Rice Genetics IV - IRRI books - International Rice Research Institute

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202224262830323436384042444648505254565860S1778 = GIR1944L612C319S14085G317R665C955T98R618C113R2151C1338C1211S10086R210R1712R2167High-resolutiongenetic mapGenomic sequenceContig mapQTL peaksCT158CT788CG532CT697CT550CT441SSR1RZ38214.419.725.826.739.144.247.854.3GA594 61.6RG811 63.6QTL mapNILs SSRsCT158CT788CT697CT550CT441GA594Fig. 6. Use of SSRs to link genotype and phenotype via the high-resolution genetic map, genomic sequence, contiged BAC andPAC clones, a QTL map targeting regions of peak LOD score, and the development of near-isogenic lines (NILs) for use inphenotypic evaluation.130 McCouch et al
provide a bridge for moving rapidly and efficiently from phenotype to sequence informationand vice versa, and providing a foundation for understanding the evolutionaryconsequences of sequence variation.The <strong>International</strong> <strong>Rice</strong> Microsatellite Initiative (IRMI) is a consortium of publicand private research groups that are working together to generate a high-resolutionset of microsatellite markers for rice. With the recent release of more than 7,000uncharacterized SSR sequences (http://www.riceresearch.org) and with new genomicsequences emerging all the time from both public and private rice sequencing efforts,opportunities for developing, characterizing, and using SSR markers in high-resolutionstudies in rice have opened up dramatically. IRMI aims to make the primer sequences,PCR conditions, polymorphism information, and map positions of thesemarkers publicly available over the Internet (www.gramene.org). To facilitate the useof SSRs in automated analyses, all primer pairs are being tested using a standard PCRprotocol and panel of rice genotypes. Results of IRMI’s decentralized effort are coordinatedin a central database in which each contributor’s input is recognized.It is of great interest not only to harness SSRs as genetic markers but also tounderstand the role they play in the biology and evolution of organisms and as contributorsto the rapidly evolving repetitive fraction of the rice genome. The power ofSSR markers resides in their abundance, co-dominance, hypervariability, and easeand economy of use in both manual and automated systems. Groups interested in therice genome can use them for evolutionary studies, to examine patterns of variation inspecific regions of the genome, compare recombination frequencies across populations,fingerprint varieties, analyze pedigree relationships, construct high-resolutiongenetic and physical maps, discover and isolate genes and QTLs, screen mutant populations,and in molecular breeding programs. By establishing a core set of publiclyavailable semiautomated SSR markers that can be readily used by independent groupsworldwide, a large amount of data bridging sequence, genotype, and phenotype canbe accumulated and readily integrated into a single database that integrates informationacross studies. Within the next few years, all SSRs in rice will likely be identifiedand their genomic locations known. This will provide the rice community with a richsource of material for addressing a wide array of scientific questions of both basicand applied interest.ReferencesAkagi H, Yokozeki Y, Inagaki A, Fujimura T. 1996. Microsatellite DNA markers for rice chromosomes.Theor. Appl. Genet. 94:61-67.Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD. 1997. Microsatellitesand a single nucleotide polymorphism differentiate apparent amylose classes in an extendedpedigree of US rice germplasm. Theor. Appl. Genet. 94:773-781.Bao, JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH. 2000. QTL mapping forthe paste viscosity characteristics in rice (Oryza sativa L.). Theor. Appl. Genet. 100:280-284.Blair MW, McCouch SR. 1997. Microsatellite and sequenced-tagged site markers diagnosticfor the rice bacterial leaf blight resistance gene xa-5. Theor. Appl. Genet. 95:174-184.Microsatellite markers in rice: . . . 131
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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.
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 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: SSRs have been used to define intro
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
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
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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
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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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