Rice Genetics IV - IRRI books - International Rice Research Institute

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Gustine DL, Sherwood RT, Huff DR. 1997. Apospory-linked molecular markers in buffelgrass.Crop Sci. 37:947-951.Haig D, Westoby M. 1991. Genomic imprinting in endosperm: its effect on seed developmentin crosses between species, and between different ploidies of the same species, and itsimplications for the evolution of apomixis. Philos. Trans. R. Soc. B 333:1-13.Han X, Teng S, Zhang XQ, Yan QS. 1999. Molecular identification of plants regenerated fromsomatic hybridization between rice and apomictic Panicum. Chin. Rice Res. Newsl. 7:3-4.Howden R, Park SK, Moore JM, Orme J, Grossniklaus U, Twell D. 1998. Selection of T-DNAtaggedmale and female gametophytic mutants by segregation distortion in Arabidopsis.Genetics 149:621-631.Huang QC, Chen QF. 1999. Basic tactics of selecting and breeding apomictic germplasm inrice. J. Fujian Agric. Univ. 28:129-134.Iwamasa M, Ueno I, Nishiura M. 1967. Inheritance of nucellar embryony in citrus. Bull. Hortic.Res. Stn. Jpn. Ser. B 7:1-8.Jefferson RA. 1994. Apomixis: a social revolution? Biotechnol. Dev. Monit. 19:14-16.Khush GS, Brar DS, Bennett J, Virmani SS. 1994. Apomixis for rice improvement. In: KhushGS, editor. Apomixis: exploiting hybrid vigor in rice. Manila (Philippines): InternationalRice Research Institute. p 1-21.Khush GS, Aquino RC, Virmani SS, Bharaj TS. 1998. Using tropical japonica germplasm toenhance heterosis in rice. In: Virmani SS, Siddiq EA, Muralidharan K, editors. Advancesin hybrid rice technology. Manila (Philippines): International Rice Research Institute.p 59-66.Kikuchi K, Chung CS, Yoshida KT. 1998. Isolation and analysis of new molecular markers forearly embryogenesis in rice (Oryza sativa L.). Plant Biotechnol. 15:77-81.Kindiger B, Bai D, Sokolov V. 1996. Assignment of a gene(s) conferring apomixis in Tripsacumto a chromosome arm: cytological and molecular evidence. Genome 39:1133-1141.Kirik V, Kolle K, Misera S, Baumlein H. 1998. Two novel MYB homologues with changedexpression in late embryogenesis-defective Arabidopsis mutants. Plant Mol. Biol. 37:819-827.Klimyuk VI, Jones JDG. 1997. AtDMC1, the Arabidopsis homologue of the yeast DMC1 gene:characterization, transposon-induced allelic variation and meiosis-associated expression.Plant J. 11:1-14.Koltunow AM. 1993. Apomixis: embryo sac and embryos formed without meiosis or fertilizationin ovules. Plant Cell 5:1425-1437.Koltunow AM, Bicknell RA, Chaudhury AM. 1995. Apomixis: molecular strategies for thegeneration of genetically identical seeds without fertilization. Plant Physiol. 108:1345-1352.Koltunow AM, Hidaka T, Robinson SP. 1996. Polyembryony in citrus: accumulation of seedstorage proteins in seeds in embryos cultured in vitro. Plant Physiol. 110:599-609.Koltunow AM, Johnson SD, Bicknell RA. 1998. Sexual and apomictic development inHieracium. Sexual Plant Reprod. 11:213-230.Kurup S, Jones HD, Holdsworth MJ. 2000. Interactions of the developmental regulator ABI3with proteins identified from developing Arabidopsis seeds. Plant J. 21:143-155.Leblanc O, Grimanelli D, Islam-Faridi N, Berthaud J, Savidan Y. 1996. Reproductive behaviorin maize-Tripsacum polyhaploid plants: implications for the transfer of apomixis into maize.J. Hered. 87:108-111.398 Bennett et al
Li JM, Yuan LP. 1999. Hybrid rice: genetics breeding and seed production. Plant Breed. Rev.17:15-156.Linnestad C, Doan DNP, Brown RC, Lemmon BE, Meyer DJ, Jung R, Olsen OA. 1998.Nucellain, a barley homolog of the dicot vacuolar-processing protease, is localized in nucellarcell walls. Plant Physiol. 118:1169-1180.Lotan T, Ohto MA, Yee KM, West MAL, Lo R, Kwong RW, Yamagishi K, Fischer RL, GoldbergRB, Harada JJ. 1998. Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryodevelopment in vegetative cells. Cell 93:1195-1205.Lund G, Ciceri P, Viotti A. 1995a. Maternal-specific demethylation and expression of specificalleles of zein genes in the endosperm of Zea mays L. Plant J. 8:571-581.Lund G, Messing J, Viotti A. 1995b. Endosperm-specific demethylation and activation of specificalleles of alpha-tubulin genes of Zea mays L. Mol. Gen. Genet. 246:716-722.Luo M, Bilodeau P, Koltunow A, Dennis ES, Peacock WJ, Chaudhury AM. 1999. Genes controllingfertilization-independent seed development in Arabidopsis thaliana. Proc. Natl.Acad. Sci. USA 96:296-301.Luo M, Bilodeau P, Dennis ES, Peacock WJ, Chaudhury A. 2000. Expression and parent-oforigineffects for FIS2, MEA, and FIE in the endosperm and embryo of developingArabidopsis seeds. Proc. Natl. Acad. Sci. USA 97:10637-10642.McCarty DR. 1995. Genetic control and integration of maturation and germination pathwaysin seed development. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:71-93.Mu XJ, Shi GC, Zhu ZQ, Cai X. 1996. Embryological observations on the apomictic rice ApIII (Shuang 13). Acta Bot. Sin. 38:969-971.Ogas J, Cheng J, Sung ZR, Somerville C. 1997. Cellular differentiation regulated by gibberellinin the Arabidopsis thaliana pickle mutant. Science 277:91-94.Ogas J, Kaufmann S, Henderson J, Somerville C. 1999. PICKLE is a CHD3 chromatin-remodelingfactor that regulates the transition from embryonic to vegetative development inArabidopsis. Proc. Natl. Acad. Sci. USA 96:13839-13844.Ohad N, Margossian L, Hsu YC, Williams C, Repetti P, Fischer RL. 1996. A mutation thatallows endosperm development without fertilization. Proc. Natl. Acad. Sci. USA 93:5319-5324.Ohad N, Yadegari R, Margossian L, Hannon M, Michaeli D, Harada JJ, Goldberg RB, FischerRL. 1999. Mutations in FIE, a WD polycomb group gene, allow endosperm developmentwithout fertilization. Plant Cell 11:407-416.Ozias-Akins P, Roche D, Hanna WW. 1998. Tight clustering and hemizygosity of apomixislinkedmolecular markers in Pennisetum squamulatum implies genetic control of aposporyby a divergent locus that may have no allelic form in sexual genotypes. Proc. Natl. Acad.Sci. USA 95:5127-5132.Parcy F, Valon C, Kohara A, Misera S, Giraudat J. 1997. The ABSCISIC ACID-INSENSITIVE3,FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects ofArabidopsis seed development. Plant Cell 9:1265-1277.Peacock WJ. 1992. Genetic engineering and mutagenesis for apomixis in rice. Apomixis Newsl.4:3-7.Peacock WJ, Ming L, Craig S, Dennis E, Chaudhury A. 1995. A mutagenesis programme forapomixis genes in Arabidopsis. In: Induced mutations and molecular techniques for cropimprovement. Proceedings, Vienna, Austria, 19-23 June 1995. International Atomic EnergyAgency, Vienna. p 117-125.Molecular tools for achieving synthetic apomixis in hybrid rice 399
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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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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
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 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
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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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