Rice Genetics IV - IRRI books - International Rice Research Institute

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<strong>Rice</strong> genetics from Mendel to functional genomics 906314445475888d-6g-1spl-5Rcv-11z-6rfsesp-7048v-8sugC09222427293036444852535455646668737576798182949599124d-4l-pl-4wxdp-1ms-1Pgd-2v-3ga-1CS-5Amp-3Est-2bl-3alkst-1Pgi-2Se-1Pi-zS-6d-9rcn-1gf-1chl-4bl-2fs-1ClPi-1ms-9Ur-1spl-4 (S)C063049515657698285101111112gh-1nl-2d-1St-2al-3spl-8al-6(t)v-10opsbglrispl-7nl-1al-2eui (L)bc-2 (S)C0140122931363965spl-1Sdh-1rl-3d-33nal-3Pox-2Acp-2Acp-1C01628Ef-1fglRf-1pglygl (L)CDn-1dp-2drp-2C09172333363738465661727795100132D-53z-1esp-2v-9sh-1Pi-aAdh-1spd-28Pgd-1v-4ladrp-7z-2d-27Pi-k5 6 7 89 10 11 12
Page 6: Retrotransposons of rice as a tool
Page 11 and 12: First, the Rice Genetics Cooperativ
Page 13 and 14: 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 27 and 28: Table 2 continued.Gene Trait Chromo
Page 29 and 30: plant resistance genes but is quite
Page 31 and 32: and the information is freely avail
Page 33: Hayano-Saito Y, Saito K, Nakamura S
Page 36 and 37: Toriyama K, Arimoto Y, Uchimiya H,
Page 39 and 40: Application of Mendelian geneticsin
Page 41 and 42: In temperate regions, breeders have
Page 43 and 44: Elongated uppermost internodeA gene
Page 45 and 46: ecent years, Katy has been used as
Page 47 and 48: Childs N. 1999. Rice situation and
Page 49 and 50: Rutger JN, Carnahan HL. 1981. A fou
Page 51 and 52: The Rockefeller Foundation’sInter
Page 53 and 54: generated from a protoplast in 1986
Page 55 and 56: Table 1. The Rockefeller Foundation
Page 57 and 58: Box no. 1The saga of Xa21THE STORY
Page 59 and 60: viruses, molecular tools made possi
Page 61 and 62: BSLLBTETBTBox no. 2Rice—the pivot
Page 63 and 64: Table 2. Types of institutions supp
Page 65 and 66: Table 3. Breakdown of number of ins
Page 67 and 68: ●●●Transformation of chloropl
Page 69 and 70: Lander ES, Weinberg RA. 2000. Genom
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Zhang J, Zheng HG, Ali ML, Tripathy
Page 74 and 75:
62 Morishima
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defined as the diploid species havi
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Interspecific relatedness was also
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Within the geographical range of O.
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Search for the immediate ancestor o
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gene pool, we performed QTL analysi
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Table 3. Changes in population para
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Kadowaki K, Yazaki K, Osumi T, Hara
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Rice: a central genomefor the genet
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Gibberellicacid-insensitiveRiceFoxt
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parative organization of the Pooide
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clear alignment of major factors co
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Gale MD, Devos KM. 1998. Plant comp
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Phylogeny of the genusOryza as reve
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Table 1. Species recognized in Oryz
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However, the subdivisional classifi
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Multiple gene trees: new insights i
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AABBBBCCCCCCDDDDKKHHKKFFHHHHJJJJGGF
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group with the diploid E genome spe
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genomes occupy the basal positions
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Donoghue MJ. 1994. Progress and pro
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Vaughan DA. 1994. The wild relative
Page 120 and 121:
The existence of TEs also demonstra
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S. Wessler, unpublished data). Othe
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parent but not in the other can be
Page 126 and 127:
ReferencesBaker B, Schell J, Lorz H
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Walker EL, Eggleston WB, Demopulos
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hypervariability make them valuable
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periments tended to detect only the
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Distribution of SSR motifsSignifica
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Association between SSRs and transp
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Molecular wt (bp)15 cultivars241 cu
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20222426283032343638404244464850525
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Blair MW, Hedetale V, McCouch SR. 2
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Semon M, Coburn J, Cadalen T, Jones
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Molecular mapping and markerassiste
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symposium (Li, this volume), here w
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Table 2 continued.Trait Gene Chromo
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markers were used for the other two
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volume). Those SSRs that can be sco
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Fukuoka S, Namai H, Okuno K. 1998.
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Naqvi NI, Chattoo BB. 1996. Molecul
Page 163:
Zhang JS, Xie C, Li ZY, Chen SY. 19
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1980s have had far-reaching effects
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Table 2. The number of detected mai
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Table 3. Relative importance of mai
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Table 6. Some nonenvironment-specif
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On average, QTL main effects were d
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Table 9. Main-effect QTLs affecting
Page 178 and 179:
Gene action of QTLsIn QTL mapping s
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tion of the parental lines; (3) enf
Page 182 and 183:
Li ZK, Paterson AH, Pinson SRM, Sta
Page 185 and 186:
Genetic and molecular basisof heter
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in Table 1 for the four traits were
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Table 2. A summary of the significa
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hybrids rather than progenies of se
Page 193 and 194:
Correlation between gene expression
Page 195 and 196:
Table 7. Numbers of cDNAs showing v
Page 197:
Saghai Maroof MA, Yang GP, Zhang Q,
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188 Sasaki et al
Page 202 and 203:
The boom in rice genome analysis is
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Selected PAC/BAC clones are culture
Page 206 and 207:
an overestimation of the gene numbe
Page 208 and 209:
Saji S, Umehara Y, Antonio BA, Yama
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BackgroundIn the random shotgun pha
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200 de la Bastide et alFig. 2. Scre
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a different sequence or contig. Fig
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ing annotation must be tagged accor
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slip in these regions, producing se
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sequencing method for us on cDNA cl
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Direct repeats Inverted repeats Tan
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iopoldat.html). The 2-kb threshold
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AppendixFinisher’s Clone Submissi
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The CUGI Rice Genome Framework Proj
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the development of a fingerprint DB
Page 232 and 233:
First inriceHexa3%Mono4%Penta12%Di2
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Contigs2712722738652742755814257782
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Table 4. CCW sequencing status for
Page 239 and 240:
Naturally occurring allelic variati
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in rice. To this end, two high-dens
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Characterization of genes at QTLs u
Page 245 and 246:
In summary, in QTL analysis of a po
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in the response to daylength in ric
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functional genomics. However, it is
Page 251 and 252:
Deletion mutants for functionalgeno
Page 253 and 254:
Although these mutants are useful f
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Table 1. Frequencies of mutations o
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ALesion length (cm)252015105IR64D6-
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However, to detect genetic variabil
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cific PCR primers to screen a DNA p
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Reardon JT, Liljestrand-Golden CA,
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insertional mutagenesis an attracti
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plants transformed with pGA1633 and
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vealed that the efficiency of GUS s
Page 272 and 273:
Table 3. GUS assay in flowers of tr
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Krizkova L, Hrouda M. 1998. Direct
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Functional genomicsThe field of fun
Page 278 and 279:
Gene detectionGene detection strate
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ice. Transgenic plants were also ge
Page 282 and 283:
ence of a single excision footprint
Page 284 and 285:
homology to known proteins. The tra
Page 286 and 287:
Transposon library generation10 sta
Page 288 and 289:
Krysan PJ, Young JC, Sussman MR. 19
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Retrotransposons of riceas a tool f
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that Tos17 is the major insertional
Page 295 and 296:
Forward and reverse genetic studies
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mutated genes by isolating the sequ
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5 kb—G1-T11 kb—5 kb—G1-T21 kb
Page 301 and 302:
Mutants identified by this method a
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Ohtsubo H, Kumekawa N, Ohtsubo E. 1
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Bioinformatics and the rice genomeB
Page 307 and 308:
total number of sequences submitted
Page 309 and 310:
Table 2 continued.Database/ URL Inf
Page 311 and 312:
Specialized databasesIn contrast to
Page 313 and 314:
more complicated traits such as QTL
Page 315 and 316:
ESTsGenetic markersMorphologicalMol
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NotesAuthors' address: Rice Genome
Page 320 and 321:
308 Valent et al
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product, or they might encode enzym
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K1 (Kiyosawa 1984) obtained Pi-ta f
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A B CFig. 2. Rice leaves showing lo
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M. griseaAVR-PitaPlant cellProcessi
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The relationship between Pi-ta and
Page 332 and 333:
ReferencesAtkins JG, Robert AL, Ada
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NotesAuthors’ addresses: B. Valen
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Role of the small GTPase Rac in dis
Page 338 and 339:
Suppression of ROS production and c
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enging activities at the level of t
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lesions appeared over the entire le
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limited amino acid sequence informa
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Structure, function, and evolution
Page 349 and 350:
trum, IRBB21 conferred a high level
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elements. Two of them were located
Page 353 and 354:
IRBB2134532703506N20-247N18-116-1N1
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Salmeron JM, Oldroyd GED, Rommens C
Page 358 and 359:
Understanding abiotic stress tolera
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Table 1. Selected cDNA libraries fr
Page 362 and 363:
Table 2. Abundance profile of expre
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Table 3 continued.Gene AbundancePut
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duction of chips is done commercial
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Microarray determination of salt st
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ConclusionsThese analyses must be c
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Table 5 continued.Open readingframe
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Lin X, Kaul S, Rounsley S, Shea TP,
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Molecular dissectionof cell death i
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lysis appeared to be larger in diam
Page 381 and 382:
Cell divisionCell elongationand exp
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extend to the S phase. Furthermore,
Page 385 and 386:
and, at 6 h, the population of S ph
Page 387 and 388:
Levine A, Tenhaken R, Dixon R, Lamb
Page 389 and 390:
Molecular tools for achievingsynthe
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ANormal sexualpathwayMegasporangium
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Tripsacum, a close relative of maiz
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used T-DNA-tagging in Arabidopsis t
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aposporous apomicts such as H. aura
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Achieving synthetic apomixisThe min
Page 401 and 402:
We isolated a rice homologue of the
Page 403 and 404:
1996), and a putative hydroxyprolin
Page 405 and 406:
The life cycle of angiosperms is pu
Page 407 and 408:
Ablation of the sexual embryoIsolat
Page 409 and 410:
Birchler JA. 1993. Dosage analysis
Page 411 and 412:
Li JM, Yuan LP. 1999. Hybrid rice:
Page 413:
Xu FX, Chye ML. 1999. Expression of
Page 416 and 417:
404 Upadhyaya et al
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yield losses per annum of about US$
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Mutant replicase. With replicase ge
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Antiviral protein-mediated resistan
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ACRTSV (positive ssRNA)12,433 nt390
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Table 2. Summary of screening for r
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esistance obtained was delayed symp
Page 430 and 431:
Finnegan J, McElroy D. 1994. Transg
Page 432 and 433:
Stam M, de Bruin R, Kenter S, van d
Page 435 and 436:
Transgenic approachesfor generating
Page 437 and 438:
LEA proteins and their effect on st
Page 439 and 440:
Table 1. Fresh and dry shoot weight
Page 441 and 442:
Table 2. Growth performance of tran
Page 443 and 444:
Table 3. The levels of green fluore
Page 445 and 446:
(Zhang and Wu 1988). Plants were re
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expression levels in young root tip
Page 449 and 450:
Kavi Kishor PB, Hong Z, Miao GH, Hu
Page 451 and 452:
High-level expression ofC 4photosyn
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(Imaizumi et al 1997). However, the
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ously. Indeed, earlier attempts to
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(Hudspeth et al 1992). Not only inc
Page 459:
Nomura M, Sentoku N, Nishimura A, L
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fects. Recent data suggest, however
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AH H H H H HEEEEEEBBBE H B UFig. 1.
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transcription through one transgene
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sertion of an adventitious DNA frag
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tin is folded into loops may result
Page 472 and 473:
Whole-plasmid DNAClean fragmentBomb
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Concluding commentsExperiments invo
Page 476 and 477:
Tinland B. 1996. The integration of
Page 478 and 479:
immune systems. Thus, restriction e
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A: p35S-CryIIIA 35SBtt CryIIIA nosB
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appealing in regard to our efforts
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1998, Kumpatla and Hall 1999). The
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HindIIIHindIIIRB 35S hpt 35S 35S in
Page 488 and 489:
ments (Francastel et al 1999), are
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ReferencesAmedeo P, Habu Y, Afsar K
Page 492 and 493:
Matzke MA, Neuhuber F, Matzke AJ. 1
Page 495 and 496:
Workshop reports483
Page 497 and 498:
Functional genomics workshopThe obj
Page 499 and 500:
Bioinformatics workshopThe Bioinfor
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