Rice Genetics IV - IRRI books - International Rice Research Institute

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Equally important as the genomic information are the germplasm resourcesthat will provide the basis for direct application of molecular tools. These resourcesrange from tester lines and mutant lines to cultivated varieties, landraces, and wildspecies maintained in various crop germplasm centers worldwide. The databaseservers provide information on acquisition, preservation, evaluation, and distributionof all available rice strains. The literature on different aspects of rice researchhas also been catalogued for searching on the Web for the user community.Informatics for the rice communityMore than 20 databases and Web sites are currently available online for ricegenomics (Table 2). Most of these databases focus on specialized and detailedinformation covering a broad range of research on rice genomics or rice biology,whereas some are designed for ordinary users and offer general information onrice. An overview of these databases is briefly given here.Rice genome databasesOne of the earliest databases that have been serving the rice community since 1993is RiceGenes (http://genome.cornell.edu/rice/). Supported by the USDA-ARS Centerfor Bioinformatics in partnership with Cornell University, this database focuseson comparative genetic maps, molecular markers, morphological markers, quantitativetrait loci (QTLs), and germplasm data. Newly added features includemicrosatellite marker data and microsatellite maps of the 12 rice chromosomes.RiceGenes is currently being converted to a relational database management systemto allow for increased data integration and greater flexibility.Table 2. Major rice genome and germplasm databases.Database/ URL Information categoriesorganization aINE http://rgp.dna.affrc.go.jp/ Genetic map, YAC physical map, ESTmap, PAC contigs, chr. 1 and 6 PAC/BAC clone sequence/annotation,IRGSP sequencing statusRiceGenes http://genome.cornell. Genetic maps, molecular markers,edu/rice/morphological markers, QTLs,comparative maps, rice varietyreleases, referencesOryzabase http://www.shigen.nig. Genetic maps, integrated maps,ac.jp/rice/oryzabase/genetic stocks, gene dictionary,mutant images, general information,referencescontinued on next page296 Antonio et al
Table 2 continued.Database/ URL Information categoriesorganization aU.S. Rice Genome http://www.usricegenome.org/ Chr. 3, 10, and 11 sequencing statusSequencingTIGR Rice http://www.tigr.org/tdb/rice/ Sequencing status, chr. 3, 10 BACDatabasesequence data, annotationClemson Univ. http://www.genome. Rice BAC libraries, BAC-endGenomics Institute clemson.edu/ sequence, rice BAC fingerprints,contig maps, chr. 3 and 10 sequencingstatus, rice blast STCsCold Spring Harbor http://nucleus.cshl.org/ Chr. 10 sequencing status, BAC (cv.Laboratory riceweb/ Tequing and Lemont) sequence/annotationPlant Genome http://www.rutgers.edu/ Chr. 10 sequencing status, BACInitiative at Rutgerssequence data, annotationKorea Rice Genome http://bioserver.myongji. Rice ESTs, genetic maps, chloroplastDatabase ac.kr/ genome sequence, chr. 1 (151.4–160.0 cM region), sequencing statusNational Center for http://www.ncgr.ac.cn/ Chr. 4 sequencing status, BAC contigGene Research, index.html map, BAC sequence data (indica)CASPlant Genome http://genome.sinica.edu.tw/ Chr. 5 sequencing status, PACCenter Academiasequence data, annotationSinicaThai Rice Genome http://jasmine.kps.ku.ac.th/ Chr. 9 sequencing statusProgramRice Gene Index http://www.tigr.org/tdb/ogi/ Rice ESTs, cDNA libraries, geneproductsRice Repeat http://www.tigr.org/tdb/rice/ Rice repeat sequences, mobileDatabase blastsearch.html elementsRiceBlastDB http://ascus.cit.cornell.edu/ Genetic/physical maps, markers,blastdb/population structure, DNA fingerprints,pathotype, mating type relatedto rice blastMAFF DNA Bank http://bank.dna.affrc.go.jp/ Rice cDNA clones, genetic map,clones/filters for distributionMAFF Genebank http://www.gene.affrc.go.jp/ Genetic stocks, evaluation dataGRIN http://www.ars-grin.gov/npgs Genetic stocks, evaluation dataSINGER http://www.cgiar.org/ Genetic stocks maintained at IRRI,http://noc1.cgiar.org/IITA, and WARDA, evaluation dataNPGRC http://www.npgrc.tari.gov.tw/ Genetic stocks, evaluation dataRiceweb http://www.riceweb.org/ General informationaTIGR = The Institute for Genomic Research, MAFF = Ministry of Agriculture, Forestry, and Fisheries,GRIN = Germplasm Resources Integrated Network, SINGER = Systemwide Information Network for GeneticResources, NPGRC = National Plant Genetic Resources Center, YAC = yeast artificial chromosome,EST = expressed sequence tag, PAC = P1-derived artificial chromosome, BAC = bacterial artificial chromosome,IRGSP = International Rice Genome Sequencing Project, QTLs = quantitative trait loci, STCs =sequence tagged connectors, IRRI = International Rice Research Institute, IITA = International Instituteof Tropical Agriculture, WARDA = West Africa Rice Development Association, CAS = Chinese Academy ofSciences.Bioinformatics and the rice genome 297
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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
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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
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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
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
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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 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
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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
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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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