Rice Genetics IV - IRRI books - International Rice Research Institute

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Saji S, Umehara Y, Antonio BA, Yamane H, Tanoue H, Baba T, Aoki H, Ishige N, Wu J, KoikeK, Matsumoto T, Sasaki T. 2001. A physical map with yeast artificial chromosome (YAC)clones covering 63 percent of the 12 rice chromosomes. Genome 44:32-37.Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K, Sasaki T. 2000. INE: a ricegenome database with an integrated map view. Nucleic Acids Res. 28:97-102.San Miguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology ofintergene retrotransposons of maize. Nat. Genet. 20:43-45.Sasaki T, Burr B. 2000. International Rice Genome Sequencing Project: the effort to completelysequence the rice genome. Curr. Opin. Plant Biol. 3:138-141.Wu J, Shimokawa T, Maehara T, Yazaki J, Harada C, Yamamoto S, Takazaki Y, Fujii F, Ono N,Koike K, Yamamoto K, Matsumoto T, Sasaki T. 1999. Current progress in rice EST mapping.Abstract of Plant & Animal Genome VII. p 163 (available at http://www.intl-pag.org/pag/7/abstracts/pag7264.html).Yamamoto K, Sasaki T. 1997. Large-scale EST sequencing in rice. Plant Mol. Biol. 35:135-144.NotesAuthors’ address: Rice Genome Research Program (RGP), NIAR/STAFF, 1-2, Kannondai2-chome, Tsukuba, Ibaraki 305-8602, Japan, E-mail: tsasaki@abr.affrc.go.jp.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.196 Sasaki et al
Strategies and techniquesfor finishing genomic sequenceM. de la Bastide, D. Johnson, V. Balija, and W.R. McCombieFinishing genomic sequence is the process of assembling and refining rawsequence data to produce a complete and accurate final sequence. The goalsof finishing are to achieve contiguity, delineate insert-vector junctions, andresolve sequence discrepancies and ambiguities such that the error rate ofthe sequence is less than one in 10,000 bases. Such a level of accuracy isoften difficult to establish due to a repetitive sequence or other secondarystructures that require the use of more complicated finishing techniques.Because of such complexities, the finishing process is the bottleneck in thesequencing queue, and as such it is extremely beneficial to make the draftdata publicly available before the sequence is completed. Much of the valuableinformation contained in the sequence can be determined from data atthis earlier stage.Finishing genomic sequence is the process of assembling and refining raw sequencedata to produce a complete and accurate final sequence. Finishing is a combination ofautomated and manual editing with directed sequencing, followed by assembly verification.The goals of sequencing are to achieve contiguity, delineate insert-vectorjunctions, and resolve sequence discrepancies and ambiguities such that the error rateof the sequence is less than one in 10,000 bases. Such a level of accuracy is oftendifficult to establish due to repetitive sequences or other secondary structures. Becauseof such complexities, the finishing process is the bottleneck in the sequencingqueue, and as such it is extremely beneficial to make the draft data publicly availablebefore the sequence is completed. Much of the valuable information contained in thesequence can be determined from data at this earlier stage. However, finishing to ahigh accuracy is an extremely valuable endeavor. Current assembly algorithms (suchas PHRAP, [Green 1996]) alone are not always sufficient to correctly assemble thesequence for gene prediction analysis, and the gene/pseudo-gene difference can be assimple as a single base change. Finished sequence provides the most complete informationfor scientific study.Strategies and techniques for finishing genomic sequence 197
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Retrotransposons of rice as a tool
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First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
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Rice genetics from Mendelto functio
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nese cultivar Nipponbare. The chrom
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Gene symbolization in riceIn the ab
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Table 2. Some examples of mapping g
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and YAC libraries, respectively. Th
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gene from wild species is the intro
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ReferencesAbbasi FM, Brar DS, Carpe
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Nagao S. 1951. Genic analysis and l
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Yoshimura S, Yamanouchi U, Katayose
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important traits for which segregat
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trolled by a single recessive gene,
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AromaAromatic rice varieties often
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Submergence tolerance is an interes
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Kinoshita T, Maekawa M. 1986. Genet
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NotesAuthors’ addresses: J.N. Rut
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The Rockefeller Foundation has a lo
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Evolution and implementation of the
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Scientific progress and outputsIn t
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Another salient example is that of
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BOX NO. 1recent international works
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For the purposes of this discussion
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Because of the great diversity (sci
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eeders where final products to enha
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Chen S, Lin XH, Xu CG, Zhang Q. 200
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Toenniessen GH. 1998. Rice biotechn
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Molecular markers,genetic diversity
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Evolution and domestication of rice
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ABCDO. barthiiO. rufipogonO. longis
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Wild(O. rufipogon)Geographical diff
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South Asia (particularly on the wes
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al 1992, Sun et al 1996a,b,c), thou
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wild and cultivated types (Est10, W
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Cai HW, Morishima H. 2000a. Diversi
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Sato YI, Tang SX, Yang LU, Tang LH.
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The solid base laid by classical ri
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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
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arthii and O. longistaminata, and t
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testing Ka/Ks between the homeologo
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Roschevicz RI. 1931. A contribution
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Miniature inverted repeattransposab
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eau and Wessler 1992, 1994), rice (
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MITEs as a source of allelic divers
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ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
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Le QH, Wright S, Yu Z, Bureau T. 20
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Microsatellite markers in rice:abun
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make the best SSR markers for rice.
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Predicted frequency100,00080,000Cla
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Relationship between SSRs and genes
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are indicated with RM locus designa
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SSRs have been used to define intro
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provide a bridge for moving rapidly
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Ishii T, McCouch SR. 2000. Microsat
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NotesAuthors’ addresses: S.R. McC
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traits of economic importance (Mack
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Table 2. Tagging and mapping of som
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even at the juvenile stage. Several
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Chen et al (2000) transferred the b
Page 158 and 159: genome sequence of rice, this will
Page 160 and 161: Kurata N, Nagamura Y, Yamamoto K, H
Page 162 and 163: Witcombe JR, Hash CT. 2000. Resista
Page 165 and 166: QTL mapping in rice:a few critical
Page 167 and 168: M-QTLsM-QTLs are defined as single
Page 169 and 170: (genetic/statistical models and cor
Page 171 and 172: Table 5. The percentage of three ty
Page 173 and 174: Table 7. Some environment-specific
Page 175 and 176: ferently to the environments. Simil
Page 177 and 178: (case 3), one may infer that this g
Page 179 and 180: Simultaneous QTL introgression and
Page 181 and 182: Doebley J, Stec A, Gustus C. 1995.
Page 183: Visscher PM, Haley CS, Thompson R.
Page 186 and 187: unavailable until recently with the
Page 188 and 189: Table 1 continued.Trait QTL a Flank
Page 190 and 191: the remaining parts of the linkage
Page 192 and 193: Table 3. QTLs detected for yield an
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: ice genome sequencing to organize a
Page 211 and 212: uses the quality values generated b
Page 213 and 214: with the advanced techniques requir
Page 215 and 216: times contain sufficient data to ma
Page 217 and 218: amplification of regions that previ
Page 219 and 220: 4. Structure problems—subcloning
Page 221 and 222: estriction maps or optical maps are
Page 223 and 224: nal assembly may point to areas tha
Page 225 and 226: McMurray AA, Sulston JE, Quail MA.
Page 227 and 228: Sequence-tagged connector/DNA finge
Page 229 and 230: 1999). The development of multiple-
Page 231 and 232: Transposable elements in the rice H
Page 233 and 234: ers, maps, mapping populations, and
Page 235 and 236: Miropeats-OSJNBa0065H03 1.2 cMThres
Page 237: NotesAuthors’ addresses: R.A. Win
Page 240 and 241: Sasaki 1997). Such analysis is ofte
Page 242 and 243: ABNipponbare × KasalathF 2QTL anal
Page 244 and 245: were classified into two groups bas
Page 246 and 247: effective at determining the genoty
Page 248 and 249: addition, some accessions of wild r
Page 250 and 251: Sasaki T, Burr T. 2000. Internation
Page 252 and 253: Mutational analysis has long been t
Page 254 and 255: marked by a deletion/chromosomal re
Page 256 and 257: 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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