Rice Genetics IV - IRRI books - International Rice Research Institute

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BOX NO. 1recent international workshops to plot future research strategy, not only for rice butalso for the five major cereals that feed human populations globally (Ito et al 1999,Ribaut and Poland 2000).The future use of molecular markers to combine or pyramid abiotic stress resistancegenes with those of disease and insect resistance, in an efficient and timelymanner, could only have been a rice breeder’s dream just a decade ago. Today, however,with Internet access to molecular genotype and phenotype databases and theinternational sharing of many different types of genetic resources (germplasm andDNA-based technologies), even such complex traits and combinations of traits areapproachable (Xu 1997).Comparative genomicsComparative genomics and the discoveries related to the study of synteny amongcereal genomes demonstrated the unequivocal superiority of DNA-based moleculartools for investigating the long-standing questions of cereal evolution. In addition, itdemonstrated what has become the ultimate discovery of the rice biotechnology adventure—thecentral role of the rice genome in understanding and technically accessingthe far-larger genomes of such major crops as maize and wheat (Box 2).Early in the 1990s, it was apparent that higher plant species must share extensive“colinearity” of DNA markers and presumably genes across genera in both dicots aswell as monocots. The prospect of conservation of linearity within linkage groupsgenerated great excitement. For, if this were true, genetic information and relatedmolecular markers might be exploited in related species with less well-developedmolecular maps and markers. From 1988 to 1993, numerous papers related the newsthat indeed colinearity was a fact across species and even genera. However, evenmore striking and fortuitous for those working with the rice genome was the developmentof comparative or consensus maps within the cereals (Bennetzen and Freeling1993). In their conceptual framework, Moore et al (1995) postulated that, based onthe alignment of 19 linkage groups/segments from rice, one could form the buildingblocks of six of the world’s major cereal food crops. A flood of research reports followedthat not only confirmed the conceptual model but also quickly illustrated howgene discovery in the rice genome, partially because of its small size and saturatedmolecular maps, could rapidly and effectively be transferred to the other cereals. By1998, Van Deynze et al (1998) had produced a set of RFLP anchor probes to facilitatecomparative mapping across grass genera. Shortly thereafter, the applications forecastearlier began to be apparent. Leister et al (1999) demonstrated the RFLP andphysical mapping of resistance gene homologues in rice and barley. Coincidentally,the R genes from rice were the genes with race-specific resistance to blast and bacterialdisease noted at the beginning of this section.These scientific advances, combined with the advent of electronic mail (an equalizerof time, space, and national origin without parallel), added a multiplier effect tothe IPRB investment that could not have been imagined 15 years earlier. Researchersworldwide have experienced research synergy unheralded over the past 50 years ofrice genetics, as rice, “the pivotal genome,” was placed in a unique position alongwith those researchers who had helped to create the science of rice biotechnology.48 O'Toole et al
BSLLBTETBTBox no. 2Rice—the pivotal genomeCOMPARATIVE GENOMICS HAS revealeda level of conservation in genecontent and order within the grasses thatsurprised even the most experiencedgeneticists. After the landmark publicationof Moore et al (1995), which indicatedthat all major cereal crop genomescould be represented by 19 segmentsfound in the rice genome, rice has takena solid position at the center of bothgraphic presentations (adapted from Galeand Devos 1998, this box) as well asresearch efforts to use map-based clon-ing for gene discovery and isolation fromthe much larger genomes of oat, wheat,and maize. The rice genome, with only400 million DNA base pairs (bp), is aboutfour times larger than Arabidopsis, themodel dicot. This, coupled with a densegenetic map of >2,500 markers, physicalmaps of the entire genome, largepublic collections of expressed sequencetags (ESTs), and the near-termprospect of the complete rice genomesequence, makes rice a model crop forthe cereals.B.3(T)B ptB.2(T)C.3(B)C ptC.2(T)B.1(T)B ptBTC.1(T)2L(t)C ptCT2S(t)22S2B(c)(t)10L(t)2L(c)10B(c)caba3VII 4105b(pt) B(pt)acVIIIbb 7c b aa 9 11 2 V52 5c(pt)a b IptIIVIII VIIXbVIIIaD 2(pt)F7J3(pt)2 44(pt)7LT BBB1SBTBBTSLBSL7STLBTTTS1 (pt)LTBSBSTTTTBBTB5LT3.12.47B5.55.42.15S4L(T)65S(d)1L(d)6S1L1S(c)1L.11BBA.2(B)A.1(B)B.4(T)B.5(B)EB2L(c)5L.45L.54S5L.15L.26LGTGBB.6(B)1L.2A ptB pt5L (pt)1 (pt)GE1 (B)E ptE 4(B)E ptOatsTriticeaeMaizePearl milletSorghumSugarcaneFoxtail milletRiceInstitutional and human resource capacity building 1Capacity building is an extremely difficult concept to define. When related to theIPRB, where it refers to national networks and institutions as well as individuals, itcan result in a great lack of clarity, which might require a full-length paper to demystify.1 This section on capacity building under the IPRB relies heavily on the report “Capacity BuildingEvaluation of the International Program on Rice Biotechnology (IPRB),” June-October 1999, byMadan Mohan, Leocadio Sebastian, Kangle Zhang, and David Norman. Rockefeller Foundation.249 p.The Rockefeller Foundation's International Program on Rice Biotechnology 49
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 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 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 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
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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
Page 250 and 251:
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
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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types of users. An annotation datab
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ReferencesAntonio BA, Fang Z, Sanch
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Gene isolation and functionEnhancin
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Enhancing deployment of genes forbl
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mochi and Tsuyuake (Wu et al 1996).
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tive indica rice varieties supports
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transcription factor, resulting in
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facilitate breeding durable resista
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(Inukai et al 1994, Yu et al 1996,
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Rossman AY, Howard RJ, Valent B. 19
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Molecular signaling in diseaseresis
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AOsRac1IED II III IV 214aaOsRac1 KC
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Japonica rice variety Kinmaze, whic
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Table 1. Characteristics of lesion-
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an effective inducer of host resist
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Takahashi A, Kawasaki T, Henmi K, S
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et al 2000). Sequence analysis of t
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612-amino acid protein, including t
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Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
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Isolation of candidate genesfor tol
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Materials and methodsPlant material
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Microarray hybridization and data a
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Table 3. Most abundant transcripts
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Microarray technologyThe rapid accu
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view of procedures, pitfalls, and n
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Log(2) ratio1.51.0OC104E01—WCP1OC
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Table 5. Strongly regulated transcr
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ReferencesAdams MD, Soares MB, Kerl
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Acknowledgments: We thank Chris Bor
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y cells separating during tissue de
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(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
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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
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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