Rice Genetics IV - IRRI books - International Rice Research Institute

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Table 3 continued.Gene AbundancePutative identification Functional category accession Score Organism (%)no. a31 Ferredoxin-nitrite reductase Metabolism JA0172 176 Z. mays 0.2532 Photosystem II Photosynthesis U86018 177 O. sativa 0.2533 Ribosomal protein l27 Protein synthesis P51419 145 A. thaliana 0.2534 GF14-c protein Transcription P49106 141 Z. mays 0.2535 Water channel protein Transport facilitation AAA69490 184 Glycine max 0.2536 Unknown Unknown AF051205 152 Picea mariana 0.2537 Beta-5 tubulin Cell growth and division CAA52719 148 Z. mays 0.2038 Histone H2B Cell growth and division P54348 165 Z. mays 0.2039 Histone H3.2 Cell growth and division AAB36496 206 Medicago sativa 0.2040 Peroxidase 1 Cell rescue and defense AAD43561 95 Gossypium hirsutum 0.2041 Ras-related protein rab7 Signal transduction Q40787 292 Pennisetum ciliare 0.2042 Enolase-phosphatase E-1 Energy AAF14866 129 Homo sapiens 0.2043 Cytochrome C reductase complex 14 kDa protein Energy P48502 164 Solanum tuberosum 0.2044 Fumarylacetoacetate hydrolase Metabolism AAC17611 118 A. thaliana 0.2045 Lipase Metabolism BAA83367 102 O. sativa 0.2046 Nucleoside diphosphate kinase I Metabolism Q07661 122 O. sativa 0.2047 Cinnamyl alcohol dehydrogenase Metabolism CAA06687 169 Z. mays 0.2048 Novel No hit – – – 0.2049 Novel No hit – – – 0.2050 Novel No hit – – – 0.20a Accession number refers to the most highly conserved sequence found by alignment of protein sequences. Sample size: 1,882 clones. Stress conditions: 150 mMNaCl, 24 h.352 Bohnert et al
Microarray technologyThe rapid accumulation of genomic sequences has been paralleled by the growth incollections of ESTs, each of which contains the partial sequence of an expressed gene(Adams et al 1993, Marra et al 1998). The public dbEST includes approximately900,000 plant EST sequences among the more than 6.6 million ESTs deposited intotal. For these sequences to be informative, the genes that they identify must beassigned biological functions. This will ultimately be a biochemical or structural function,but many sequences are now annotated in descriptive terms that must not bemistaken for a functional identity. Realistically, we know the precise function of maybea quarter of all genes and we know some characteristics for about another quarter. Atleast one-half of all genes, however, remain functionally unknown. Expression profilingusing DNA microarrays provides a powerful tool for correlating some aspectsof gene functions, such as tissue-, developmental-, or external manipulation-specificexpression, with sequences. DNA microarrays are also useful for identifying differentiallyexpressed genes in organisms for which genomic DNA sequences are limited.The use of microarrays for expression profiling is based on two fundamental principles.The first is that, for many genes, a predominant factor underlying changes inexpression is an alteration in the abundance of the cognate mRNA. It is clear thatpost-transcriptional factors also affect gene expression but the analysis of these factorsis not amenable through microarray analysis. The second principle is that onlyDNA strands possessing complementary sequences can hybridize to each other toform a stable, double-stranded molecule. Microarrays exploit this property throughthe immobilization of single-strand copies of a gene as individual array elements onsurfaces such as glass slides coated with polylysine. These elements are termed the“probe” (Phimister 1999). After incubation with a mixture of (radioactively orfluorescently) labeled DNA molecules (termed “target”), representing a proportionalrepresentation of all genes present in a given (tissue) sample, the labeled moleculesthat represent the same gene as the immobilized DNA elements can form heteroduplexes.By measuring the amount of label that is bound to each array element at theend of the hybridization reaction, the relative transcript abundance of each gene canbe determined. In this way, RNA abundance levels for thousands of genes can bemeasured in a single experiment. Patterns of gene expression can be correlated withparticular tissues or experimental conditions by comparing abundance levels fromdifferent experiments.Two types of microarrays, which differ primarily in the length of the probes thatmake up the array elements and in the production of these elements, are being usedfor expression profiling. For DNA microarrays, printed on membranes or glass, theelements are large gene fragments (approximately 400 to 2,000 bp or more), typicallyproduced through polymerase chain reaction (PCR) amplification. In contrast, oligonucleotide-basedarrays (termed “chips”) (Lipshutz et al 1999) contain elements madeup of short synthetic DNA molecules. These are synthesized such that a set of 10 ormore oligonucleotide fragments report the presence of one gene and they includecontrols, which have one base mismatch for each of the selected fragments. The pro-Isolation of candidate genes for tolerance of abiotic stresses 353
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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
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For drought-response screening, our
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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
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Although mutants with discrete gene
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Generation of T-DNA insertionaltagg
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Aprobe AEEprobe BpGA1633RBgus Tn p3
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Number of loci36%224%170%010 20 30F
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Table 2. GUS assay in roots of tran
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1999, Krysan et al 1999, Sato et al
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Transposons and functionalgenomics
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cesses. To study the interactions a
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Constructs were made with the aim o
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RBcis-effect of the adjacent strong
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Ac knockout mutagenesisThe Ac lines
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Table 2 summarizes the transformati
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ReferencesBaldwin D, Crane V, Rice
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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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
Page 359 and 360: Materials and methodsPlant material
Page 361 and 362: Microarray hybridization and data a
Page 363: Table 3. Most abundant transcripts
Page 367 and 368: view of procedures, pitfalls, and n
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Page 371 and 372: Table 5. Strongly regulated transcr
Page 373 and 374: ReferencesAdams MD, Soares MB, Kerl
Page 375: Acknowledgments: We thank Chris Bor
Page 378 and 379: y cells separating during tissue de
Page 380 and 381: (Erwee and Goodwin 1983). The sympl
Page 382 and 383: tion between the abundance of CDK t
Page 384 and 385: in a complex of 105 kDa. These resu
Page 386 and 387: Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389: Umeda M, Umeda-Hara C, Yamaguchi M,
Page 390 and 391: asexual reproduction through apomix
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Page 394 and 395: Search for apomixis in riceThere ar
Page 396 and 397: Issues related to achieving synthet
Page 398 and 399: come and may use imprinting to achi
Page 400 and 401: Embryo-inducing geneInactive ablati
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Page 404 and 405: embryos, several genes characterist
Page 406 and 407: Our search for a rice homologue of
Page 408 and 409: sequenced the two rice DMC1 genes a
Page 410 and 411: Gustine DL, Sherwood RT, Huff DR. 1
Page 412 and 413: 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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