Rice Genetics IV - IRRI books - International Rice Research Institute

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hypervariability make them valuable as genetic markers (Weber and May 1989). Inrice, more than 500 microsatellite markers have been developed and used to constructgenetic maps (Wu and Tanksley 1993, Akagi et al 1996, Panaud et al 1995, 1996,Chen et al 1997, Temnykh et al 2000, 2001). These markers provide important codominantlandmarks that are well distributed throughout the rice genome. SSRs havebeen widely used in rice genetics to fingerprint accessions, analyze diversity, identifyintrogressions in interspecific crosses, trace pedigrees, locate genes and QTLs on ricechromosomes, and in marker-assisted selection. In sequencing and genomics applications,SSRs are increasingly useful as sequence tag connectors (STCs) linking thephysical and genetic maps of rice.SSR marker developmentIn the past, the advantages of microsatellite markers were partially offset by the difficultyinherent in marker development, as laborious iterations of genomic DNA libraryscreening with radio-labeled probes were required to isolate SSR-containingsequences. In rice, the growing pool of DNA sequence information being generatedby the <strong>International</strong> <strong>Rice</strong> Genome Sequencing Project (IRGSP) and by independentorganizations (see, for example, www.rice-research.org and www.syngenta.com) providesthe basis for efficient, high-throughput in silico identification of SSR loci. Thepublic availability of genomic sequences has dramatically altered the strategies usedfor marker development and has largely removed the technical and economic limitationsthat previously limited the number of SSR loci that were available for rice.To facilitate the development of new microsatellite markers using publicly availableDNA sequence information, a set of computer programs has been developed forsemiautomated identification of nonredundant SSR loci and for primer design. Thescript consists of two parts and is publicly available at http://ars-genome.cornell.edu/rice/tools.html. The searching script identifies all microsatellites of a user-definedminimum repeat length in a set of downloaded sequences; records the database ID(i.e., GenBank accession number), motif type, number of perfect repeats, and sequencecoordinates for each SSR; does a redundancy search based on flanking sequenceidentity; and reports the results in an output file. Primers are then designedusing the program Primer 0.5 (Daly et al 1991). The search can be used to identifySSRs in different types and lengths of DNA sequence, including relatively short sequences(300–700 bp) derived from the ends of cDNA clones (known as expressedsequence tags, or ESTs), or from the ends of rice genomic DNA cloned into bacterialartificial chromosomes (BACs), or long contigs assembled from fully sequenced BACand P1-derived artificial chromosome (PAC) clones that may be up to 1 Mb in length(Temnykh et al 2001).Based on information about the frequency and average length of specific SSRmotifs in rice, classes of SSRs most likely to provide good genome coverage and highlevels of polymorphism can be selected for primer design and used as DNA markers.Akagi et al (1996) first noted that AT-rich microsatellites tended to show more lengthvariation than tracts consisting of GC-rich motifs and suggested that these would118 McCouch et al
make the best SSR markers for rice. Cho et al (2000) demonstrated that, on average,long SSRs tend to be more polymorphic than shorter ones, no matter what the motifis, and this characteristic was in agreement with studies in human and other species(Weber 1990, Goldstein and Clark 1995).Length classification of SSRs and relationship to polymorphismBecause the length of the SSR repeat unit in any single genome has proven to be areasonably good predictor of overall polymorphism in related genotypes, microsatelliteloci in this study were categorized into two groups based on the length of the repeatmotif. As summarized in Figure 1, class I consists of hypervariable markers, classifiedas perfect SSRs >20 nt in length, and class II consists of potentially variablemarkers, defined as SSRs >12 nt and
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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
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 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: Microsatellite markers in rice:abun
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
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
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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
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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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