Rice Genetics IV - IRRI books - International Rice Research Institute

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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, Pi-tPi-fM-Pi-zPi-se-1 (Rb-1)Pi-ix-1 (Rb-1)CDO127RZ638RZ400RG118Adh1S2AS3I1S2AS3A1RG1094r6b(NBS-LRR)Pi-aRG167Npb44XLRin12A4RG247NLRfrA2ZMDRTScr11b(NBS-LRR)r11a(NBS-LRR)r4b(NBS-LRR)r12(NBS-LRR)1700b (Rp1)1700a (Rp1)RG103r6a(NBS-LRR)RG1109ZMDRTSdZMDRTSer10(NBS-LRR)r2(NBS-LRR)Npb186RZ536r5(NBS-LRR)r3(NBS-LRR)XLRfrA7XLRfrABBBphenchr 114.06.97.31.45.93.36.56.96.50.80.60.63.25.41.70.51.14.723.34.60.91.711.86.02.88.40.02.93.05.10.03.30.09.3R4R12R5Fig. 4. Assigning nucleotide-binding site and leucine-rich repeat (NBS-LRR) sequencesto loss-in-resistance mutants. Fast neutron (FN) and gamma ray (GR)mutants with a loss in resistance to blast were analyzed for deletion in NBS-LRRsequences that have been mapped on chromosome 11. DNA from progeny of themutant line GR131 showed a smaller fragment when probed with R4, indicating adeletion at this locus.Gamma ray and fast neutron induced mutantsGR131 R4 deletionIR64GR131 susceptible to 3 blast pathogen isolates248 Leung et al
cific PCR primers to screen a DNA pool of deletion lines. If the target gene has adeletion bracketed by the primers, a length polymorphism would be detected in thePCR products. More recently, McCallum et al (2000a,b) described a technique calledtargeting induced local lesions in genomes (TILLING) to detect base-pair mismatches.In this case, primers are designed to bracket the target gene. A single base-pair mismatchbetween the mutant and wild-type DNA sequences results in a heteroduplexthat can be detected by denaturing high-performance liquid chromatography (DHPLC)or by specific enzyme cleavage precisely at the 3’-end of the mismatch (Oleykowskiet al 1998, Colbert et al 2001). The TILLING procedure is attractive as it is wellsuited for high-throughput screening. Furthermore, the high density of mutations inducedby EMS makes it possible to cover the genome with relatively few individuals(approximately 10,000 lines). We have generated a collection of EMS-induced mutantsand DNA pools are being produced and subjected to TILLING. Successful applicationof a reverse genetics system to the IR64 mutants will greatly enhance thevalue of the collection of mutants and increase our ability to assign sequences to eachof the mutant lines.IR64 mutant databaseWe have systematically collected phenotypic information on the mutant stocks withthe goal of linking such information to genomic databases. As rice genome data becomeavailable, we envision that all mutant lines can be assigned to one or morephysical locations on the sequence map. Together with other collections of mutants, itis feasible to assign an allelic series of insertions, deletions, and point mutations toevery gene in the genome.As a first step, we have used the <strong>International</strong> Crop Information System (ICIS)database to document phenotypic and molecular data on the IR64 mutant stocks. Anontology of component traits of mutant phenotypes is being defined to allow structuredsearches of the database. The database of mutants has about 200 phenotypicallydescribed mutants. A prototype Web interface (www.cgiar.org/irri/genomics/index.htm)has been developed to allow users to search the database according to mutant phenotypes.The next phase of database development will involve linking phenotypic datato molecular characterization of the mutants to facilitate the identification of candidategenes.ConclusionsThe IR64 mutant collection provides a needed resource for gene discovery, particularlyfor indica varieties that contain many adaptive traits for rice grown in the tropics.Our data suggest that the IR64 mutants exhibit a wide range of variability usefulfor detecting conditional mutants. We will expand the mutant collection with a rangeof deletion sizes and point mutations such that an efficient reverse genetics systemcan be developed using high-throughput genotyping methods. Through database linkages,we will place these mutants onto the chromosomal regions by association withknown mutants or traits and by reverse genetics.Deletion mutants for functional genomics: . . . 249
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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
Page 209 and 210: Strategies and techniquesfor finish
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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 and 236: Miropeats-OSJNBa0065H03 1.2 cMThres
Page 237: NotesAuthors’ addresses: R.A. Win
Page 240 and 241: Sasaki 1997). Such analysis is ofte
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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 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
Page 298 and 299: primers (G1, G2) and two Tos17-spec
Page 300 and 301: of insertion mutants by sequencing
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 308 and 309: 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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