Walter AM, Rafalski A, Chumley FG. 1993. Genetic mapof the rice blast fungus Magnaporthe grisea. In: O’Brien SJ, editor. Genetic maps. Plainview,NY (USA): Cold Spring Harbor Laboratory Press. p 3.112-3.117.Tatsumi H, Murakami S, Tsuji RF, Ishida Y, Murakami K, Masaki A, Kawabe H, Arimura H,Nakano E, Motai H. 1991. Cloning and expression in yeast of a cDNA clone encodingAspergillus oryzae neutral protease II, a unique metalloprotease. Mol. Gen. Genet. 228:97-103.Wu KS, Martínez C, Lentini Z, Tohme J, Chumley FG, Scolnik PA, Valent B. 1996. Cloning ablast resistance gene by chromosome walking. In: Khush GS, editor. Rice genetics III.Proceedings of the Third International Rice Genetics Symposium, 16-20 Oct 1995, Manila,Philippines. Los Baños (Philippines): International Rice Research Institute. p 669-674.Xia JQ, Correll JC, Lee FN, Marchetti MA, Rhoads DD. 1993. DNA fingerprinting to examinemicrogeographic variation in the Magnaporthe grisea (Pyricularia grisea) population intwo rice fields in Arkansas. Phytopathology 83:1029-1035.Yamada M. 1985. Pathogenic specialization of rice blast fungus in Japan. Jpn. Agric. Res. Q.19:178-183.Yamada M, Kiyosawa S, Yamaguchi T, Hirano T, Kobayashi T, Kushibuchi K, Watanabe S.1976. Proposal of a new method for differentiating races of Pyricularia oryzae Cavara inJapan. Ann. Phytopathol. Soc. Jpn. 42:216-219.Yu ZH, Mackill DJ, Bonman JM, McCouch SR, Guiderdoni E, Notteghem JL, Tanksley SD.1996. Molecular mapping of genes for resistance to rice blast (Pyricularia grisea Sacc.).Theor. Appl. Genet. 93:859-863.Zeigler RS, Cuoc LX, Scott RP, Bernardo MA, Chen DH, Valent B, Nelson RJ. 1995. Therelationship between lineage and virulence in Pyricularia grisea in the Philippines. Phytopathology85:443-451.Zeigler RS, Leong SA, Teng PS, editors. 1994. Rice blast disease. Wallingford (UK): CABInternational. 626 p.Zheng KL, Zhuang JY, Lu J, Qian HR, Lin HX. 1996. Identification of DNA markers tightlylinked to blast resistance genes in rice. In: Khush GS, editor. Rice genetics III. Proceedingsof the Third International Rice Genetics Symposium, 16-20 Oct 1995, Manila, Philippines.Los Baños (Philippines): International Rice Research Institute. p 565-569.Enhancing deployment of genes for blast resistance: . . . 321
Page 6:
Retrotransposons of rice as a tool
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First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
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Rice genetics from Mendelto functio
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nese cultivar Nipponbare. The chrom
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Gene symbolization in riceIn the ab
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Table 2. Some examples of mapping g
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and YAC libraries, respectively. Th
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gene from wild species is the intro
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ReferencesAbbasi FM, Brar DS, Carpe
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Nagao S. 1951. Genic analysis and l
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Yoshimura S, Yamanouchi U, Katayose
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important traits for which segregat
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trolled by a single recessive gene,
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AromaAromatic rice varieties often
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Submergence tolerance is an interes
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Kinoshita T, Maekawa M. 1986. Genet
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NotesAuthors’ addresses: J.N. Rut
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The Rockefeller Foundation has a lo
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Evolution and implementation of the
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Scientific progress and outputsIn t
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Another salient example is that of
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BOX NO. 1recent international works
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For the purposes of this discussion
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Because of the great diversity (sci
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eeders where final products to enha
Page 68 and 69:
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
Page 87 and 88:
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
Page 281 and 282: RBcis-effect of the adjacent strong
Page 283 and 284: Ac knockout mutagenesisThe Ac lines
Page 285 and 286: Table 2 summarizes the transformati
Page 287 and 288: ReferencesBaldwin D, Crane V, Rice
Page 289: NotesAuthors’ addresses: R. Greco
Page 292 and 293: These include T-DNA (Azpiroz-Leehan
Page 294 and 295: polyproteins and two identical 138-
Page 296 and 297: mutant. The mutation in the ent-kau
Page 298 and 299: primers (G1, G2) and two Tos17-spec
Page 300 and 301: of insertion mutants by sequencing
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: (Inukai et al 1994, Yu et al 1996,
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
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tion between the abundance of CDK t
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in a complex of 105 kDa. These resu
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Drew MC, Jackson MB, Giffard S. 197
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Umeda M, Umeda-Hara C, Yamaguchi M,
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asexual reproduction through apomix
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MPManual pollination by breeders×
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Search for apomixis in riceThere ar
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Issues related to achieving synthet
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come and may use imprinting to achi
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Embryo-inducing geneInactive ablati
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M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
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embryos, several genes characterist
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Our search for a rice homologue of
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sequenced the two rice DMC1 genes a
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Gustine DL, Sherwood RT, Huff DR. 1
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Peel MD, Carman JG, Leblanc O. 1997
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TransformationEngineering for virus
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Engineering for virusresistance in
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proteins, (2) the expression of dys
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Antisense and cosuppression RNA. Ex
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Table 1. Transgenic rice with patho
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the disease symptoms. Efforts from
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an ambisense coding strategy (Fig.
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first produced and shown to have vi
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McLean GD, Evans G. 1997. Some pote
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Waterhouse PM, Upadhyaya NM. 1998.
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duction in response to dehydration
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(KIKEKLPG) in the carboxyl terminus
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These three plasmids were used to t
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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
Page 481 and 482:
Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
Page 483 and 484:
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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