Rice Genetics IV - IRRI books - International Rice Research Institute

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Table 4. CCW sequencing status for year 1.Goal CUGI CSHL WUGSC CCW Sequence (Mb)Finishing 12 20 0 32 4.17Finished 3 5 1 9 1.39In finishing 12 16 4 32 4.72In production 0 0 0 0 0.00In library 0 0 0 0 0.00Total 15 21 5 41 6.11Sequence (Mb) 2.17 3.21 0.74 6.11immediate access to the rice genome for positional cloning and marker-assistedselection. Moreover, it would allow the IRGSP to provide a set of defined BAC clonesto sequence to each member of the IRGSP based on sequencing capacity and funding.Such a scheme would accelerate the completion of the sequencing of the rice genome,possibly as early as 2004.ReferencesArumuganathan K, Earle E. 1991. Nuclear DNA content of some important plant species. PlantMol. Biol. Rep. 9:208-219.Budiman M. 1999. Chapter III: Construction and characterization of a BAC library of Oryzasativa L. subsp. japonica cv. Nipponbare for genomic studies. PhD dissertation. TexasA&M University, College Station, Texas, USA. p 50-80.Cheng Z, Presting G, Buell C, Wing R, Jiang J. 2001. High resolution pachytene chromosomemapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromerelocation and the distribution of genetic recombination along chromosome 10 ofrice. Genetics 157:1749-1757.Mao L, Wood T, Yu Y, Budiman M, Woo S, Sasinowski M, Goff S, Dean R, Wing R. 2000. Ricetransposable elements: a survey of 73,000 sequence-tagged-connectors (STCs). GenomeRes. 10:982-990.Marra M, Kucaba T, Dietrich N, Green E, Brownstein B, Wilson R, McDonald K, Hillier L,McPherson J, Waterston R. 1997. High throughput fingerprint analysis of large-insert clones.Genome Res. 7:1072-1084.Sasaki T, Burr B. 2000. International Rice Genome Sequencing Project: the effort to completelysequence the rice genome. Curr. Opin. Plant Biol. 3:138-141.Soderlund C, Humphray S, Dunham A, French L. 2000. Contigs built with fingerprints, markersand FPC V4.7. Genome Res. 10:1772-1787.Sulston J, Mallett F, Durbin R, Horsnell T. 1989. Image analysis of restriction enzyme fingerprintautoradiograms. CABIOS 13:101-106.Venter C, Smith H, Hood L. 1996. A new strategy for genome sequencing. Science 381:364-366.Yuan Q, Liang F, Hsiao J, Zismann V, Benito M, Quackenbush J, Wing R, Buell R. 2000.Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Res. 28:3636-3641.224 Wing et al
NotesAuthors’ addresses: R.A. Wing, Yeisoo Yu, G. Presting, D. Frisch, T. Wood, Sung-Sick Woo,M. Arief Budiman, Long Mao, Hye Ran Kim, T. Rambo, E. Fang, B. Blackmon,J.L. Goicoechea, S. Higingbottom, M. Sasinowski, J. Tomkins, R.A. Dean, C. Soderlund,Clemson University Genomics Institute, 100 Jordan Hall, Clemson, SC 29634;W.R. McCombie, R. Martienssen, M. de la Bastide, Cold Spring Harbor Laboratory, 1Bungtown Rd., Cold Spring Harbor, NY, 11724; R. Wilson, D. Johnson, Washington UniversityGenome Sequencing Center, 4444 Forest Park Boulevard, St. Louis, MO 63108.Acknowledgments: The authors would like to acknowledge financial support from the RockefellerFoundation for BAC library development (RF98001#630 to RAW), the NSF Plant GenomeProgram for the CUGI BAC/EST Resource Center (#DBI-987276 to RAW, RAD,DF, MS), the Novartis Foundation for the fingerprint and STC databases, and the USDA-CSREES/NSF–Rice Genome Sequencing Project for the physical mapping, sequencing,and annotation of the short arms of chromosomes 10 and 3 (#99-35317-8505). We alsothank the staff of CUGI, CSHL, and WU-GSC, past and present, for their hard work anddedication to the project. Finally, we especially thank T. Sasaki and members of the JapaneseRice Genome Program for providing access to their valuable molecular genetic resources.Citation: Khush GS, Brar DS, Hardy B, editors. 2001. Rice genetics IV. Proceedings of theFourth International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines.New Delhi (India): Science Publishers, Inc., and Los Baños (Philippines): InternationalRice Research Institute. 488 p.Sequence-tagged connector/DNA fingerprint . . . 225
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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.
Page 186 and 187: unavailable until recently with the
Page 188 and 189: Table 1 continued.Trait QTL a Flank
Page 190 and 191: 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
Page 213 and 214: with the advanced techniques requir
Page 215 and 216: times contain sufficient data to ma
Page 217 and 218: amplification of regions that previ
Page 219 and 220: 4. Structure problems—subcloning
Page 221 and 222: estriction maps or optical maps are
Page 223 and 224: 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: Miropeats-OSJNBa0065H03 1.2 cMThres
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
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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
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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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