Rice Genetics IV - IRRI books - International Rice Research Institute

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Walker EL, Eggleston WB, Demopulos D, Kermicle J, Dellaporta SL. 1997. Insertions of anovel class of transposable elements with a strong target site preference at the r locus ofmaize. Genetics 146:681-693.Wessler SR, Bureau TE, White SE. 1995. LTR-retrotransposons and MITEs: important playersin the evolution of plant genomes. Curr. Opin. Genet. Dev. 5:814-821.Yoder JI. 1990. Rapid proliferation of the maize transposable element Activator in transgenictomato. Plant Cell 2:723-730.Zhang Q, Arbuckle J, Wessler SR. 2000. Recent, extensive and preferential insertion of membersof the miniature inverted-repeat transposable element family Heartbreaker (Hbr) intogenic regions of maize. Proc. Natl. Acad. Sci. USA 97:1160-1165.NotesAuthors’ addresses: S.R. Wessler, A. Nagel, Department of Botany, University of Georgia,Athens, GA 30602, USA, phone: 706-542-1870, fax: 706-542-1805, E-mail:sue@dogwood.botany.uga.edu; A. Casa, present address: Institute for Genomic Diversityand Department of Plant Breeding, Cornell University, 153 Biotechnology Building, Ithaca,NY 14853, USA.Acknowledgments: We thank Svieta Temnykh and Susan McCouch for rice genomic DNAused for transposon display and Cedric Feschotte for critical reading of the manuscript.MITE research is supported by grants from the National Institutes of Health, Pioneer Hi-Bred Int. (to S.R.W.), and a National Science Foundation Research Training Grant (toA.N).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.116 Wessler et al
Microsatellite markers in rice:abundance, diversity, and applicationsS.R. McCouch, S. Temnykh, A. Lukashova, J. Coburn, G. DeClerck,S. Cartinhour, S. Harrington, M. Thomson, E. Septiningsih, M. Semon,P. Moncada, and Jiming LiA well-distributed set of 500 microsatellite markers has been geneticallymapped onto the rice genome. These markers link the genetic and physicalmaps with the genomic sequence of rice, facilitating studies that seek todetermine the relationship between the structure and function of genes andgenomes. To facilitate the development of new microsatellite markers usingpublicly available DNA sequence information, a simple sequence repeat identificationtool (SSRIT) has been developed for semiautomated identificationof nonredundant simple sequence repeat (SSR) loci and for primer design(available at http://www.gramene.org/microsat/). Using this script, a totalof 57.8 Mb of DNA sequence from rice was searched to determine the frequencyand distribution of different SSRs in the genome. Because the lengthof the SSR unit in any single genome has proven to be a reasonably goodpredictor of overall polymorphism in related genotypes, SSR loci were categorizedinto two groups (class I and class II) based on the length of therepeat motif. Microsatellites with poly(AT)n repeats represented the mostabundant and polymorphic class of SSRs but were frequently associatedwith the Micropon family of miniature inverted repeat transposable elements(MITEs) and were difficult to amplify. Estimates of total microsatellite frequenciesin rice suggested that there were approximately 28,340 Class Iand 70,530 Class II SSRs, or about 100,000 di-, tri-, and tetra-nucleotideSSR motifs in the rice genome. The distribution of SSR sequences showedthat regions of the rice genome that were richer in expressed genes alsotended to be richer in SSR sequences, underscoring their usefulness asgenetic markers. Applications of SSRs in variety protection, diversity analysis,gene and QTL identification, marker-assisted selection, physical mapping,and gene isolation will be discussed.Simple sequence repeats (SSRs), commonly referred to as microsatellites, are tandemlyrepeated mono- to hexa-nucleotide motifs that are ubiquitous in eukaryotic genomesand exhibit highly variable numbers of repeats at a locus. Their abundance andMicrosatellite markers in rice: . . . 117
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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
Page 77 and 78: ABCDO. barthiiO. rufipogonO. longis
Page 79 and 80: Wild(O. rufipogon)Geographical diff
Page 81 and 82: South Asia (particularly on the wes
Page 83 and 84: al 1992, Sun et al 1996a,b,c), thou
Page 85 and 86: wild and cultivated types (Est10, W
Page 87 and 88: Cai HW, Morishima H. 2000a. Diversi
Page 89: Sato YI, Tang SX, Yang LU, Tang LH.
Page 92 and 93: The solid base laid by classical ri
Page 94 and 95: The synthesis shown in Figure 1 is
Page 96 and 97: Arabidopsis, long heralded as a “
Page 98 and 99: Monocots and eudicots: Is there sti
Page 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 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: Le QH, Wright S, Yu Z, Bureau T. 20
Page 131 and 132: make the best SSR markers for rice.
Page 133 and 134: Predicted frequency100,00080,000Cla
Page 135 and 136: Relationship between SSRs and genes
Page 139 and 140: are indicated with RM locus designa
Page 141 and 142: SSRs have been used to define intro
Page 143 and 144: provide a bridge for moving rapidly
Page 145 and 146: Ishii T, McCouch SR. 2000. Microsat
Page 147: NotesAuthors’ addresses: S.R. McC
Page 150 and 151: traits of economic importance (Mack
Page 152 and 153: Table 2. Tagging and mapping of som
Page 154 and 155: even at the juvenile stage. Several
Page 156 and 157: Chen et al (2000) transferred the b
Page 158 and 159: genome sequence of rice, this will
Page 160 and 161: Kurata N, Nagamura Y, Yamamoto K, H
Page 162 and 163: Witcombe JR, Hash CT. 2000. Resista
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
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Simultaneous QTL introgression and
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Doebley J, Stec A, Gustus C. 1995.
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Visscher PM, Haley CS, Thompson R.
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unavailable until recently with the
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Table 1 continued.Trait QTL a Flank
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the remaining parts of the linkage
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Table 3. QTLs detected for yield an
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Table 6. Correlations of various pa
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The functions of these sequences ne
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Structural and functional genomicsT
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The International Rice GenomeSequen
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the RGP, a PAC (P1-derived artifici
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Progress of sequencing in the RGPWe
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ice genome sequencing to organize a
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Strategies and techniquesfor finish
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uses the quality values generated b
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with the advanced techniques requir
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times contain sufficient data to ma
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amplification of regions that previ
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4. Structure problems—subcloning
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estriction maps or optical maps are
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nal assembly may point to areas tha
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McMurray AA, Sulston JE, Quail MA.
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Sequence-tagged connector/DNA finge
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1999). The development of multiple-
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Transposable elements in the rice H
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ers, maps, mapping populations, and
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Miropeats-OSJNBa0065H03 1.2 cMThres
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NotesAuthors’ addresses: R.A. Win
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Sasaki 1997). Such analysis is ofte
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ABNipponbare × KasalathF 2QTL anal
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were classified into two groups bas
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effective at determining the genoty
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addition, some accessions of wild r
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Sasaki T, Burr T. 2000. Internation
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Mutational analysis has long been t
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marked by a deletion/chromosomal re
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analysis suggests that the mutation
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For drought-response screening, our
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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
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Although mutants with discrete gene
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Generation of T-DNA insertionaltagg
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Aprobe AEEprobe BpGA1633RBgus Tn p3
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Number of loci36%224%170%010 20 30F
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Table 2. GUS assay in roots of tran
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1999, Krysan et al 1999, Sato et al
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Transposons and functionalgenomics
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cesses. To study the interactions a
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Constructs were made with the aim o
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RBcis-effect of the adjacent strong
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Ac knockout mutagenesisThe Ac lines
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Table 2 summarizes the transformati
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ReferencesBaldwin D, Crane V, Rice
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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types of users. An annotation datab
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ReferencesAntonio BA, Fang Z, Sanch
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Gene isolation and functionEnhancin
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Enhancing deployment of genes forbl
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mochi and Tsuyuake (Wu et al 1996).
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tive indica rice varieties supports
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transcription factor, resulting in
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facilitate breeding durable resista
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(Inukai et al 1994, Yu et al 1996,
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Rossman AY, Howard RJ, Valent B. 19
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Molecular signaling in diseaseresis
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AOsRac1IED II III IV 214aaOsRac1 KC
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Japonica rice variety Kinmaze, whic
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Table 1. Characteristics of lesion-
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an effective inducer of host resist
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Takahashi A, Kawasaki T, Henmi K, S
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et al 2000). Sequence analysis of t
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612-amino acid protein, including t
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Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
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Isolation of candidate genesfor tol
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Materials and methodsPlant material
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Microarray hybridization and data a
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Table 3. Most abundant transcripts
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Microarray technologyThe rapid accu
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view of procedures, pitfalls, and n
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Log(2) ratio1.51.0OC104E01—WCP1OC
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Table 5. Strongly regulated transcr
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ReferencesAdams MD, Soares MB, Kerl
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Acknowledgments: We thank Chris Bor
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y cells separating during tissue de
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(Erwee and Goodwin 1983). The sympl
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tion between the abundance of CDK t
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in a complex of 105 kDa. These resu
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Drew MC, Jackson MB, Giffard S. 197
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Umeda M, Umeda-Hara C, Yamaguchi M,
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asexual reproduction through apomix
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MPManual pollination by breeders×
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Search for apomixis in riceThere ar
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Issues related to achieving synthet
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come and may use imprinting to achi
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Embryo-inducing geneInactive ablati
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M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
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embryos, several genes characterist
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Our search for a rice homologue of
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sequenced the two rice DMC1 genes a
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Gustine DL, Sherwood RT, Huff DR. 1
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Peel MD, Carman JG, Leblanc O. 1997
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TransformationEngineering for virus
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Engineering for virusresistance in
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proteins, (2) the expression of dys
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Antisense and cosuppression RNA. Ex
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Table 1. Transgenic rice with patho
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the disease symptoms. Efforts from
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an ambisense coding strategy (Fig.
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first produced and shown to have vi
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McLean GD, Evans G. 1997. Some pote
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Waterhouse PM, Upadhyaya NM. 1998.
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duction in response to dehydration
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(KIKEKLPG) in the carboxyl terminus
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These three plasmids were used to t
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We now show the effects of the toba
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Since one major goal of plant scien
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Table 4. Copy number of transgenes
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Chan M-T, Chang H-H, Ho S-L, Tang W
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NotesAuthors’ address: Department
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initially fixed by phosphoenolpyruv
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High-level expression of maize C 4-
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The effect of illumination on PPDK
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ate in 2% O 2 can be limited by Pi
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Transgene integration,organization,
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duced by organogenesis, somatic emb
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ing transgene organization. FISH an
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ments and the integration of exogen
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Level 2: activation of local repair
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strongly suggested that plant facto
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other cases it was not. We observed
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Gorbunova V, Levy AA. 1997. Non-hom
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Gene silencing and itsreactivation
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Carbofuran (trade name, Furadan) is
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Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
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ABCDhptuidAmUbi1kb10.08.05.04.13.0F
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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
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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