Rice Genetics IV - IRRI books - International Rice Research Institute

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testing Ka/Ks between the homeologous loci of the allotetraploid and the genes of thediploid species with the corresponding genomes will determine which homeologouslocus has undergone adaptive evolution.Recurrent formation of an allotetraploid genome. Multiple independent formationsof an allopolyploid genome or species from different populations of the diploidprogenitors have been observed in both plants and animals (Soltis and Soltis 2000).The O. officinalis complex with the B, C, and BC genomes is well known for itstaxonomic complexity in Oryza, and the polyploids, in particular, are difficult to group(Vaughan 1989). A recent study using Adh and matK genes suggested that the BCgenome originated independently in Africa and Asia (Ge et al 1999). The BC genomemay have also formed multiple times within each continent. The recurrent formationof the BC genome is probably responsible for the taxonomic difficulty in the speciescomplexes containing the B, C, and BC genomes (Tateoka and Pancho 1963, Tateoka1965b). Because allotetraploids in Oryza involved many genomes and originated fromdifferent lineages and at different times, Oryza should serve as a good model systemfor studying various aspects of polyploid genome evolution.Beyond its agronomic importance, rice has become a model organism for biologicalresearch. Because of its small genome size, Oryza sativa will be the first monocotand the second plant species (following Arabidopsis thaliana) with the entire genomesequenced (Sasaki 1998). The genus Oryza thus offers an excellent system for studiesof plant evolution at the genomic level. This will allow us to examine genomic changesthat are adaptively or agriculturally important. The availability of genomic informationof the selected nuclear gene markers, such as chromosomal locations, will allowus to investigate genome evolution. This will, on the one hand, help address a fundamentalquestion of which genomic consequences have provided adaptive advantagesfor allopolyploids and have made this mode of speciation so prevalent in angiosperms(Wendel 2000). On the other hand, with a robust phylogeny and multiple gene markers,many intriguing questions involving the biogeography of particular species, thegenome, and the whole genus can be addressed.ReferencesAbe T, Edanami T, Adachi E, Sasahara T. 1999. Phylogenetic relationships in the genus Oryzabased on mitochondrial RFLPs. Genes Genet. Syst. 74:23-27.Aggarwal RK, Brar DS, Khush GS. 1997. Two new genomes in the Oryza complex identifiedon the basis of molecular divergence analysis using total genomic DNA hybridization.Mol. Gen. Genet. 254:1-12.Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS. 1999. Phylogenetic relationships amongOryza species revealed by AFLP markers. Theor. Appl. Genet. 98:1320-1328.Brar DS, Khush GS. 1997. Alien introgression in rice. Plant Mol. Biol. 35:35-44.Cordesse F, Grellet F, Reddy AS, Delseny M. 1992. Genome specificity of rDNA spacer fragmentsfrom Oryza sativa L. Theor. Appl. Genet. 83:864-870.Dally AM, Second G. 1990. Chloroplast DNA diversity in wild and cultivated species of rice(genus Oryza, section Oryza): cladistic-mutation and genetic-distance analysis. Theor. Appl.Genet. 80:209-222.102 Song Ge et al
Donoghue MJ. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Mo. Bot.Gard. 81:405-418.Doyle JJ, Kanazin V, Shoemaker RC. 1996. Phylogenetic utility of histone H3 intron sequencesin the perennial relatives of soybean (Glycine: Leguminosae). Mol. Phylogen. Evol. 6:438-447.Fukui K, Shishido R, Kinoshita T. 1997. Identification of the rice D-genome chromosomes bygenomic in situ hybridisation. Theor. Appl. Genet. 95:1239-1245.Gaut BS, d’Ennequin MLT, Peek AS, Sawkins MC. 2000. Maize as a model for the evolutionof plant nuclear genomes. Proc. Natl. Acad. Sci. USA 97:7008-7015.Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin ofmaize. Proc. Natl. Acad. Sci. USA 94:6809-6814.Ge S, Sang T, Lu BR, Hong DY. 1999. Phylogeny of rice genomes with emphasis on origins ofallotetraploid species. Proc. Natl. Acad. Sci. USA 96:14400-14405.Hillis DM, Huelsenbeck JP. 1995. Assessing molecular phylogenies. Science 267:255-256.Ishii T, Nakano T, Maeda H, Kamijima O. 1996. Phylogenetic relationships in A-genome speciesof rice as revealed by RAPD analysis. Genes Genet. Syst. 71:195-201.Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS. 2000. Genetic diversity and phylogeneticrelationship as revealed by inter simple sequence repeat (ISSR) polymorphism inthe genus Oryza. Theor. Appl. Genet. 100:1311-1320.Khush GS. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35:25-34.Kihara H. 1924. Cytologische und genetische Studien bei wichtigen Getreidearten mit besondererRucksicht auf das Verhalten der Chromosomen und die Sterilitat in den Bastarden. Mem.Coll. Sci. Kyoto Imp. Univ., Ser. B 1:1-200.Launert E. 1965. A survey of the genus Leersia in Africa. Senckenbergiana Biol. 46:129-153.Li HW. 1964. Studies on genetic and cytogenetic evidence for species relationships in theRepublic of China. In: Rice genetics and cytogenetics. Proceedings of the Symposium onRice Genetics and Cytogenetics. Amsterdam (Netherlands): Elsevier Publishing Company.p 119-131.Li WH. 1997. Molecular evolution. Sunderland, Mass. (USA): Sinauer Associates, Inc.Linnaeus C. 1753. Species plantarum. Vol. 1. Stockholm, Sweden.Lu BR. 1999. Taxonomy of the genus Oryza (Poaceae): historical perspective and current status.Int. Rice Res. Notes 24:4-8.Masterson J. 1994. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms.Science 264:421-424.McIntyre CL, Winberg BC. 1998. A rapid means of identifying wild rice species DNA usingdot blots and genome-specific rDNA probes. Genome 41:391-395.Morinaga T. 1943. Cytogenetical studies on Oryza sativa L. VI. The cytogenetics of F 1 hybridsof O. minuta Presl. and O. latifolia. Jpn. J. Bot. 12:347-357.Morinaga T. 1964. Cytogenetical investigations on Oryza species. In: Rice genetics and cytogenetics.Proceedings of the Symposium on Rice Genetics and Cytogenetics. Amsterdam(Netherlands): Elsevier Publishing Company. p 91-102.Morishima H, Oka HI. 1960. The pattern of interspecific variation in the genus Oryza: itsquantitative representation by statistical methods. Evolution 14:153-165.Morishima H, Sano Y, Oka HI. 1992. Evolutionary studies in cultivated rice and its wild relatives.Oxford Surv. Evol. Biol. 8:135-184.Nayar NM. 1973. Origin and cytogenetics of rice. Adv. Genet. 17:153-292.Prodoehl A. 1922. Oryzeae monographice describuntur. Bot. Arch. 1:211-224, 231-256.Phylogeny of the genus Oryza . . . 103
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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
Page 64 and 65: Because of the great diversity (sci
Page 66 and 67: eeders where final products to enha
Page 68 and 69: Chen S, Lin XH, Xu CG, Zhang Q. 200
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 73 and 74: Molecular markers,genetic diversity
Page 75 and 76: Evolution and domestication of rice
Page 77 and 78: ABCDO. barthiiO. rufipogonO. longis
Page 79 and 80: Wild(O. rufipogon)Geographical diff
Page 81 and 82: South Asia (particularly on the wes
Page 83 and 84: al 1992, Sun et al 1996a,b,c), thou
Page 85 and 86: wild and cultivated types (Est10, W
Page 87 and 88: Cai HW, Morishima H. 2000a. Diversi
Page 89: Sato YI, Tang SX, Yang LU, Tang LH.
Page 92 and 93: The solid base laid by classical ri
Page 94 and 95: The synthesis shown in Figure 1 is
Page 96 and 97: Arabidopsis, long heralded as a “
Page 98 and 99: Monocots and eudicots: Is there sti
Page 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 116 and 117: Roschevicz RI. 1931. A contribution
Page 119 and 120: Miniature inverted repeattransposab
Page 121 and 122: eau and Wessler 1992, 1994), rice (
Page 123 and 124: MITEs as a source of allelic divers
Page 125 and 126: ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
Page 127 and 128: Le QH, Wright S, Yu Z, Bureau T. 20
Page 129 and 130: Microsatellite markers in rice:abun
Page 131 and 132: make the best SSR markers for rice.
Page 133 and 134: Predicted frequency100,00080,000Cla
Page 135 and 136: Relationship between SSRs and genes
Page 139 and 140: are indicated with RM locus designa
Page 141 and 142: SSRs have been used to define intro
Page 143 and 144: provide a bridge for moving rapidly
Page 145 and 146: Ishii T, McCouch SR. 2000. Microsat
Page 147: NotesAuthors’ addresses: S.R. McC
Page 150 and 151: traits of economic importance (Mack
Page 152 and 153: Table 2. Tagging and mapping of som
Page 154 and 155: even at the juvenile stage. Several
Page 156 and 157: Chen et al (2000) transferred the b
Page 158 and 159: genome sequence of rice, this will
Page 160 and 161: Kurata N, Nagamura Y, Yamamoto K, H
Page 162 and 163: 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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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
Page 485 and 486:
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
Page 496 and 497:
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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