Ray Wu, CONVENER
Section of Biochemistry, Molecular and Cell
Biology, Cornell University,
Ithaca, New York 14853, U.S.A.
Between August 1988-1989, approximately 15 papers on the molecular analysis of rice genes were published and reviewed in Volume 6 of the RGN; between August 1989-1990, approximately 30 papers were published and reviewed in Volume 7 of the RGN. However, between August 1990-August 1991, over 90 papers on rice gene analysis were published. Therefore, it is no longer practical to review each paper within the limited size of this article. Thus, for this report, I have only listed these papers according to their topic and have given the full reference so that anyone interested in reading any of the papers can readily find them. The list of papers is not complete. Short notes and abstracts of papers have not been included. In addition, only papers published in English have been included. If any papers have been left out, I apologize for not including them in the references of this report.
I. Cloning and sequencing of nuclear genes
Anderson et al. (1990); Lei and Wu (1991); Rothenberg and Wu (1991); Shimada and Tada (1991); Shyur and Chen (1990); Wang et al. (1990c)
II. Transcriptional analysis of genes in vitro
Kim and Wu (1990); Takaiwa and Oono (1990)
III. Transcriptional analysis of genes in vivo; Linkage
Anderson et al. (1991); Ishii et al. (1990); Jena and Kochert (1991); Phom et al. (1990); Ricard et al. (1991); Second (1991)
IV. Regeneration of rice plants
Cho and Zapata (1990); Dutta et al. (1990a, 1990b), Guiderdoni (1991); Hayashimoto et al. (1990); Higuchi and Maeda (1990); Lyznik et al. (1991)
V. Transgenic rice; Transcriptional analysis of genes in transgenic
Battraw and Hall (1990); Cao et al. (1990); Claes et al. (1991); Izawa et al. (1991); Lee et al. (1991); Meijer et al. (1991); Nagatani et al. (1991); Peng et al. (1990); Tada et al. (1990); Tada et al. (1991); Takaiwa et al. (1991); Wu (1991); Wu et al. (1990); Zhang et al. (1991)
VI. Somaclonal variation; Recombination; Molecular changes
in regenerated plants or cultured cells
Brown et al. (1990); Cao et al. (1991); Castiglione et al. (1991); Higashitani et al. (1990)
VII. Hormone regulated genes
Huang et al. (1990); Karrer et al. (1991); Kobayashi et al. (1990); O'Neill et al. (1990); Sutliff et al. (1991); Yamaguchi-Shinozaki et al. (1990); Su et al. (1990)
VIII. Repetitive DNAs; rDNAs; Chromosome mapping
Cuzzoni et al. (1990); Dutta et al. (1991); Fukui and Iijima (1991); Iijima et al. (1991); Sano and Sano (1990); Takaiwa et al. (1990); Wu et al. (1991)
IX. Chitinase; Stress-related genes
Huang et al. (1991); Nishizawa and Hibi (1991); Zhu and Lamb (1991)
X. Evolutionary relationship
Barbier et al. (1991); Dehesh et al. (1991); Kemmerer et al. (1991)
XI. Genes of rice viruses
Gao et al. (1990); Hay et al. (1991); Suzuki et al. (1990)
XII. Chloroplast and mitochondrial genes
Chen et al. (1990); Chowdhury et al. (1990); Dally and Second (1990); Hirai (1991); Kadowaki et al. (1990a, 1990b); Matsuoka (1990); Sakamoto et al. (1990); Shimada et al. (1990); Shimada and Sugiura (1991); Wang et al. (1990a, 1990b)
XIII. Nutritional improvement; Miscellaneous
Bajai (1991); Flowers et al. (1990); Huebner et al. (1990); Ludlow and Muchow (1990); Sano (1990); Schmitz and Lorz (1990); Sobral et al. (1990); Uchimiya and Toriyama (1991)
XIV. Protease inhibitors; Other proteins
Arai et al. (1991); Chen (1990); Chiba et al. (1990); Giordano et al. (1991); Liang et al. (1991); Masumura et al. (1991); Mawal et al. (1990); Nakamura et al. (1991); Shirata and Takagishi (1990)
Anderson, J. M., J. Hnilo, R. Larson, T. W. Okita, M. Morell and J. Preiss, 1990. The encoded primary sequence of a rice seed ADP-glucose pyrophosphorylase subunit and its homology to the bacterial enzyme. J. Biol- Chem. 264: 12238-12242.
Anderson, J. M., R. Larson, D. Laudencia, W. T. Kim, D. Morrow, T. W. Okita and J. Preiss, 1991. Molecular characterization of the gene encoding a rice endosperm-specific ADP glucose pyrophosphorylase subunit and its developmental pattern of transcription. Gene 97: 199- 205.
Arai, S., H. Watanabe, H. Kondo, Y. Emori and K. Abe, 1991. Papain-inhibitory activity of oryzacystain, a rice seed cysteine proteinase inhibitor, depends on the central glu-val-val- ala-gly region conserved among cystain superfamily members. J. Biochem. 109: 294-298.
Bajaj, S., 1991. Biotechnology in nutritional improvement of rice. In Biotech. of Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 508-523.
Barbier, P., H. Morishima, and A. Ishihama, 1991.Phylogenetic-relationships of annual and perennial wild riceprobing by direct DNA sequencing. Theor. Appl. Genet. 81: 693-702.
Battraw, M. J. and T. C. Hall, 1990. Histochemical analysis of CaMV 35S promoter-β-glucuronidase gene expression in transgenic rice plants. Plant Mol. Biol. 15: 527-538.
Brown, P.T.H., J. Kyozuka, Y. Sukekiyo, Y. Kimura, K. Shimamoto and H. Lorz, 1990. Molecular changes in protoplast-derived rice plants. Mol. Gen. Genet. 223: 324-328.
Cao, J., Y.C. Wang, T. M. Klein, J. Sanford and R. Wu, 1990. Transformation of rice and maize using the biolistic process. In Plant Gene Transfer, C. J. Lamb and R. N. Beachy (eds.), pp. 21-33.
Cao, J., M. C. Rush, M. W. Nabors, Q. J. Xie, T. P. Croughan and E. Nowick, 1991. Development and inheritance of somaclonal variation in rice. In Biological Nitrogen Fixation Associated with Rice Production, S. K. Dutta and C. Sloger (eds.), pp. 385-419.
Castiglione, S., E. Cuzzoni, M. L. Marchesi, K. L. Zheng, C. Morandi, L. Ferretti and F. Sala, 1991. Plasticity of the rice genome: DNA amplfication in cultured cells. In Biotech. in Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 447-456.
Chen, S.C. G., M.C. Cheng, J. Chen and L.Y. Hwang, 1990. Organization of the rice chloroplast psaA-psaB-rpsl4 gene and the presence of sequence heterogeneity in this gene cluster. Plant Sci. 68: 213-221.
Chen, S. H., 1990. Comparative study of pollen proteins of rice by isoelectric focusing and high- performance liquid chromatography. Cereal Chem. 68: 91-94.
Chiba, Y. M., M. Ui, Y. Kato, T. Nakajima and E. Ichishima, 1990. Two groups of intracellular α-amylase isoenzymes from cultured rice cells. Phytochem. 29: 2075-2078.
Cho, M. S. and F. J. Zapata, 1990. Plants regenerated from isolated microspore of indica rice. Plant Cell Physiol. 31: 881-885.
Chowdhury, M. K. U., G. W. Schaeffer, R. L. Smith, L. R. DeBonte and B. F. Mattews, 1990. Mitochondrial DNA variation in long-term tissue cultured rice lines. Theor. Appl. Genet. 80: 81 -87.
Claes, B., J. Smalle, R. Dekeyser, M. Van Montagu and A. Caplan, 1991. Organ-dependent regulation of a plant promoter isolated from rice by promoter-trapping in tobacco. The Plant J. 1: 15-26.
Cuzzoni, E., L. Ferretti, C. Giordani, S. Castiglione and F. Sela, 1990. A repeated chromosomal DNA sequence is amplified as a circular extrachromosomal molecule in rice. Mol. Gen. Genet. 222: 58-64.
Dally, A. M. and G. Second, 1990. Chloroplast DNA diversity in wild rice and cultivated species of rice (genus Oryza, section Oryza). Cladistic-mutation and genetic distance analysis. Theor. Appl. Genet. 80: 209-222.
Dehesh, K., J. Tepperman, A. H. Christensen and P. H. Quail, 1991. phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots. Mol. Gen. Genet. 225: 305-313.
Dutta, S. K., A. Peterhans, K. Datta and I. Potrykus, 1990a. Genetically engineering fertile indica-rice recovered from protoplasts. Bio/Technology 8: 736-740.
Dutta, S. K., K. Datta and I. Potrykus, 1990b. Fertile indica rice plant regenerated from protoplasts isolated from microspore derived cell suspension. Plant Cell Rep. 9: 253-256.
Dutta, S. K., S. Bhansaly, B. Ghosh, R. K. Chaudhuri and M. Verma, 1991. Restriction fragment length polymorphism of rice ribosomal RNA genes. In: Biological Nitrogen Fixation Associated with Rice Production, S. K. Dutta and C. Sloger (eds.), pp. 377-383.
Flowers, T. J., S. A. Flowers, M. A. Hajibagheri, 1990. Salt tolerance in the halophytic wild rice Porteresia coarctata Tateoka. New Phytol. 114: 675-684.
Fukui, K. and K. Iijima, 1991. Somatic chromosome map of rice by imaging methods. Theor. Appl. Genet. 81: 589-596.
Gao, Q., Y. X. Ou, W. Liu, N. S. Pan and Z. L. Chen, 1990. Partial complementary cloning and nucleotide sequence of rice dwarf virus genome. Acta Bot. Sinica 32: 13-18.
Giordano, M., M. E. Mattachini, R. Cella and G. Pedralinoy, 1991. Purification and properties of a novel DNA methyltransferase from cultured rice cells. Biochem. Biophys. Res. Commun. 177: 711-719.
Guiderdoni, E., 1991. Gametic selection in anther culture of rice. Theor. Appl. Genet. 81: 406- 412.
Hay, J.M., M. C. Jones, M.L. Blakebrough, I. Dasgupta, J.W. Davies and R. Hull, 1991. An analysis of the sequence of an infectious clone of rice tungro bacilliform virus. Nucl. Acids. Res. 19: 2615-2621.
Hayashimoto, A., Z. Li and N. Mural, 1990. A polyethylene glycol-mediated protoplast transformation system for production of fertile transgenic rice plants. Plant Physiol. 53: 857-863.
Higashitani, A., S. Tamamoto, S. Tabata, K. Oono and Y. Hotta, 1990. D-loop forming activity and general recombinatory activity in extracts from shoot, flower and callus of varieties of rice. Jpn J. Genet. 65: 53-64.
Higuchi, N. and E. Maeda, 1990. Enhanced plant regeneration in rice callus cultures following abscisic acid treatment. Japan J. Crop Sci. 59: 359-368.
Hirai, A., 1991. Molecular structure of chroloplast DNA from rice. In Biotech. in Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 458-466.
Huang, N., N. Koizumi, S. Reinl and R. L. Rodriguez, 1990. Structural organization and differential expression of rice alpha-amylase genes. Nucl. Acids Res. 18: 7007-7014.
Huang, J. K., L. Wen, M. Swegl, H. C. Tran, T. H. Thin, H. M. Naylor, S. Muthukrishnan and G. R. Reeck, 1991. Nucleotide sequence of a rice genomic clone that encodes a class I endochitinase. Plant Mol. Biol. 16: 479-480.
Huebner, F. R., J. A. Bietz, B. D. Webb and B.O. Juliano, 1990. Rice cultivar identification by high-performance liquid chromatography of endosperm proteins. Cereal Chem. 67: 129- 135.
Iijima, K., K. Kekeda and K. Fukui, 1991. Identification and characterization of somatic rice chromosomes by imaging methods. Theor. Appl. Genet. 81: 597-605.
Ishii, T., O. Panaud, D. S. Brar and G. S. Khush, 1990. Use ofnon-radioactive digoxigenin-labeled DNA probe for RFLP analysis in rice. Plant Mol. Biol. Rep. 8: 167-179.
Izawa, T., C. Miyazaki, M. Yamamoto, R. Terada, S. Iida and K. Shimamoto, 1991. Introduction and transposition of the maize transposable element Ac in rice (Oryza sativa L). Mol. Gen. Genet. 227: 391-396.
Jena, K. K. and G. Kochert, 1991. Restriction fragment length polymorphism analysis of CCDD genome species of the genus Oryza L. Plant Mol. Biol. 16: 831-840.
Kadowaki, K., T. Suzuki and S. Kagawa, 1990a. A chimeric gene containing the 5' portion of atp6 is associated with cytoplasmic male-sterility in rice. Mol. Gen. Genet. 224: 10-16.
Kadowaki, K. and K. Harada, 1990b. Heterogeneity of mitochondrial plasmid-like DNAs in cytoplasmically male-sterile rice. Jpn. J. Breed. 39: 439-447.
Karrer, E. E., J. C. Litts and R. Rodriguez, 1991. Differential expression of α-amylase genes in germinating rice and barley seeds. Plant Mol. Biol. 16: 797-805.
Kemmerer, E. C., M. Lei and R. Wu, 199 1. Isolation and molecular evolutionary analysis of a cytochrome c gene from Oryza sativa (rice). Mol. Biol. Evol. 8: 212-226.
Kim, S. Y. and R. Wu, 1990. Multiple protein factors bind to a rice glutelin promoter region. Nucl. Acids Res. 18: 6845-6852.
Kobayashi, M., Y. Kamiya, A. Sakurai, H. Saka and N. Takahashi, 1990. Metabolism of gibberellins in cell-free extracts of anthers from normal and dwarf rice. Plant Cell Physiol. 31: 289-293.
Lee, N., Y. Wang, J. Yang, K. Ge, S. Huang, J. Tan and D. Testa, 1991. Efficient transformation and regeneration of rice small cell groups. Proc. Natl. Acad. Sci. USA 88: 6389-6393.
Lei, M. and R. Wu, 1991. A novel glycine-rich cell wall protein gene in rice. Plant Mol. Biol. 16: 187-198.
Liang, C., G. Brookhart, G. H. Feng, G. R. Reeck and K. J. Kramer, 1991. Inhibition of digestive proteinases of stored grain coleoptera by oryzacystatin, a cystein proteinase inhibitor from rice seed. FEBS 278: 139-142.
Ludlow, M. M. and R. C. Muchow, 1990. A critical evaluation of traits for improving crop yields in water-limited environments. Advances in Agronomy 43: 107-153.
Lyznik L. A. J. Peng and T. K. Hodges, 1991. Simplified procedure for transient transformation of plant protoplasts using ployethylene glycol treatment. Bio Techniques 10: 294-300.
Masumura, T., N. Mitsukawa, K. Tanaka and S. Fujii, 1991. Rice storage proteins: genetic analysis of accumulation process. In Biotech. in Agric. and Forestry Y. P. S. Bajaj (ed.) 14: 495-506.
Matsuoka, M., 1990. Classification and characterization of cDNA that encodes the light-harvesting chlorophyll A-B binding protein of photosystem II from rice. Plant Cell Physiol. 31: 519-526.
Mawal, Y. R., M. R. Mawal, M. N. Sainani and P. K. Ranjekar, 1990. Rice seed storage proteins: a structural insight. Plant Sci. 70: 73-80.
Meijer, E. G. M., R. A. Schilperoot, S. RLieb, P. E. Vanosruygrok and L. A. M. Hensgens, 1991. Transgenic rice cell lines and plants expression of transferred chimeric genes. Plant Mol. Biol. 16: 807-820.
Mural, N., Z. Li, Y. Kawagoe and A. Hayashimoto, 1991. Transposition of the maize activator element in transgenic rice plants. Nucl. Acids Res. 19: 617-622.
Nagatani, A., S. A. Kay, M. Deak, N. H. Chua and M. Furuya, 1991. Rice type-1 phytochrome regulates hypocotyl elongation in transgenic tobacco seedlings. Proc. Natl. Acad. Sci. USA 88: 5207-5211.
Nakamura, A., H. Hirano and F. Kikuchi, 1991. Identification and genetic analysis of semidwarfism-related proteins in rice. Theor. Appl. Genet. 81: 376-380.
Nishizawa, Y. and T. Hibi, 1991. Rice chitinase gene cDNA cloning and stress-induced expression. Plant Science 76: 211-218.
O'Neill, S. D., M. H. Kumagai, A. Majumdar, N. Huang, T. D. Sutliff and R. L. Rodriguez, 1990.The α-amylase genes in Oryza sativa: characterization of cDNA clones and mRNA expression during seed germination. Mol. Gen. Genet. 221: 235-244.
Peng, J., L. A. Lyznik, L. Lee and T. K. Hodges, 1990. Co-transformation of indica rice protoplasts with gusa and neo genes. Plant Cell Reports 9: 168-172.
Pham, J. L., J. C. Glaszmann, R. Sano, P. Barbier, A. Ghesquiere and G. Second, 1990. Isozyme markers in rice: genetic analysis and linkage relationships. Genome 33: 348-359.
Ricard, B., J. Rivoal, A. Spiteri and A. Pradet, 1991. Anaerobic stress induces the transcription and translation of sucrose synthase in rice. Plant Physiol. 95: 669-674.
Rothenberg, M. and R. Wu, 1991. Molecular analysis of rice genes and methods for gene transfer. In Biotech. in Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 422-442.
Sakamoto, W., K. Kadowaki, S. Tano and T. Yabuno, 1990. Analysis of mitochondrial DNAs from Oryza glaberrima and its cytoplasmic substituted line for Oryza sativa associated with cytoplasmic male sterility. Jpn J. Genet. 65: 1-6.
Sano, Y., 1990. The genic nature of gamete elimination in rice. Genetics 125: 183-191.
Sano, Y. and R. Sano, 1990. Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33: 209-218.
Schmitz, U. and H. Lorz, 1990. Nutrient uptake in suspension cultures of Gramineae. II. Suspension cultures of rice (Oryza sativa L.). Plant Sci. 66: 95-111.
Second, G., 1991. Molecular markers in rice systematics. In Biotech. in Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 468-491.
Shimada, H., M. Fukuta, M. Ishikawa and M. Sugiura, 1990. Rice chloroplast RNA polymerase genes: the absence of an intron in rpoC1 and the presence of an extra sequence in rpoC2. Mol. Gen. Genet. 221: 395-402.
Shimada, H. and Y. Tada, 1991. Rapid isolation of a rice waxy sequence: a single PCR method for the analysis of recombinant plasmids from intact E. coli. Gene 98: 243-248.
Shimada, H. and M. Sugiura, 1991. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucl. Acids Res. 19: 983-995.
Shirata, K. and H. Takagishi, 1990. Salt-induced accumulation of 26 and 27 kD proteins in cultured cells of rice plant. Soil Sci. Plant Nutr. 36: 153-157.
Shyur, L.F. and C.S. Chen, 1990. Nucleotide sequence of two rice protamin cDNAs. Nucl. Acids Res. 19: 6683.
Sobral, W.S., R.J. Honey, Agate and M. Macmillan, 1990. Analysis of rice (Oryza sativa L.) genome using pulsed-field gel electrophoresis and rare-cutting restriction enounces. Plant Mol. Biol. Report 8: 253-275.
Sutliff, T. D., N. Huang, J. C. Litts and R. L. Rodriguez, 1991. Characterization of an alpha-amylase multi gene cluster in rice. Plant Mol. Biol. 16: 579-591.
Suzuki, N., Y. Watanabe, T. Ku sano and Y. Kitbag, 1990. Sequence analysis of the rice dwarf photogravures segment S3 transcript. Virology 179: 455-459.
Tada, Y., M. Sakamoto and T. Fujiwara, 1990. Efficient gene introduction into rice by electroplating and analysis of transgenic plants. Theor. Appl. Genet. 80: 475-480.
Tada, Y., M. Sakamoto, M. Matsuoka and T. Fujiwara, 1991. Expression of a monocot LHCP promoter in rice. EMBO J. 10: 1803-1808.
Takaiwa, F. and K. Oono, 1990. Interaction of an immature seed-specific trans-acting factor with the 5' upstream region of a rice glutelin gene. Mol. Gen. Genet. 224: 289-293.
Takaiwa, F., S. Kikuchi and K. Oono, 1990. The complete nucleotide sequence of the intergenic spacer between 25S and 17S rDNAs in rice. Plant Mol. Biol. 15: 933-935.
Takaiwa, F., K. Oono and A. Kato, 1991. Analysis of the 5' flanking region responsible for the endosperm-specific expression of a rice glutelin chimeric gene in transgenic tobacco. Plant Mol. Biol. 16: 49-58.
Uchimiya, H. and K. Toriyama, 1991. Transformation, molecular biology and nutritional improvement. In Biotech. in Agric. and Forestry, Y. P. S. Bajaj (ed.) 14: 415-421.
Wang, B., Y. N. Li, X. W. Zhang, L. Hun and J. Z. Wang, 1990a. Double-stranded RNA and male sterility in rice. Theor. Appl. Genet. 79: 556-560.
Wang, G., W. Wang, Y. N. Li and D. D. Li, 1990b. Some physiochemical properties of rice mitochondrial DNA. Theor. Appl. Genet. 77: 581-586.
Wang, Z. Y., Z. L. Wu, Y. Y. Axing, F. G. Zheng, X. L. Gu, W. G. Zhang and M. M. Hong, 1990c. Nucleotide sequence of rice waxy gene. Nucl. Acids Res. 18: 5898.
Wu, H. K., M. C. Chung, T. Wu, C. N. Ming and R. Wu, 1991. Localization of specific repetitive DNA sequences in individual rice chromosomes. Chromosomal100: 330-338.
Wu, R., 1991. Genetic manipulation of the rice genome by introducing cloned genes into rice. In Biological Nitrogen Fixation Associated with Rice Production, S. K. Dutta and C. Sloger (eds.), pp. 371-376.
Wu, R., E. Kemmerer and D. McElroy, 1990. Transformation and regeneration of important crop plants: rice as the model system for monocots. In Gene Manipulation in Plant Improvement II, J. P. Gustafson (ed.), pp. 251-263.
Yamaguchi-Shinozaki, K., M. Mino, J. Mundy and N.H. Chua, 1990. Analysis of an ABA- responsive rice gene promoter in transgenic tobacco. Plant Mol. Biol. 15: 905-912.
Yu, S. M., Y. S. Tai, S. Goldman, Y. J. Chu, T. M. Ou-Lee and R. Wu, 1990. Analysis of the promoter region of rice α-amylase genes. In Structure and Function of Nucleic Acids and Proteins, F. Y. H. Wu and C. W. Wu (eds), pp. 287-295.
Zhang, J. L., X. M. Lou, R. Z. Cai, R. X. Huang and M. M. Hong, 1991. Transposition of maize transposable element activator in rice. Plant Sci. 73: 191-198.
Zhu, Q. and C. J. Lamb, 1991. Isolation and characterization of a rice gene encoding a basic chitinase. Mol. Gen. Genet. 226: 289-296.