Rice Genetics IV - IRRI books - International Rice Research Institute

More documents

Recommendations

Info

Monocots and eudicots: Is there still colinearity between rice and Arabidopsis?The close alignment of genes between genomes spread over 60 million years of cerealevolution begs the question as to whether synteny remains over the 140–200-million-year monocot-eudicot divide. Significant residual colinearity would mean thatmany cereal genomics approaches could be serviced by the Arabidopsis DNA sequence.This question has been addressed by several studies (Paterson et al 1996, Devoset al 1999, van Dodeweerd et al 1999). The consensus is that, although there is someevidence of residual synteny in some regions of the genome, gene sequences andorders have diverged so much that very little predictive power remains in the comparisons.The recent revelations of extensive local chromosome segment duplicationthat was preceded by a polyploidization event in Arabidopsis (The Arabidopsis GenomeInitiative 2000) would seem to definitely preclude the wide-scale use ofArabidopsis gene orders to approach cereal genetics. Nevertheless, the question shouldremain open a little longer as enough contiguous genomic rice sequence becomesavailable to compare directly with that of the model eudicot.ReferencesAhn SN, Tanksley SD. 1993. Comparative linkage maps of the rice and maize genomes. Proc.Natl. Acad. Sci. USA 90:7980-7984.Bennetzen JL. 2000. Comparative sequence analysis of plant nuclear genomes: microcolinearityand its many exceptions. Plant Cell 12:1021-1029.Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD. 1989. RFLP-basedgenetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78:495-504.Chen M, San Miguel P, Bennetzen JL. 1998. Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435-443.Devos KM, Atkinson MD, Chinoy CN, Francis HA, Harcourt RL, Koebner RMD, Liu CJ,Masojc P, Xie DX, Gale MD. 1993. Chromosomal rearrangements in the rye genome relativeto that of wheat. Theor. Appl. Genet. 85:673-680.Devos KM, Beales J, Nagamura Y, Sasaki T. 1999. Arabidopsis-rice: Will colinearity allowgene prediction across the eudicot-monocot divide? Genome Res. 9:825-829.Devos KM, Pittaway TS, Reynolds A, Gale MD. 2000. Comparative mapping reveals a complexrelationship between the pearl millet genome and those of foxtail millet and rice.Theor. Appl. Genet. 100:190-198.Devos KM, Wang ZM, Beales J, Sasaki T, Gale MD. 1998. Comparative genetic maps offoxtail millet (Setaria italica) and rice (Oryza sativa). Theor. Appl. Genet. 96:63-68.Dufour M, Deu M, Grivet L, D’Hont A, Paulet F, Glaszmann JC, Hamon P. 1997. Constructionof a composite sorghum genome map and comparison with sugarcane, a related complexpolyploid. Theor. Appl. Genet. 94:409-418.Feuillet C, Keller B. 1999. High gene density is conserved at syntenic loci of small and largegrass genomes. Proc. Natl. Acad. Sci. USA 96:8265-8270.Foote T, Roberts M, Kurata N, Sasaki T, Moore G. 1997. Detailed comparative mapping ofcereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics 147:801-807.86 Gale et al
Gale MD, Devos KM. 1998. Plant comparative genetics after 10 years. Science 282:656-659.Gale M, Moore G, Devos K. 2001. Rice—the pivotal genome in cereal comparative genetics.Chichester (England): John Wiley & Sons. p 46-52. Copyright© Novartis Foundation 2001.Glaszmann JC, Dufour P, Grivet L, D’Hont A, Deu M, Paulet F, Hamon P. 1997. Comparativegenome analysis between several tropical grasses. Euphytica 96:13-21.Kennard W, Phillips RL, Porter R, Grombacher A. 1999. A comparative map of wild rice (Zizaniapalustris L. 2n=2x=30). Theor. Appl. Genet. 99:793-799.Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale MD. 1994. Conservationof genome structure between rice and wheat. Bio/Technology 12:276-278.Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos KM, Graner A, Schulze-Lefert P.1998. Rapid reorganisation of resistance gene homologues in cereal genomes. Proc. Natl.Acad. Sci. USA 95:370-375.Moore G, Devos KM, Wang ZM, Gale MD. 1995. Cereal genome evolution: Grasses, line upand form a circle. Curr. Biol. 5:737-739.Nagamura Y, Inoue T, Antonio BA, Shimano T, Kajiya H, Shomura A, Lin SY, Kuboki Y,Harushima Y, Kurata N, Minobe Y, Yano M, Sasaki T. 1995. Conservation of duplicatedsegments between rice chromosomes 11 and 12. Breed. Sci. 45:373-376.Paterson AH, Lan T-H, Reischmann KP, Chang C, Lin Y-R, Liu S-C, Burow MD, Kowalski SP,Katsar CS, Del Monte TA, Feldmann KA, Schertz KF, Wendel JF. 1996. Toward a unifiedgenetic map of higher plants transcending the monocot-dicot divergence. Nat. Genet. 14:380-382.Riley R, Chapman V. 1964. Cytological determination of the homoeology of chromosomes ofTriticum aestivum. Nature 203:156-158.Roberts MA, Reader SM, Dalgliesh C, Miller TE, Foote TN, Fish LJ, Snape JW, Moore G.1999. Induction and characterization of Ph1 wheat mutants. Genetics 153:1909-1918.Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A. 2000. The complete sequence of 340kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maizechromosome 4. Plant Cell 12:381-391.The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the floweringplant Arabidopsis thaliana. Nature 408:796-815.Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z. 1999.Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc.Natl. Acad. Sci. USA 96:7409-7414.Toenniessen GH. 1998. Rice biotechnology capacity building in Asia. In: Ives CL, BedfordBM, editors. Agricultural biotechnology in international development. Wallingford (UK):CAB International. p 201-212.Van Deynze AE, Nelson JC, O’Donoughue LS, Ahn S, Siripoonwiwat W, Harrington SE,Yglesias ES, Braga DP, McCouch SR, Sorrells ME. 1995a. Comparative mapping in grasses:oat relationships. Mol. Gen. Genet. 249:349-356.Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, SorrellsME. 1995b. Comparative mapping in grasses: wheat relationships. Mol. Gen. Genet.248:744-754.van Dodeweerd AM, Hall AM, Bent EG, Johnson SJ, Bevan MW, Bancroft I. 1999. Identificationand analysis of homoeologous segments of the genomes of rice and Arabidopsis. Genome42:887-892.Wang ZM, Thierry A, Panaud O, Gale MD, Sarr A, Devos KM. 2001. Trait mapping in foxtailmillet. Theor. Appl. Genet. (In press.)Rice: a central genome for the genetics of all cereals 87
Page 6:
Retrotransposons of rice as a tool
Page 11 and 12:
First, the Rice Genetics Cooperativ
Page 13 and 14:
OverviewRice genetics from Mendel t
Page 15 and 16:
Rice genetics from Mendelto functio
Page 17 and 18:
nese cultivar Nipponbare. The chrom
Page 19:
Gene symbolization in riceIn the ab
Page 26 and 27:
Table 2. Some examples of mapping g
Page 28 and 29:
and YAC libraries, respectively. Th
Page 30 and 31:
gene from wild species is the intro
Page 32 and 33:
ReferencesAbbasi FM, Brar DS, Carpe
Page 35 and 36:
Nagao S. 1951. Genic analysis and l
Page 37:
Yoshimura S, Yamanouchi U, Katayose
Page 40 and 41:
important traits for which segregat
Page 42 and 43:
trolled by a single recessive gene,
Page 44 and 45:
AromaAromatic rice varieties often
Page 46 and 47:
Submergence tolerance is an interes
Page 48 and 49: Kinoshita T, Maekawa M. 1986. Genet
Page 50 and 51: NotesAuthors’ addresses: J.N. Rut
Page 52 and 53: The Rockefeller Foundation has a lo
Page 54 and 55: Evolution and implementation of the
Page 56 and 57: Scientific progress and outputsIn t
Page 58 and 59: Another salient example is that of
Page 60 and 61: BOX NO. 1recent international works
Page 62 and 63: For the purposes of this discussion
Page 64 and 65: Because of the great diversity (sci
Page 66 and 67: eeders where final products to enha
Page 68 and 69: Chen S, Lin XH, Xu CG, Zhang Q. 200
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 73 and 74: Molecular markers,genetic diversity
Page 75 and 76: 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 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 114 and 115: testing Ka/Ks between the homeologo
Page 116 and 117: Roschevicz RI. 1931. A contribution
Page 119 and 120: Miniature inverted repeattransposab
Page 121 and 122: eau and Wessler 1992, 1994), rice (
Page 123 and 124: MITEs as a source of allelic divers
Page 125 and 126: ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
Page 127 and 128: Le QH, Wright S, Yu Z, Bureau T. 20
Page 129 and 130: Microsatellite markers in rice:abun
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
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 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
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 292 and 293:
These include T-DNA (Azpiroz-Leehan
Page 294 and 295:
polyproteins and two identical 138-
Page 296 and 297:
mutant. The mutation in the ent-kau
Page 298 and 299:
primers (G1, G2) and two Tos17-spec
Page 300 and 301:
of insertion mutants by sequencing
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-
Page 343 and 344:
an effective inducer of host resist
Page 345:
Takahashi A, Kawasaki T, Henmi K, S
Page 348 and 349:
et al 2000). Sequence analysis of t
Page 350 and 351:
612-amino acid protein, including t
Page 352 and 353:
Genetic dissection of the Xa21-medi
Page 354 and 355:
ReferencesAnderson PA, Lawrence GJ,
Page 357 and 358:
Isolation of candidate genesfor tol
Page 359 and 360:
Materials and methodsPlant material
Page 361 and 362:
Microarray hybridization and data a
Page 363 and 364:
Table 3. Most abundant transcripts
Page 365 and 366:
Microarray technologyThe rapid accu
Page 367 and 368:
view of procedures, pitfalls, and n
Page 369 and 370:
Log(2) ratio1.51.0OC104E01—WCP1OC
Page 371 and 372:
Table 5. Strongly regulated transcr
Page 373 and 374:
ReferencesAdams MD, Soares MB, Kerl
Page 375:
Acknowledgments: We thank Chris Bor
Page 378 and 379:
y cells separating during tissue de
Page 380 and 381:
(Erwee and Goodwin 1983). The sympl
Page 382 and 383:
tion between the abundance of CDK t
Page 384 and 385:
in a complex of 105 kDa. These resu
Page 386 and 387:
Drew MC, Jackson MB, Giffard S. 197
Page 388 and 389:
Umeda M, Umeda-Hara C, Yamaguchi M,
Page 390 and 391:
asexual reproduction through apomix
Page 392 and 393:
MPManual pollination by breeders×
Page 394 and 395:
Search for apomixis in riceThere ar
Page 396 and 397:
Issues related to achieving synthet
Page 398 and 399:
come and may use imprinting to achi
Page 400 and 401:
Embryo-inducing geneInactive ablati
Page 402 and 403:
M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
Page 404 and 405:
embryos, several genes characterist
Page 406 and 407:
Our search for a rice homologue of
Page 408 and 409:
sequenced the two rice DMC1 genes a
Page 410 and 411:
Gustine DL, Sherwood RT, Huff DR. 1
Page 412 and 413:
Peel MD, Carman JG, Leblanc O. 1997
Page 415 and 416:
TransformationEngineering for virus
Page 417 and 418:
Engineering for virusresistance in
Page 419 and 420:
proteins, (2) the expression of dys
Page 421 and 422:
Antisense and cosuppression RNA. Ex
Page 423 and 424:
Table 1. Transgenic rice with patho
Page 425 and 426:
the disease symptoms. Efforts from
Page 427 and 428:
an ambisense coding strategy (Fig.
Page 429 and 430:
first produced and shown to have vi
Page 431 and 432:
McLean GD, Evans G. 1997. Some pote
Page 433:
Waterhouse PM, Upadhyaya NM. 1998.
Page 436 and 437:
duction in response to dehydration
Page 438 and 439:
(KIKEKLPG) in the carboxyl terminus
Page 440 and 441:
These three plasmids were used to t
Page 442 and 443:
We now show the effects of the toba
Page 444 and 445:
Since one major goal of plant scien
Page 446 and 447:
Table 4. Copy number of transgenes
Page 448 and 449:
Chan M-T, Chang H-H, Ho S-L, Tang W
Page 450 and 451:
NotesAuthors’ address: Department
Page 452 and 453:
initially fixed by phosphoenolpyruv
Page 454 and 455:
High-level expression of maize C 4-
Page 456 and 457:
The effect of illumination on PPDK
Page 458 and 459:
ate in 2% O 2 can be limited by Pi
Page 461 and 462:
Transgene integration,organization,
Page 463 and 464:
duced by organogenesis, somatic emb
Page 465 and 466:
ing transgene organization. FISH an
Page 467 and 468:
ments and the integration of exogen
Page 469 and 470:
Level 2: activation of local repair
Page 471 and 472:
strongly suggested that plant facto
Page 473 and 474:
other cases it was not. We observed
Page 475 and 476:
Gorbunova V, Levy AA. 1997. Non-hom
Page 477 and 478:
Gene silencing and itsreactivation
Page 479 and 480:
Carbofuran (trade name, Furadan) is
Page 481 and 482:
Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
Page 483 and 484:
ABCDhptuidAmUbi1kb10.08.05.04.13.0F
Page 485 and 486:
Fig. 4. X-gluc staining of germinat
Page 487 and 488:
eflect different causes for silenci
Page 489 and 490:
Table 4. Suppressors of silencing f
Page 491 and 492:
Garrick D, Fiering S, Martin DI, Wh
Page 493:
Xu Y, Buchholz WG, DeRose RT, Hall
Page 496 and 497:
Rice molecular breeding workshopThi
Page 498 and 499:
the working group can develop a net
Page 500:
Rice genetics cooperativeA meeting
show all

Rice Genetics IV - IRRI books - International Rice Research Institute

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?