Rice Genetics IV - IRRI books - International Rice Research Institute

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Witcombe JR, Hash CT. 2000. Resistance gene deployment strategies in cereal hybrids usingmarker-assisted selection: gene pyramiding, three-way hybrids, and synthetic parent populations.Euphytica 112:175-186.Wu KS, Martinez C, Lentini Z, Tohme J, Chumley FG, Scolnik PA, Valent B. 1996. Cloning ablast resistance gene by chromosome walking. In: Khush GS, editor. Rice genetics III.Proceedings of the Third International Rice Genetics Symposium, 16-20 Oct 1995, Manila,Philippines. Los Baños (Philippines): International Rice Research Institute. p 669-674.Xu K, Mackill DJ. 1996. A major locus for submergence tolerance mapped on rice chromosome9. Mol. Breed. 2:219-224.Yamaguchi Y, Ikeda R, Hirasawa H, Minami M, Ujihara A. 1997. Linkage analysis ofthermosensitive genic male sterility gene, tms-2, in rice (Oryza sativa L.). Breed. Sci. 47:371-373.Yamasaki M, Tsunematsu H, Yoshimura A, Iwata N, Yasui H. 1999. Quantitative trait locusmapping of ovicidal response in rice (Oryza sativa L.) against whitebacked planthopper(Sogatella furcifera Horvath). Crop Sci. 39:1178-1183.Yanagihara S, McCouch SR, Ishikawa K, Ogi Y, Maruyama K, Ikehashi H. 1995. Molecularanalysis of the inheritance of the S-5 locus, conferring wide compatibility in indica/japonicahybrids of rice (O. sativa L.). Theor. Appl. Genet. 90:182-188.Yang DC, Magpantay GB, Mendoza M, Huang N, Brar DS. 1997. Construction of a contig fora fertility restorer gene, Rf2, in rice using BAC library and its sequence with Rf2 gene ofmaize. Rice Genet. Newsl. 14:116-117.Yano M, Sasaki T. 1997. Genetic and molecular dissection of quantitative traits in rice. PlantMol. Biol. 35:145-153.Yao FY, Xu CG, Yu SB, Li JX, Gao YJ, Li XH, Zhang QF. 1997. Mapping and genetic analysisof two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice(Oryza sativa L.). Euphytica 98:183-187.Yoshimura S, Yoshimura A, Iwata N, McCouch SR, Abenes ML, Baraoidan MR, Mew TW,Nelson RJ. 1995. Tagging and combining bacterial blight resistance genes in rice usingRAPD and RFLP markers. Mol. Breed. 1:375-387.Yoshimura S, Yoshimura A, Saito A, Kishimoto N, Kawase M, Yano M, Nakagahra M, OgawaT, Iwata N. 1992. RFLP analysis of introgressed chromosomal segments in three nearisogeniclines of rice for bacterial blight resistance genes, Xa-1, Xa-3 and Xa-4. Jpn. J.Genet. 67:29-37.Young ND, Tanksley SD. 1989. Restriction fragment length polymorphism maps and the conceptof graphical genotypes. Theor. Appl. Genet. 77:95-101.Yu ZH, Mackill DJ, Bonman JM, McCouch SR, Guiderdoni E, Notteghem JL, Tanksley SD.1996. Molecular mapping of genes for resistance to rice blast (Pyricularia grisea Sacc.).Theor. Appl. Genet. 93:859-863.Yu ZH, Mackill DJ, Bonman JM, Tanksley SD. 1991. Tagging genes for blast resistance in ricevia linkage to RFLP markers. Theor. Appl. Genet. 81:471-476.Zhang G, Angeles ER, Abenes MLP, Khush GS, Huang N. 1996. RAPD and RFLP mapping ofthe bacterial blight resistance gene xa-13 in rice. Theor. Appl. Genet. 93:65-70.Zhang G, Bharaj TS, Lu Y, Virmani SS, Huang N. 1997. Mapping of the Rf-3 nuclear fertilityrestoringgene for WA cytoplasmic male sterility in rice using RAPD and RFLP markers.Theor. Appl. Genet. 94:27-33.Zhang GY, Guo Y, Chen SL, Chen SY. 1995. RFLP tagging of a salt tolerance gene in rice.Plant Sci. 110:227-234.150 Mackill and Junjian Ni
Zhang JS, Xie C, Li ZY, Chen SY. 1999. Expression of the plasma membrane H + -ATPase genein response to salt stress in a rice salt-tolerant mutant and its original variety. Theor. Appl.Genet. 99:1006-1011.Zhang Q, Shen BZ, Dai XK, Mei MH, Saghai Maroof MA, Li ZB. 1994. Using bulked extremesand recessive class to map genes for photoperiod-sensitive genic male sterility inrice. Proc. Natl. Acad. Sci. USA 91:8675-8679.Zheng K, Subudhi PK, Domingo J, Magpantay G, Huang N. 1995. Rapid DNA isolation formarker assisted selection in rice breeding. Rice Genet. Newsl. 12:255-258.Zheng KL, Zhuang JY, Lu J, Qian HR, Lin HX. 1996. Identification of DNA markers tightlylinked to blast resistance genes in rice. In: Khush GS, editor. Rice genetics III. Proceedingsof the Third International Rice Genetics Symposium, 16-20 Oct 1995, Manila, Philippines.Los Baños (Philippines): International Rice Research Institute. p 565-569.Zhu LH, Chen Y, Xu YB, Xu JC, Cai HM, Ling ZZ. 1993. Construction of a molecular map ofrice and gene mapping using a double haploid population of a cross between Indica andJaponica varieties. Rice Genet. Newsl. 10:132-134.NotesAuthors’ address: USDA-ARS, Department of Agronomy and Range Science, University ofCalifornia, Davis, CA 95616, USA.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.Molecular mapping and marker-assisted selection . . . 151
Page 6:
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
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 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 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
Page 194 and 195: Table 6. Correlations of various pa
Page 196 and 197: The functions of these sequences ne
Page 199 and 200: Structural and functional genomicsT
Page 201 and 202: The International Rice GenomeSequen
Page 203 and 204: the RGP, a PAC (P1-derived artifici
Page 205 and 206: Progress of sequencing in the RGPWe
Page 207 and 208: ice genome sequencing to organize a
Page 209 and 210: Strategies and techniquesfor finish
Page 211 and 212: 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
Page 250 and 251:
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
Page 341 and 342:
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,
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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
Page 386 and 387:
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
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
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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
Page 467 and 468:
ments and the integration of exogen
Page 469 and 470:
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
Page 493:
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
Page 500:
Rice genetics cooperativeA meeting
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