Rice Genetics IV - IRRI books - International Rice Research Institute

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Although mutants with discrete genetic lesions are ideal genetic materials forassigning function to a particular gene, there are only two possible alleles at a locus ineach parental genotype. The success of a mutant screening therefore depends on discriminatingthe phenotypic effect of changing a single allele. Some mutated allelesmay not have observable phenotypes because of minor effects or gene redundancy.The production of double or triple mutants is probably needed to understand the effectsand interactions of multiple genes. Even after a sequence is assigned to a mutantby reverse genetics, phenotyping, possibly guided by the known disrupted sequence,remains the critical step for assigning function. With the availability of genetic toolsand sequence information, ample opportunities exist to make use of the allelic diversitycreated in mutants together with the natural variability present in breeding materialsand raw germplasm to better understand the pathways that control complex traits.ReferencesAguirrezabalaga I, Nivard MJM, Comendador MA, Vogel EW. 1995. The cross-linking agenthexamethylphosphoramide predominantly induces intra-locus and multi-locus deletionsin postmeiotic germ cells of Drosophila. Genetics 139:649-658.Bruggemann E, Handwerger K, Essex C, Storz G. 1996. Analysis of fast neutron-generatedmutants at the Arabidopsis thaliana HY4 locus. Plant J. 10:755-760.Clough SJ, Fengler KA, Yu I-c, Lippok B, Smith Jr. RK, Bent AF. 2000. The Arabidopsis dnd1“defense, no death” gene encodes a mutated cyclic nucleotide-gated ion channel. Proc.Natl. Acad. Sci. USA 97:9323-9328.Colbert TG, Till BJ, Tompa R, Reynolds SH, Steine MN, Yeung AT, McCallum CM, Comai L,Henikoff S. 2001. High-throughput screening for induced point mutations. Plant Physiol.(In press.)Krysan PJ, Young JC, Tax F, Sussman MR. 1996. Identification of transferred DNA insertionswithin Arabidopsis genes involved in signal transduction and ion transport. Proc. Natl.Acad. Sci. USA 93:8145-8150.Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P. 1998.Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl. Acad.Sci. USA 95:370-375.Liu LX, Spoerke JM, Milligan EL, Chen J, Reardon B, Westlund B, Sun L, Abel K, ArmstrongB, Hardiman G, King J, McCague L, Basson M, Clover R, Johnson CD. 1999. Highthroughputisolation of Caenorhabditis elegans deletion mutants. Genome Res. 9:859-867.Martienssen RA. 1998. Functional genomics: probing plant gene function and expression withtransposons. Proc. Natl. Acad. Sci. USA 95:2021-2026.McCallum CM, Comai L, Green EA, Henikoff S. 2000a. Targeting induced local lesions ingenomes (TILLING) for plant functional genomics. Plant Physiol. 123:439-442.McCallum CM, Comai L, Green EA, Henikoff S. 2000b. Targeted screening for induced mutations.Nature Biotechnol. 18:455-457.Okubara PA, Anderson PA, Ochoa OE, Michelmore RW. 1994. Mutants of downy mildewresistance in Lactuca sativa (lettuce). Genetics 137:867-874.Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT. 1998. Mutation detection usinga novel plant endonuclease. Nucleic Acids Res. 26:4597-4602.250 Leung et al
Reardon JT, Liljestrand-Golden CA, Dusenbery RL, Smith PD. 1987. Molecular analysis ofdiepoxybutane-induced mutations at the rosy locus of Drosophila melanogaster. Genetics115:323-331.Shirley BS, Hanley S, Goodman HM. 1992. Effects of ionizing radiation on a plant genome:analysis of two Arabidopsis transparent testa mutations. Plant Cell 4:333-347.Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrandiz C,Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, Wang ZY, Xia Y, DixonRA, Harrison MJ, Lamb C, Yanofsky M, Chory J. 2000. Activation tagging in Arabidopsis.Plant Physiol. 122:1003-1013.Wurtzel ET, Luo R, Yatou O. 2001. A simple approach to identify the first rice mutants blockedin carotenoid biosynthesis. J. Exp. Bot. 52:161-166.Yandell MD, Edgar LG, Wood WB. 1994. Trimethylpsoralen induces small deletion mutationsin Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 91:1381-1385.Yin Z, Chen J, Zeng L, Goh M, Leung H, Khush GS, Wang GL. 2000. Characterization of ricelesion mimic mutants and identification of a mutant with broad-spectrum resistance to riceblast and bacterial blight. Mol. Plant-Microbe Interact. 13:869-876.NotesAuthors’ addresses: H. Leung, C. Wu, M. Baraoidan, A. Bordeos, M. Ramos, S. Madamba, P.Cabauatan, C. Vera Cruz, A. Portugal, G. Reyes, R. Bruskiewich, G. McLaren, R. Lafitte,G. Gregorio, J. Bennett, D. Brar, G. Khush, International Rice Research Institute, DAPOBox 7777, Metro Manila, Philippines; P. Schnable, Department of Agronomy, Iowa StateUniversity, Ames, IA 50011, USA; G. Wang, Department of Plant Pathology, Ohio StateUniversity, Columbus, OH 43210, USA; J. Leach, Department of Plant Pathology, KansasState University, Manhattan, KS 66506-5502, USA.Acknowledgments: This work has been supported by IRRI core research funds and in part bygrants from the Rockefeller Foundation, United States Department of Agriculture, andUnited States Agency for International Development.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.Deletion mutants for functional genomics: . . . 251
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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
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 and 236: Miropeats-OSJNBa0065H03 1.2 cMThres
Page 237: NotesAuthors’ addresses: R.A. Win
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 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
Page 310 and 311: 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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