Rice Genetics IV - IRRI books - International Rice Research Institute

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Blair MW, Hedetale V, McCouch SR. 2001. Fluorescent-labeled microsatellite panels usefulfor detecting allelic diversity in cultivated rice (Oryza sativa L.). Theor. Appl. Genet. (Inpress.)Bligh HFJ, Till RI, Jones CA. 1995. A microsatellite sequence closely linked to the Waxy geneof Oryza sativa. Euphytica 86:83-85.Bligh HFJ, Roach PS, Jones CA, Larkin PD, Fu H, Park WD. 1998. Use of alternate splice sitesin granule bound starch synthase mRNA from low amylose rice varieties. Plant Mol. Biol.38:407-415.Brar DS, Abbasi FM, McNally R, Talag J, Corral M, Molinawe J, Li Z, Khush GS. 2000.Molecular characterization of introgression and alien gene tranfer in rice. In: Abstracts.International Rice Genetics Symposium, International Rice Research Institute, Los Baños,Philippines, Oct. 2000. p 56.Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR. 1997. Development of a microsatelliteframework map providing genome-wide coverage in rice (Oryza sativa L.). Theor. Appl.Genet. 95:553-567.Chin EC, Senior ML, Shu H, Smith JSC. 1996. Maize simple repetitive DNA sequences: abundanceand allele variation. Genome 39:866-873.Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, CartinhourS. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequencesin rice (Oryza sativa L.). Theor. Appl. Genet. 100:713-721.Coburn JR, Temnykh SV, McCouch SR. 2001. Chromosome-specific panels of microsatellitemarkers for semi-automated genotyping of rice (Oryza sativa L.). Crop Sci. (Submitted.)Daly MJ, Lincoln SE, Lander ES. 1991. “PRIMER,” unpublished software, Whitehead Institute/MITCenter for Genome Research. Available at http://www-genome.wi.mit.edu/ftp/pub/software/primer.0.5, and via anonymous ftp to ftp-genome.wi.mit.edu, directory/pub/software/primer.0.5.Doyle JJ, Morgante M, Tingey SV, Powell W. 1998. Size homoplasy in chloroplast microsatellitesof wild perennial relatives of soybean (Glycine subgenus Glycine). Mol. Biol. Evol. 15:215-218.Goldstein DB, Clark AG. 1995. Microsatellite variation in North American populations ofDrosophila melanogaster. Nucleic Acids Res. 23:3882-3886.Guiderdoni E, Galinato E, Luistro J, Vergara G. 1992. Anther culture of tropical japonica ×indica hybrids of rice (Oryza sativa L.). Euphytica 62:219-224.Hahn WJ, Grifo FT. 1996. Molecular markers in plant conservation genetics. In: Sobral BWS,editor. The impact of plant molecular genetics. New York, N.Y. (USA): Birkhaeuser Boston,Inc.Harrington S. 2000. A survey of genetic diversity of eight AA genome species of Oryza usingmicrosatellite markers. MS thesis. Cornell University, Ithaca, NY.He Y, Zhou P, Tan Y, Xu C, Zhang Q. 2000. Improvement of cooking and eating quality ofZhenshan 97, an elite maintainer line of hybrid rice, by molecular marker-assisted selection.In: Abstracts. International Rice Genetics Symposium, International Rice ResearchInstitute, Los Baños, Philippines, Oct. 2000. p 94.Hua JP, Xing YZ, Xu CG, Sun ZL, Zhang Q. 2000. Analyzing genetic basis of heterosis usingan immortalized F 2 population. In: Abstracts. International Rice Genetics Symposium, InternationalRice Research Institute, Los Baños, Philippines, Oct. 2000. p 13.Huang N, McCouch SR, Mew MT, Parco A, Guiderdoni E. 1994. Development of a RFLP mapfrom a double haploid population in rice. Rice Genet. Newsl. 11:134-137.132 McCouch et al
Ishii T, McCouch SR. 2000. Microsatellites and microsynteny in the chloroplast genomes ofOryza and eight other Gramineae species. Theor. Appl. Genet. 100:1257-1266.Ishii T, Xu Y, McCouch SR. 2001. Nuclear and chloroplast microsatellite variation in A-genomespecies of rice (Oryza spp.). Genome. (In press.)Ji HS, Koh HJ, Park SU, McCouch SR. 1998. Varietal identification in Japonica rice usingmicrosatellite DNA markers. Korean J. Breed. 30:350-360.Kwon SJ, Ahn SN, Yang CI, Hong HC, Kim YK, Suh JP, Hwang HG, Moon HP, Choi HC.2000. Genetic diversity of Korean Japonica rice cultivars. In: Abstracts. International RiceGenetics Symposium, International Rice Research Institute, Los Baños, Philippines, Oct.2000. p 41.Larkin PL, Park WD. 1999. Transcript accumulation and utilization of alternate and non-consensussplice sites in rice granule bound starch synthase is temperature-sensitive and controlledby a single nucleotide polymorphism. Plant Mol. Biol. 40:719-727.Lorieux M, Ndjiondjop M-N, Ghesquiere A. 2000. A first interspecific Oryza sativa × Oryzaglaberrima microsatellite-based genetic map. Theor. Appl. Genet. 100:591-601.McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M. 1997.Microsatellite marker development, mapping and applications in rice genetics and breeding.Plant Mol. Biol. 35:89-99Mitchell SE, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK. 1997. Applicationof multiplex PCR and fluorescence-based, semi-automated allele sizing technology forgenotyping plant genetic resources. Crop Sci. 37:617-624.Moncada P, Martinez CP, Borrero J, Chatel M, Gauch Jr. H, Guimaraes E, Tohme J, McCouchSR. 2000. Quantitative trait loci for yield and yield components in an Oryza sativa × Oryzarufipogon BC 2 F 2 population evaluated in an upland environment. Theor. Appl. Genet.102:441-452.Ni J, Colowit PM, Oster JJ, Mackill DJ. 2001. Evaluation of genetic diversity in rice subspeciesusing SSLP markers. Crop Sci. (Submitted.)Olufowote JO, Xu Y, Chen X, Park WO, Beachell HM, Dilday RH, Goto M, McCouch SR.1997. Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) usingmicrosatellite and RFLP markers. Genome 40:370-378.Panaud O, Chen X, McCouch SR. 1995. Frequency of microsatellite sequences in rice (Oryzasativa L.). Genome 38:1170-1176.Panaud O, Chen X, McCouch SR. 1996. Development of microsatellite markers and characterizationof simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol.Gen. Genet. 252:597-607.Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. 1996. A comparisonof RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis.Mol. Breed. 2:225-238.Provan J, Corbett G, Waugh R, McNicol JW, Morgante M, Powell W. 1996. DNA fingerprintsof rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats.Proc. R. Soc. Lond. B 263:1275-1281.Provan J, Corbett G, McNicol JW, Powell W. 1997. Chloroplast DNA variability in wild andcultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats.Genome 40:104-110.Pupko T, Graur D. 1999. Evolution of microsatellites in the yeast Saccharomyces cerevisiae:role of length and number of repeated units. J. Mol. Evol. 48:313-316.Microsatellite markers in rice: . . . 133
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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
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 114 and 115: testing Ka/Ks between the homeologo
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: provide a bridge for moving rapidly
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
Page 165 and 166: QTL mapping in rice:a few critical
Page 167 and 168: M-QTLsM-QTLs are defined as single
Page 169 and 170: (genetic/statistical models and cor
Page 171 and 172: Table 5. The percentage of three ty
Page 173 and 174: Table 7. Some environment-specific
Page 175 and 176: ferently to the environments. Simil
Page 177 and 178: (case 3), one may infer that this g
Page 179 and 180: Simultaneous QTL introgression and
Page 181 and 182: Doebley J, Stec A, Gustus C. 1995.
Page 183: Visscher PM, Haley CS, Thompson R.
Page 186 and 187: unavailable until recently with the
Page 188 and 189: Table 1 continued.Trait QTL a Flank
Page 190 and 191: the remaining parts of the linkage
Page 192 and 193: Table 3. QTLs detected for yield an
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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,
Page 333 and 334:
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
Page 352 and 353:
Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
Page 357 and 358:
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
Page 408 and 409:
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
Page 419 and 420:
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
Page 427 and 428:
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
Page 452 and 453:
initially fixed by phosphoenolpyruv
Page 454 and 455:
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
Page 461 and 462:
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
Page 473 and 474:
other cases it was not. We observed
Page 475 and 476:
Gorbunova V, Levy AA. 1997. Non-hom
Page 477 and 478:
Gene silencing and itsreactivation
Page 479 and 480:
Carbofuran (trade name, Furadan) is
Page 481 and 482:
Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
Page 483 and 484:
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
Page 489 and 490:
Table 4. Suppressors of silencing f
Page 491 and 492:
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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