Rice Genetics IV - IRRI books - International Rice Research Institute

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Molecular markers,genetic diversity, and evolutionEvolution and domestication of rice 61
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
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 68 and 69: Chen S, Lin XH, Xu CG, Zhang Q. 200
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 74 and 75: 62 Morishima
Page 76 and 77: defined as the diploid species havi
Page 78 and 79: Interspecific relatedness was also
Page 80 and 81: Within the geographical range of O.
Page 82 and 83: Search for the immediate ancestor o
Page 84 and 85: gene pool, we performed QTL analysi
Page 86 and 87: Table 3. Changes in population para
Page 88 and 89: Kadowaki K, Yazaki K, Osumi T, Hara
Page 91 and 92: Rice: a central genomefor the genet
Page 93 and 94: Gibberellicacid-insensitiveRiceFoxt
Page 95 and 96: parative organization of the Pooide
Page 97 and 98: clear alignment of major factors co
Page 99 and 100: Gale MD, Devos KM. 1998. Plant comp
Page 101 and 102: Phylogeny of the genusOryza as reve
Page 103 and 104: Table 1. Species recognized in Oryz
Page 105 and 106: However, the subdivisional classifi
Page 107 and 108: Multiple gene trees: new insights i
Page 109 and 110: AABBBBCCCCCCDDDDKKHHKKFFHHHHJJJJGGF
Page 111 and 112: group with the diploid E genome spe
Page 113 and 114: genomes occupy the basal positions
Page 115 and 116: Donoghue MJ. 1994. Progress and pro
Page 117: 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
Page 149 and 150:
Molecular mapping and markerassiste
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symposium (Li, this volume), here w
Page 153 and 154:
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
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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
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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
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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
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Correlation between gene expression
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Table 7. Numbers of cDNAs showing v
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Saghai Maroof MA, Yang GP, Zhang Q,
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188 Sasaki et al
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The boom in rice genome analysis is
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Selected PAC/BAC clones are culture
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an overestimation of the gene numbe
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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
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First inriceHexa3%Mono4%Penta12%Di2
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Contigs2712722738652742755814257782
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Table 4. CCW sequencing status for
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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
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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
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Deletion mutants for functionalgeno
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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
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Gene detectionGene detection strate
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ice. Transgenic plants were also ge
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ence of a single excision footprint
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homology to known proteins. The tra
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Transposon library generation10 sta
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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
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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
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total number of sequences submitted
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Table 2 continued.Database/ URL Inf
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Specialized databasesIn contrast to
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more complicated traits such as QTL
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ESTsGenetic markersMorphologicalMol
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NotesAuthors' address: Rice Genome
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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
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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
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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
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trum, IRBB21 conferred a high level
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elements. Two of them were located
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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
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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
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Cell divisionCell elongationand exp
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extend to the S phase. Furthermore,
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and, at 6 h, the population of S ph
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Levine A, Tenhaken R, Dixon R, Lamb
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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
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We isolated a rice homologue of the
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1996), and a putative hydroxyprolin
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The life cycle of angiosperms is pu
Page 407 and 408:
Ablation of the sexual embryoIsolat
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Birchler JA. 1993. Dosage analysis
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Li JM, Yuan LP. 1999. Hybrid rice:
Page 413:
Xu FX, Chye ML. 1999. Expression of
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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
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Stam M, de Bruin R, Kenter S, van d
Page 435 and 436:
Transgenic approachesfor generating
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LEA proteins and their effect on st
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Table 1. Fresh and dry shoot weight
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Table 2. Growth performance of tran
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Table 3. The levels of green fluore
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(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
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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
Page 474 and 475:
Concluding commentsExperiments invo
Page 476 and 477:
Tinland B. 1996. The integration of
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immune systems. Thus, restriction e
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A: p35S-CryIIIA 35SBtt CryIIIA nosB
Page 482 and 483:
appealing in regard to our efforts
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1998, Kumpatla and Hall 1999). The
Page 486 and 487:
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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