Rice Genetics IV - IRRI books - International Rice Research Institute

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Peel MD, Carman JG, Leblanc O. 1997. Megasporocyte callose in apomictic buffelgrass, Kentuckybluegrass, Pennisetum squamulatum Fresen, Tripsacum L., and weeping lovegrass.Crop Sci. 37:724-732.Perry SE, Nichols KW, Fernandez DE. 1996. The MADS domain protein AGL15 localizes tothe nucleus during early stages of seed development. Plant Cell 8:1977-1989.Pessino SC, Ortiz JPA, Leblanc O, Do Valle CB, Evans C, Hayward MD. 1997. Identificationof a maize linkage group related to apomixis in Brachiaria. Theor. Appl. Genet. 94:439-444.Pessino SC, Evans C, Ortiz JPA, Armstead I, Do Valle CB, Hayward MD. 1998. A genetic mapof the apospory-region in Brachiaria hybrids: identification of two markers closely associatedwith the trait. Hereditas 128:153-158.Roche D, Cong P, Chen Z, Hanna WW, Gustine DL, Sherwood RT, Ozias-Akins P. 1999. Anapospory-specific genomic region is conserved between Buffelgrass (Cenchrus ciliaris L.)and Pennisetum squamulatum Fresen. Plant J. 19:203-208.Savidan Y. 2000. Apomixis: genetics and breeding. Plant Breed. Rev. 18:13-86.Schiefthaler U, Balasubramanian S, Sieber P, Chevalier D, Wisman E, Schneitz K. 1999. Molecularanalysis of NOZZLE, a gene involved in pattern formation and early sporogenesisduring sex organ development in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96:11664-11669.Scott RJ, Spielman M, Bailey J, Dickinson HG. 1998. Parent-of-origin effects on seed developmentin Arabidopsis thaliana. Development 125:3329-3341.Sharma KK, Thorpe TA. 1995. Asexual embryogenesis in vascular plants in nature. In: In vitroembryogenesis in plants. In: Thorpe TA, editor. Current plant science and biotechnology inagriculture. Vol. 20. Dordrecht (Netherlands): Kluwer Academic Publishers. p 17-72.Shi GC, Ni PC, Song JX, Mu XJ, Liang TB. 1996. A cytoembryological study on rice 84-15, arice line presumed to be apomictic. Acta Agron. Sin. 22:657-660.Sturaro M, Linnestad C, Kleinhofs A, Olsen OA, Doan DNP. 1998. Characterization of a cDNAencoding a putative extensin from developing barley grains (Hordeum vulgare L.). J. Exp.Bot. 49:1935-1944.Sokolov VA, Khatypova IV. 1999. Inactivation of the imprinting effects in maize-Tripsacumhybrids. Maize Genet. Coop. Newsl. 73:74-76.Tan W, Guo XX, Kong FL. 1994. A study of the influence of genetic background on the frequencyof twin seedlings in the apomictic rice genotype C1001. J. Southwest Agric. Univ.16:369-372.Tsaftaris AS, Polidoros AN. 2000. DNA methylation and plant breeding. Plant Breed. Rev.18:87-176.Tsukaya H, Shoda K, Kim GT, Uchimiya H. 2000. Heteroblasty in Arabidopsis thaliana (L.)Heynh. Planta 210:536-542.Van Dijk P, Van Damme J. 2000. Apomixis technology and the paradox of sex. Trends PlantSci. 5:81-84.Vinkenoog R, Spielman M, Adams S, Fischer RL, Dickinson HG, Scott RJ. 2000.Hypomethylation promotes autonomous endosperm development and rescuespostfertilization lethality in fie mutants. Plant Cell 12:2271-2282.Virmani SS. 1994. Heterosis and hybrid rice breeding. New York, N.Y. (USA): Springer-Verlag.West MAL, Matsudaira-Yee K, Danao J, Zimmerman JL, Fischer RL, Goldberg RB, HaradaJJ. 1994. Leafy cotyledon1 is an essential regulator of late embryogenesis and cotyledonidentity in Arabidopsis. Plant Cell 6:1731-1745.400 Bennett et al
Xu FX, Chye ML. 1999. Expression of cysteine proteinase during developmental events associatedwith programmed cell death in brinjal. Plant J. 17:321-327.Yao JL, Cai DT, Ma PF, Zhu H. 1997. Embryological studies on apospory in rice HDAR. Chin.J. Rice Sci. 11:113-117.Ye XL, Chen ZL, Li YQ. 1994. Polyembryogenesis in apomixis parent IV of rice. J. Trop.Subtrop. Bot. 2:67-72.Ye XL, Chen ZL, Li YQ. 1995. The characteristics of apomictic PDER rice variety and thedevelopment of diploid embryo sac. J. Trop. Subtrop. Bot. 3:36-42.Zuo J, Niu QW, Moller SG, Chua NH. 2001. Chemical-regulated, site-specific DNA excisionin transgenic plants. Nat. Biotechnol. 19:157-161.NotesAuthors’ address: Plant Breeding, Genetics, and Biochemistry Division, International RiceResearch Institute, DAPO Box 7777, Metro Manila, Philippines.Acknowledgments: This research was supported by a grant from the Australian Centre for InternationalAgricultural Research. AK thanks the Natural Science and Engineering ResearchCouncil of Canada for a fellowship. We thank the Rice Genome Research Project ofJapan for cDNA clones and Zhikang Li and his staff for assistance in isolation of bacterialartificial chromosome clones. We are grateful to Darshan Brar, Abed Chaudhury, Liz Dennis,Anna Koltunow, Jim Peacock, and Sant Virmani for advice and to Beng Albano, EvelynLiwanag, and Nards Estanor for technical assistance. We thank Darshan Brar and AnnaKoltunow for comments on the manuscript.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.Molecular tools for achieving synthetic apomixis in hybrid rice 401
Page 6:
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
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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 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,
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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
Page 481 and 482:
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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