Rice Genetics IV - IRRI books - International Rice Research Institute

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Direct repeats Inverted repeats Tandem repeatsUniquesequenceUniquesequenceIndependentreadsIncorrectsequencealignmentsA B CFig. 7. (A) Direct repeats are regions of highly identical sequence that lie in the same orientation. Direct repeats are often mistakenly alignedon top of each other, thereby eliminating the unique sequence that lies between the repeat copies. (B) Inverted repeats are regions of highlyidentical sequence that lie in opposite orientations. Inverted repeats often cause physical gaps in the sequence. Secondary bonding betweenthe repeat units results in hairpin loops, which may be both unstable to clone and notoriously difficult to sequence through. (C) Tandemrepeats are regions of highly similar sequence with little or no unique sequence separating the repeat copies. Tandem repeats are oftenincorrectly aligned on top of each other and are difficult to sort. Most polymerases are unable to sequence through multiple copies withoutslipping.210 de la Bastide et al
nal assembly may point to areas that were incorrectly sorted by the finisher. One mustalways remember not to rely entirely on assembly algorithms, however, as they arenot always adept at sorting high-identity repeat sequences. Combined PHRAP qualityvalues can be generated for each base in the assembly based on the quality, strand,and chemistry of the underlying primary data. PHRAP scores of 40 or better indicatean extremely accurate sequence. Overlapping data from clones that share a commonportion of sequence can be independently finished, and the resulting data can be comparedfor differences and discrepancies. Analysis of the assembly using alternate navigationsoftware (such as Gap4 from the Staden package [Staden et al 1998]) andindependent resequencing of questionable areas within the assembly can also be informative.The sequencing pipeline, finishing time, and data releaseIn most if not all large-scale sequencing operations, an assembly line is constructed.In these labs, clones are processed one group after another from beginning until end.The first step is the making of subclone libraries. This typically takes 1 to 2 weeks perclone. Following subclone library construction is a phase of production sequencing.As an example, in our lab, the production phase typically takes 1 to 2 weeks as well.The next phase is the finishing phase, which involves assembly, resolution of problems,filling of gaps, and verification of the assembled sequence. On an uncomplicatedclone, this might take about 3–5 weeks. Some complicated clones might takemonths or longer to complete. Some of the clones we sequenced from the centromereof Arabidopsis chromosome <strong>IV</strong> took more than 1 year to finish (Mayer et al 1999).Following finishing and validation of the clones, the sequence is analyzed.Several factors concerning this process need to be emphasized. First, this is anextremely parallel process, that is, many clones, 10 or more, may be processed atabout the same time. The clones are not done sequentially. Second, most of the dataare available after the production-sequencing phase. The gaps and ambiguities remainingprior to finishing often account for only a small percentage of the total sequence.Although the data are definitely more difficult to use prior to finishing, theyare mostly complete, and hence very valuable. Last, as a result of the process at mostlarge sequencing centers, a very large amount of partially finished sequence is availableat any given time. In fact, it would not be surprising if the amount of unfinishedsequence exceeds the amount of finished sequence available for much of the life of aproject, even if the sequence is being finished as rapidly as possible. This is the resultof the parallel nature of the process, the bottleneck of finishing, and the typical gradualincrease in sequencing capacity. This phenomenon has been known since large-scalesequencing began in the early 1990s.Aware of this phenomenon, virtually all groups doing large-scale genome sequencingsince 1995 have agreed to a policy of immediate release of assembled contiguousfragments of a sequence of more than 2 kilobases. This is the currently acceptedinternational standard for data release referred to as the Bermuda Standards (Bentley1996, Guyer 1998, HUGO Web site at http://www.gene.ucl.ac.uk/hugo/publicationsreports.html;Wellcome Trust Web site at http://www.wellcome.ac.uk/en/1/Strategies and techniques for finishing genomic sequence 211
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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
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genome sequence of rice, this will
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Kurata N, Nagamura Y, Yamamoto K, H
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Witcombe JR, Hash CT. 2000. Resista
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QTL mapping in rice:a few critical
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M-QTLsM-QTLs are defined as single
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(genetic/statistical models and cor
Page 171 and 172: Table 5. The percentage of three ty
Page 173 and 174: Table 7. Some environment-specific
Page 175 and 176: ferently to the environments. Simil
Page 177 and 178: (case 3), one may infer that this g
Page 179 and 180: Simultaneous QTL introgression and
Page 181 and 182: Doebley J, Stec A, Gustus C. 1995.
Page 183: Visscher PM, Haley CS, Thompson R.
Page 186 and 187: unavailable until recently with the
Page 188 and 189: Table 1 continued.Trait QTL a Flank
Page 190 and 191: the remaining parts of the linkage
Page 192 and 193: Table 3. QTLs detected for yield an
Page 194 and 195: Table 6. Correlations of various pa
Page 196 and 197: The functions of these sequences ne
Page 199 and 200: Structural and functional genomicsT
Page 201 and 202: The International Rice GenomeSequen
Page 203 and 204: the RGP, a PAC (P1-derived artifici
Page 205 and 206: Progress of sequencing in the RGPWe
Page 207 and 208: ice genome sequencing to organize a
Page 209 and 210: Strategies and techniquesfor finish
Page 211 and 212: uses the quality values generated b
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: estriction maps or optical maps are
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
Page 258 and 259: For drought-response screening, our
Page 260 and 261: Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
Page 262 and 263: Although mutants with discrete gene
Page 265 and 266: Generation of T-DNA insertionaltagg
Page 267 and 268: Aprobe AEEprobe BpGA1633RBgus Tn p3
Page 269 and 270: Number of loci36%224%170%010 20 30F
Page 271 and 272: 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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