Rice Genetics IV - IRRI books - International Rice Research Institute

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These include T-DNA (Azpiroz-Leehan and Feldmann 1997, Krysan et al 1999) andmaize transposable elements Ac/Ds (Parinov et al 1999) and En/Spm (Speulman et al1999, Tissier et al 1999). Mutant populations induced by these mutagens are beingused for forward and reverse genetics. Since these lines induced by the exogenousinsertional mutagens are transgenic plants, it is necessary to grow them under theregulation of recombinant DNA experiments. Because rice plants are relatively large,it is not easy to handle thousands of transgenic rice plants in a greenhouse. Therefore,it is desirable to use endogenous insertional mutagens. Ac/Ds-, En/Spm-, and Mu-likeelements (Hirochika and Fukuchi 1992, Motohashi et al 1996, R. Ishikawa and M.Freeling, personal communication) have been identified by molecular analysis in rice.Most of them, however, appear to be inactive due to accumulation of mutations. Consistentwith these results, none of the spontaneous waxy mutations were induced bytransposable elements (Okagaki and Wessler 1988). This finding does not necessarilymean that active transposable elements do not exist in the rice genome. We haveshown that the retrotransposon of rice, named Tos17, is highly active only duringtissue culture and that the activation of Tos17 is responsible for tissue-culture-inducedmutations (Hirochika et al 1996). Unique features of Tos17 suggest that it canbe used for forward and reverse genetic studies (Hirochika 1997, 1999). Here, wereport features of Tos17 as an insertional mutagen and the current status of forwardand reverse genetic studies of rice using Tos17.Isolation of active retrotransposons of riceAlthough more than 40 families of long terminal repeats (LTR)-retrotransposons havebeen found in rice (Tos1-Tos32: Hirochika et al 1992, 1996, unpublished; RIRE1-RIRE8: Noma et al 1997, Ohtsubo et al, 1999, H. Ohtsubo et al, personal communication;Rrt1-Rrt23: Wang et al 1997), only five of them were shown to be active. Tos10,Tos17, Tos19, Tos25, and Tos27, which were isolated by using polymerase chain reaction(PCR) or reverse transcript (RT)-PCR, are silent during normal growth conditionsand become active only during tissue culture (Hirochika et al 1996, Hirochika etal, unpublished). The PCR method is based on the conservation of certain amino acidsequences in the reverse transcriptase domain among Ty1-copia group retrotransposons.Four out of the five active retrotransposons were isolated by using RT-PCR, indicatingthat this method is very effective for isolating active retrotransposons. This methodis based on the fact that most inactive plant retrotransposons are not transcribed andactive retrotransposons are transcribed only under certain stress conditions (Hirochika1993). Among the five active retrotransposons, Tos17 has been shown to be the mostactive (Fig. 1, Hirochika et al 1996, Hirochika, unpublished). As the transcript ofTos17 was only detected under tissue culture conditions, the transposition of Tos17must be regulated mainly at the transcriptional level as in the case of tobaccoretrotransposons such as Tnt1 (Pouteau et al 1991, Grandbastien 1998) and Tto1(Hirochika 1993, Takeda et al 1998). To compare the activities of Tos17 and Tos19under the same culture conditions, the DNA gel blot used in Figure 1 was rehybridizedwith a Tos19 probe. An increase in copy number ranging from one to three was foundonly in those plants regenerated from 16-mo-old culture (data not shown), indicating280 Hirochika et al
that Tos17 is the major insertional mutagen among the rice retrotransposons examined.As shown in Figure 2, Tos17 is 4,114 bp long (Okamoto and Hirochika, unpublished)and carries one open reading frame (ORF) corresponding to Gag and PolkbControl3-mo-oldRegenerated plants9-mo-old16-mo-old23.1—9.4—6.6—4.4—2.3—2.0—Fig. 1. Activation of Tos17 by tissue culture. DNAs were prepared from leaves of normallypropagated rice plants (control) and plants regenerated from 3-, 9-, and 16-mo-oldcultures and analyzed by DNA blot hybridization with a Tos17-specific probe after digestionwith XbaI. (This figure is adapted from Hirochika et al 1996.)5’-LTR(138 bp)gagpol3’-LTR(138 bp)(integrase, reverse transcriptase, RNaseH)1RNA4,114120ORF625 3,960Fig. 2. Structure deduced from the complete nucleotide sequence and transcription ofTos17. Long terminal repeats (LTRs) are boxed. The thick arrow indicates the transcript ofTos17 and the open arrow indicates the longest open reading frame (ORF) starting withthe ATG. The pol gene encodes integrase, reverse transcriptase, and RNaseH.Retrotransposons of rice as a tool . . . 281
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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
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Table 5. The percentage of three ty
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Table 7. Some environment-specific
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ferently to the environments. Simil
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(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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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
Page 273 and 274: 1999, Krysan et al 1999, Sato et al
Page 275 and 276: Transposons and functionalgenomics
Page 277 and 278: cesses. To study the interactions a
Page 279 and 280: Constructs were made with the aim o
Page 281 and 282: RBcis-effect of the adjacent strong
Page 283 and 284: Ac knockout mutagenesisThe Ac lines
Page 285 and 286: Table 2 summarizes the transformati
Page 287 and 288: ReferencesBaldwin D, Crane V, Rice
Page 289: NotesAuthors’ addresses: R. Greco
Page 294 and 295: polyproteins and two identical 138-
Page 296 and 297: mutant. The mutation in the ent-kau
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Page 302 and 303: Grandbastien M-A, Spielman A, Caboc
Page 304 and 305: NotesAuthors’ addresses: H. Hiroc
Page 306 and 307: human endeavor, greatly contributed
Page 308 and 309: Equally important as the genomic in
Page 310 and 311: Oryzabase is one of the most recent
Page 312 and 313: Database structureA characteristic
Page 314 and 315: types of users. An annotation datab
Page 316 and 317: ReferencesAntonio BA, Fang Z, Sanch
Page 319 and 320: Gene isolation and functionEnhancin
Page 321 and 322: Enhancing deployment of genes forbl
Page 323 and 324: mochi and Tsuyuake (Wu et al 1996).
Page 325 and 326: tive indica rice varieties supports
Page 327 and 328: transcription factor, resulting in
Page 329 and 330: facilitate breeding durable resista
Page 331 and 332: (Inukai et al 1994, Yu et al 1996,
Page 333 and 334: Rossman AY, Howard RJ, Valent B. 19
Page 335 and 336: Molecular signaling in diseaseresis
Page 337 and 338: AOsRac1IED II III IV 214aaOsRac1 KC
Page 339 and 340: Japonica rice variety Kinmaze, whic
Page 341 and 342: 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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