Rice Genetics IV - IRRI books - International Rice Research Institute

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Chen S, Lin XH, Xu CG, Zhang Q. 2000. Improvement of bacterial blight resistance of ‘Minghui63’, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Crop Sci.40:239-244.Cohen JL, Falconi C, Komen J. 1998. Proprietary biotechnology inputs and international agriculturalresearch. ISNAR Briefing Paper No. 38. The Hague (Netherlands): InternationalService for National Agricultural Research.Conway G, Toenniessen GH. 1999. Feeding the world in the twenty-first century. Nature402(suppl):C55-C58.Courtois B, McLaren G, Sinha PK, Prasad K, Yadav R, Shen L. 2000. Mapping QTLs associatedwith drought avoidance in upland rice. Mol. Breed. 6:55-66.Devos KM, Gale MD. 2000. Genome relationships: the grass model in current research. PlantCell 12:637-646.Evenson RE, Herdt RW, Hossain M, editors. 1996. Rice research in Asia: progress and priorities.Manila (Philippines): International Rice Research Institute, and Wallingford (UK):CAB International. 418 p.Falconi C. 1999. What is agricultural biotechnology research capacity in developing countries?ISNAR Discussion Paper No. 99-10. The Hague (Netherlands): International Service forNational Agricultural Research.Gale MD, Devos KM. 1998. Plant comparative genetics after 10 years. Science 282:656-658.Herdt RW. 1986. Information needs for research resource allocation. Prepared for the workshopon Biotechnology for Crop Improvement, 13-17 Oct. 1986, International Rice ResearchInstitute (IRRI). Los Baños (Philippines): IRRI. 32 p.Herdt RW. 1987. Equity considerations in setting priorities for Third World rice biotechnologyresearch. Dev. Seeds Change 4:19-24.Herdt RW. 1991. Research priorities for rice biotechnology. In: Khush GS, Toenniessen GH,editors. Rice biotechnology. Manila (Philippines); International Rice Research Institute,and Wallingford (UK): CAB International. p 19-54.Herdt RW, Rieley Jr. R. 1987. International rice research priorities: implications for biotechnologyinitiatives. Prepared for the Rockefeller Foundation Workshop on Allocating Resourcesfor Developing Country Agricultural Research, 6-10 July 1987, Bellagio, Italy.78 p.Hossain MA, Huq E, Grover A, Dennis E, Peacock WJ, Hodges TK. 1996. Characterization ofpyruvate decarboxylase genes from rice. Plant Mol. Biol. 31:761-770.Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, BennettJ, Khush GS. 1997. Pyramiding of bacterial blight resistance genes in rice: marker-assistedselection using RFLP and PCR. Theor. Appl. Genet. 95:313-320.Huq E, Harrington S, Hossain MA, Wen F, McCouch SR, Hodges TK. 1999. Molecular characterizationof pdc2 and mapping of three pdc genes from rice. Theor. Appl. Genet. 98:815-824.Ito O, O'Toole J, Hardy B, editors. 1999. Genetic improvement of rice for water-limited environments.Proceedings of the Workshop on Genetic Improvement of Rice for Water-LimitedEnvironments, 1-3 December 1998, Los Baños, Philippines. Manila (Philippines): InternationalRice Research Institute. 353 p.Kearl B, Adkisson P, McNamara R. 1982. A review of the Rockefeller Foundation Conquest ofHunger Program. New York (USA): Rockefeller Foundation.Khush GS, Bacalangco E, Ogawa T. 1991. A new gene for resistance to bacterial blight from O.longistaminata. Rice Genet. Newsl. 7:121-122.56 O'Toole et al
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Page 6:
Retrotransposons of rice as a tool
Page 11 and 12:
First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
Page 15 and 16:
Rice genetics from Mendelto functio
Page 17 and 18: nese cultivar Nipponbare. The chrom
Page 19: Gene symbolization in riceIn the ab
Page 26 and 27: Table 2. Some examples of mapping g
Page 28 and 29: and YAC libraries, respectively. Th
Page 30 and 31: gene from wild species is the intro
Page 32 and 33: ReferencesAbbasi FM, Brar DS, Carpe
Page 35 and 36: Nagao S. 1951. Genic analysis and l
Page 37: Yoshimura S, Yamanouchi U, Katayose
Page 40 and 41: important traits for which segregat
Page 42 and 43: trolled by a single recessive gene,
Page 44 and 45: AromaAromatic rice varieties often
Page 46 and 47: Submergence tolerance is an interes
Page 48 and 49: Kinoshita T, Maekawa M. 1986. Genet
Page 50 and 51: NotesAuthors’ addresses: J.N. Rut
Page 52 and 53: The Rockefeller Foundation has a lo
Page 54 and 55: Evolution and implementation of the
Page 56 and 57: Scientific progress and outputsIn t
Page 58 and 59: Another salient example is that of
Page 60 and 61: BOX NO. 1recent international works
Page 62 and 63: For the purposes of this discussion
Page 64 and 65: Because of the great diversity (sci
Page 66 and 67: eeders where final products to enha
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 73 and 74: Molecular markers,genetic diversity
Page 75 and 76: Evolution and domestication of rice
Page 77 and 78: ABCDO. barthiiO. rufipogonO. longis
Page 79 and 80: Wild(O. rufipogon)Geographical diff
Page 81 and 82: South Asia (particularly on the wes
Page 83 and 84: al 1992, Sun et al 1996a,b,c), thou
Page 85 and 86: wild and cultivated types (Est10, W
Page 87 and 88: Cai HW, Morishima H. 2000a. Diversi
Page 89: Sato YI, Tang SX, Yang LU, Tang LH.
Page 92 and 93: The solid base laid by classical ri
Page 94 and 95: The synthesis shown in Figure 1 is
Page 96 and 97: Arabidopsis, long heralded as a “
Page 98 and 99: Monocots and eudicots: Is there sti
Page 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 114 and 115: testing Ka/Ks between the homeologo
Page 116 and 117: Roschevicz RI. 1931. A contribution
Page 119 and 120:
Miniature inverted repeattransposab
Page 121 and 122:
eau and Wessler 1992, 1994), rice (
Page 123 and 124:
MITEs as a source of allelic divers
Page 125 and 126:
ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
Page 127 and 128:
Le QH, Wright S, Yu Z, Bureau T. 20
Page 129 and 130:
Microsatellite markers in rice:abun
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make the best SSR markers for rice.
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Predicted frequency100,00080,000Cla
Page 135 and 136:
Relationship between SSRs and genes
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are indicated with RM locus designa
Page 141 and 142:
SSRs have been used to define intro
Page 143 and 144:
provide a bridge for moving rapidly
Page 145 and 146:
Ishii T, McCouch SR. 2000. Microsat
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NotesAuthors’ addresses: S.R. McC
Page 150 and 151:
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
Page 156 and 157:
Chen et al (2000) transferred the b
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genome sequence of rice, this will
Page 160 and 161:
Kurata N, Nagamura Y, Yamamoto K, H
Page 162 and 163:
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
Page 169 and 170:
(genetic/statistical models and cor
Page 171 and 172:
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
Page 179 and 180:
Simultaneous QTL introgression and
Page 181 and 182:
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
Page 192 and 193:
Table 3. QTLs detected for yield an
Page 194 and 195:
Table 6. Correlations of various pa
Page 196 and 197:
The functions of these sequences ne
Page 199 and 200:
Structural and functional genomicsT
Page 201 and 202:
The International Rice GenomeSequen
Page 203 and 204:
the RGP, a PAC (P1-derived artifici
Page 205 and 206:
Progress of sequencing in the RGPWe
Page 207 and 208:
ice genome sequencing to organize a
Page 209 and 210:
Strategies and techniquesfor finish
Page 211 and 212:
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
Page 221 and 222:
estriction maps or optical maps are
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nal assembly may point to areas tha
Page 225 and 226:
McMurray AA, Sulston JE, Quail MA.
Page 227 and 228:
Sequence-tagged connector/DNA finge
Page 229 and 230:
1999). The development of multiple-
Page 231 and 232:
Transposable elements in the rice H
Page 233 and 234:
ers, maps, mapping populations, and
Page 235 and 236:
Miropeats-OSJNBa0065H03 1.2 cMThres
Page 237:
NotesAuthors’ addresses: R.A. Win
Page 240 and 241:
Sasaki 1997). Such analysis is ofte
Page 242 and 243:
ABNipponbare × KasalathF 2QTL anal
Page 244 and 245:
were classified into two groups bas
Page 246 and 247:
effective at determining the genoty
Page 248 and 249:
addition, some accessions of wild r
Page 250 and 251:
Sasaki T, Burr T. 2000. Internation
Page 252 and 253:
Mutational analysis has long been t
Page 254 and 255:
marked by a deletion/chromosomal re
Page 256 and 257:
analysis suggests that the mutation
Page 258 and 259:
For drought-response screening, our
Page 260 and 261:
Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
Page 262 and 263:
Although mutants with discrete gene
Page 265 and 266:
Generation of T-DNA insertionaltagg
Page 267 and 268:
Aprobe AEEprobe BpGA1633RBgus Tn p3
Page 269 and 270:
Number of loci36%224%170%010 20 30F
Page 271 and 272:
Table 2. GUS assay in roots of tran
Page 273 and 274:
1999, Krysan et al 1999, Sato et al
Page 275 and 276:
Transposons and functionalgenomics
Page 277 and 278:
cesses. To study the interactions a
Page 279 and 280:
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 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 and 340:
Japonica rice variety Kinmaze, whic
Page 341 and 342:
Table 1. Characteristics of lesion-
Page 343 and 344:
an effective inducer of host resist
Page 345:
Takahashi A, Kawasaki T, Henmi K, S
Page 348 and 349:
et al 2000). Sequence analysis of t
Page 350 and 351:
612-amino acid protein, including t
Page 352 and 353:
Genetic dissection of the Xa21-medi
Page 354 and 355:
ReferencesAnderson PA, Lawrence GJ,
Page 357 and 358:
Isolation of candidate genesfor tol
Page 359 and 360:
Materials and methodsPlant material
Page 361 and 362:
Microarray hybridization and data a
Page 363 and 364:
Table 3. Most abundant transcripts
Page 365 and 366:
Microarray technologyThe rapid accu
Page 367 and 368:
view of procedures, pitfalls, and n
Page 369 and 370:
Log(2) ratio1.51.0OC104E01—WCP1OC
Page 371 and 372:
Table 5. Strongly regulated transcr
Page 373 and 374:
ReferencesAdams MD, Soares MB, Kerl
Page 375:
Acknowledgments: We thank Chris Bor
Page 378 and 379:
y cells separating during tissue de
Page 380 and 381:
(Erwee and Goodwin 1983). The sympl
Page 382 and 383:
tion between the abundance of CDK t
Page 384 and 385:
in a complex of 105 kDa. These resu
Page 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 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 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
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
Page 498 and 499:
the working group can develop a net
Page 500:
Rice genetics cooperativeA meeting
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