Rice Genetics IV - IRRI books - International Rice Research Institute

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initially fixed by phosphoenolpyruvate carboxylase (PEPC) in the mesophyll cell toform a C 4 compound, oxaloacetate (OAA). OAA is subsequently converted to malate.Malate is then transferred to the bundle sheath cell and then decarboxylated by NADPdependentmalic enzyme (NADP-ME). CO 2 released from this decarboxylation reactionis refixed in the Calvin cycle by Rubisco, as in C 3 plants. To complete the cycle,pyruvate produced by the malate decarboxylation is transferred to the mesophyll chloroplastand phosphorylated to phosphoenolpyruvate (PEP) via pyruvate, orthophosphatedikinase (PPDK) (Fig. 1).The introduction of C 4 traits through genetic engineering into rice (C 3 plant) wouldimprove photosynthetic efficiency. One of the major objectives in improving riceyield is to enhance the plant’s photosynthetic efficiency. It is necessary to developprotocols to express C 4 enzymes at high levels in C 3 plants. We report here the mechanismof evolution of C 4 photosynthesis genes, and the strategy for the high-levelexpression of C 4 genes in C 3 plants based on characteristics of C 4 genes.Evolution of a C 4-type PPDK geneThe genes involved in C 4 photosynthesis have been found in a variety of organisms,not only in C 4 and Crassulacean acid metabolism (CAM) plants, but also in C 3 plantsRuBP2 PGAC 3 pathwayMesophyll cellCO 2RubiscoC 3 pathwayPyruvateRubiscoNADP-MECO 2Bundle sheath cellCO 2fixationPPDKPEPC 4 pathwayMalatePEPCOAAMesophyll cellCO 2concentrationCO 2Fig. 1. Comparison of C 3 and C 4 pathways. The C 3 pathway is locatedin mesophyll cells in C 3 plants, whereas the C 3 cycle is located inbundle sheath cells in C 4 plants. The major function of the C 4 pathwayis to concentrate CO 2 in the inner bundle sheath cells where Rubiscois located and thus suppress its oxygenase activity and the associatedphotorespiration. OAA = oxaloacetate, NADP-ME = NADP-malicenzyme, PEP = phosphoenolpyruvate, PGA = phosphoglycerate, RuBP= ribulose-1,5-bisphosphate.440 Matsuoka et al
(Imaizumi et al 1997). However, the activities of C 4 enzymes such as PPDK are muchlower in C 3 plants than in C 4 plants. It is thus important to identify C 4 -type genes withhigh-level expression.Glackin and Grula (1990) and Sheen (1991) found that the C 4 -type PPDK gene inmaize is transcribed from two different initiation sites under the control of two differentpromoters; the first promoter produces the larger transcript encoding the C 4 -typeenzyme with the chloroplast transit peptide and the second promoter produces the smallertranscript encoding the C 3 -type enzyme that is localized in the cytoplasm. Thelarger transcript is started from exon 1 by the first promoter, whereas the smaller transcriptis started from exon 2 by the second promoter (Fig. 2). We isolated and characterizedthe PPDK gene homologous to the maize C 4 -type gene from rice.The deduced amino acid sequence of rice PPDK is 88% homologous to the maizeC 4 -type PPDK in the mature peptide region (Imaizumi et al 1997). The rice gene issimilar to that of maize except that it has two extra introns (Fig. 2).The transcription activity of the promoters of the rice and maize PPDK was studied.In transgenic rice, both rice and maize promoters directed GUS expression in photosyntheticorgans in a light-dependent manner. However, the maize promoter exhibited amuch higher transcriptional activity than the rice promoter did (Matsuoka et al 1993,Nomura et al 2000). The high-level expression of C 4 -specific genes in rice is not limitedto the PPDK gene, but another C 4 photosynthetic gene for PEPC was also expressedin mesophyll cells in light-grown tissue (Matsuoka et al 1994). These results indicatethat rice contains trans-acting elements that are required for expression of both the C 4PPDK gene and C 4 PEPC gene. It is possible that rice contains most of the trans-actingelements required for the expression of C 4 -specific photosynthetic genes.<strong>Rice</strong>11’12–50 kb2 33’ 4 5 6 7 8 9 101112 13 14 15 16 1718 19ATGATGTGA1’Maize 6 kb2 34 5 6 7 8 9 10 1112 13141516 1718 19ATG ATG TGA1 kbFig. 2. Exon-intron structure of the genes for PPDK. In both rice and maize genes, transcriptionstarts at the two sites indicated by curved arrows. The common coding regions of the large andsmall transcripts are represented by filled boxes and the 5’ and 3’ noncoding regions are representedby open boxes. Dotted boxes in rice exon 2 and maize exon 1 represent the region thatencodes the transit peptide, and dotted boxes in rice exon 3 and maize exon 2 represent thecoding region unique to the small transcripts. The positions of the initiation and terminationcodons are indicated by ATG and TGA, respectively. The broken lines linking the first and seconddiagrams indicate the presence of two extra introns in the rice gene. (From Matsuoka et al2000.)High-level expression of C 4photosynthetic genes in transgenic rice 441
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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
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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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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 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
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