Abstract
To investigate the rearrangement of the plastid genome during tissue culture, DNA from rice callus lines, which had been derived individually from single protoplasts isolated from seed or pollen callus (protoclones), was analyzed by Southern hybridization with rice chloroplast DNA (ctDNA) clones as probes. Among 44 long-term cultured protoclones, maintained for 4, 8 or 11 years, 28 contained plastid DNA (ptDNA) from which portions had been deleted. The ptDNA of all protoclones that had been maintained for 11 years had a deletion that covered a large region of the plastid genome. The deletions could be classified into 15 types from their respective sizes and positions. By contrast, no deletions were found in the ptDNA of 38 protoclones that had been maintained for only 1 month. These results indicate that long-term culture causes deletions in the plastid genome. Detailed hybridization experiments revealed that plastid genomes with deletions in several protoclones were organized as head-to-head or tail-to-tail structures. Furthermore, ptDNAs retained during long-term culture all had a common terminus at one end, where extensive rearrangement is known to have occurred during the speciation of rice and tobacco. Morphological analysis revealed the accumulation of starch granules in plastids and amyloplasts in protoclones in which the plastid genome had undergone deletion. Our observations indicated that novel structural changes in the plastid genome and morphological changes in the plastid had occurred in rice cells during long-term tissue culture. Moreover, the morphological changes in plastids were associated with deletions in the plastid genome.
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Arnhold-Schmitt B (1993) Rapid changes in amplification and methylation pattern of genomic DNA in culture carrot root explants (Daucus carota L.) Theor Appl Genet 85:793–800
Blackely LM, Steward FC (1964) Growth and organized development of cultured cells. 7. Cellular variation. Am J Bot 51:809–820
Boynton JE, Gillham NW, Harris EH, Hosler JP, Johnson AM, Jones AR, Randolph-Anderson BL, Robertson D, Klein TM, Shark KB, Sanford JC (1988) Chloroplast transformation in Chlamydomonas with high-velocity microprojectiles. Science 240:1534–1538.
Brown PTH, Gobel E, Lorz H (1991) RFLP analysis of Zea mays callus cultures and their regenerated plants. Theor Appl Genet 81:227–232
Chen Z, Liang GH, Muthukrishnan S, Kofoid KD (1993) A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum. Mol Gen Genet 236:251–259
Day A, Ellis THN (1984) Chloroplast DNA deletion associated with wheat plants regenerated from pollen: possible basis for maternal inheritance of chloroplasts. Cell 39:359–368
de Haas JM, Boot KJM, Haring MA, Kool AdJ, Nijkamp HJJ (1986) A Petunia hybrida chloroplast DNA region, close to one of the inverted repeats, shows a sequence homology with the Euglena gracilis chloroplast DNA region that carries the putative replication origin. Mol Gen Genet 202:48–54
dePamphillis, Palmer JD (1990) Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348:337–339
Ellis THN, Day A (1986) A hairpin plastid genome in barley. EMBO J 5:2769–2774
Harada T, Ishikawa R, Niizeki M, Saito K (1991) Large-scale deletions of rice plastid DNA in anther culture. Theor Appl Genet 81:157–161
Harada T, Ishikawa R, Niizeki M, Saito K (1992) Pollen-derived rice calli that have large deletions in plastid DNA do not require protein synthesis in plastids for growth. Mol Gen Genet 233:145–150
Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa L.) chloroplast genome; intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185–194
Ishii T, Terachi T, Tsunewaki K (1993) Comparative study on the chloroplast, mitochondrial and nuclear genome differentiation in two cultivated rice species, Oryza sativa and O. glaberrima, by RFLP analyses. Theor Appl Genet 86:88–96
Karp A (1991) On the current understanding of somaclonal variation. In: Milfin BJ (ed) Oxford Surveys of Plant Molecular Cell Biology, vol 7. Oxford University Press, London, pp 1–58
Kawata M, Harada S, Antonio B, Oono K (1992) Protoclonal variation of plant regeneration in rice. Plant Cell Tissue Org Cult 28:1–10
Kenneth HW, Clifford WM, Palmer JD (1992) Function and evolution of a minimal plastid genome from a nonphotosynthetic plant. Proc Natl Acad Sci USA 89:10648–10652
Kikuchi S, Takaiwa F, Oono K (1987) Variable copy number DNA sequences in rice. Mol Gen Genet 210:373–380
Kobayashi H (1990) The molecular biology of plastids. In: Bogorad L, Vasil IK (eds) Cell culture and somatic cell genetics of plants, vol. 7. Academic Press, San Diego, pp 345–353
Larkin PJ, Scowcroft LVR (1981) Somaclonal variation, a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–204
Lee M, Phillips RL (1988) The chromosomal basis of somaclonal variation. Annu Rev Plant Physiol Plant Mol Biol 39:413–437
Maruta I, Kikuchi S, Oono K (1994) Unspliced precursor mRNA of the plastid rpl2 gene cluster accumulates in rice (Oryza sativa L.) albino pollen plants (in press)
Matthews BF, DeBonte LR (1985) Chloroplast and mitochondrial DNAs of carrot and its wild relatives. Plant Mol Biol Rep 3:12–14
Medgyesy P, Fejes E, Maliga P (1985) Interspecific chloroplast recombination in a Nicotiana somatic hybrid. Proc Natl Acad Sci USA 82:6960–6964
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497
Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight DNA. Nucleic Acids Res 8:4321–4325
Ngernprasirtsiri J, Kobayashi H, Akazawa T (1988) DNA methylation as a mechanism of transcriptional regulation in non-photosynthetic plastids in plant cells. Proc Natl Acad Sci USA 85:4750–4754
Ogihara Y, Tsunewaki K (1979) Tissue culture in Haworthia-Setata. 3. Occurrence of callus variants during sub-cultures and its mechanism. Jpn J Genet 54:271–294
Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S-1, Inokuchi H and Ozeki H (1986) Chloroplast genome organization deduced from complete sequence of liverwort (Marchantia polymorpha) chloroplast DNA. Nature 322:572–574
Oono K (1975) Production of haploid plants of rice (Oryza sativa L.) by anther culture and their use for breeding. Bull Natl Inst Agric Sci D26:139–222
Orton TJ (1984) Genetic variation in somatic tissues; method or madness? Adv Plant Pathol 2:153–189
Palmer JD (1983) Chloroplast DNA exists in two orientations. Nature 301:92–93
Paven MCM, Henry Y, Buyser JD, Corre F, Hartmann C, Rode A (1992) Organ/tissue-specific changes in the mitochondrial genome organization of in vitro cultures derived from different explants of a single wheat variety. Theor App Genet 85:1–8
Peschke VM, Phillips RL (1991) Activation of the maize transposable element Suppressor-mutator (Spm) in tissue culture. Theor Appl Genet 81:90–97
Peschke VM, Phillips RL (1992) Genetic implications of somaclonal variation in plants. Adv Gent 30:41–76
Pollard-Knight D, Read CA, Downes M, Howard LA, Leadbetter MR, Pheby SA, McNaughton E, Syms A, Brady MAW (1990) Nonradioactive nucleic acid detection by enhanced chemiluminescence using probes directly labeled with horseradish peroxidase. Anal Biochem 185:84–89
Reed KC, Mann DA (1985) Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res 1:7207–7221
Rode A, Hartmann C, Dron M, Picard E and Ouetier F (1985) Organelle genome stability in anther-derived doubled haploids of wheat (Triticum aestivum L., cv “Moisson”). Theor Appl Genet 71:320–324
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning; a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Scott NS, Tymmis MJ, Possingham JV (1984) Plastid-DNA levels in the different tissues of plants. Planta 161:12–19
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome; its gene organization and expression. EMBO J 5:2043–2049
Walsh MA, Rechel EA, Popovich TM (1980) Observation on plastid fine-structure in the holoparasitic angiosperm Epifagus virginiana. Am J Bot 67:833–837
Wang XH, Lazzeri PA, Lorz H (1992) Chromosomal variation in dividing protoplasts derived from cell suspensions of barley (Hordteum vulgare L.). Theor Appl Genet 85:181–185
Zurawski G, Clegg MT (1987) Evolution of higher-plant chloroplast DNA-encoded genes; implications for structure-function and phylogenic studies. Annu Rev Plant Physiol 38:391–418
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Kawata, M., Ohmiya, A., Shimamoto, Y. et al. Structural changes in the plastid DNA of rice (Oryza sativa L.) during tissue culture. Theoret. Appl. Genetics 90, 364–371 (1995). https://doi.org/10.1007/BF00221978
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DOI: https://doi.org/10.1007/BF00221978