Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/89497
標題: Study on the relationship between waxy mutant and transposition of transposon Pong of TNG67 rice variety
水稻台農67號糯性突變體與轉位子Pong轉位 關係之探討
作者: 田妮可
Ni-Ke Tien
關鍵字: transposon Pong;waxy mutant;轉位子Pong;糯性突變體
引用: 周琪英。2002。利用差異表現法自水稻突變體篩選抗褐飛蝨相關基因。國立中興大學農藝研究所碩士論文。台中。 林玫珠。1998。水稻台農67號疊氮化鈉誘變後代突變性狀之鑑定及稻胚特異基因突變體之篩選。國立中興大學農藝研究所碩士論文。台中。 陳治官、黃真生。1984。疊氮化鈉對水稻台農67號之誘變效應。中華農業研究33: 345-353。 許育嘉。2010。水稻台農67號疊氮化鈉突變體與轉位子活化及轉位關係之研究。國立中興大學農藝研究所博士論文。台中。 劉志偉。2012。糯性水稻蛋白質體分析與質譜鑑定磷酸化胜肽技術之改進。國立中興大學分子生物學研究所博士論文。台中。 An, X.L., Y.L. Cai, J.G. Wang, G.Q. Wang, and H.Y. Sun. 2003. Chemical mutagen and its application in plant breeding. Acta Agriculturae Nucleatae sinica 17: 239-242. Arenaz, P., R.A. Nilan, and A. Kleinhofs. 1983. Lack of induction of single-strand breaks in mammalian cells by sodium azide and its proximal mutagen. Mutat. Res. 116: 423-9. Bennetzen, J.L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269. Barker, R.F., D.V. Thompson, D.R. Talbot, J. Swanson, and J.L. Bennetzen. 1984. Nucleotide sequence of the maize transposable element Mul. Nucleic Acids Res. 12: 5955-5967. Bie'mont, C. and C. Vieira. 2006. Junk DNA as an evolutionary force. Nature 443: 521-524. Chung, C.T., S.L. Niemela, and R.H. Miller. 1989. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. USA 86: 2172-2175. Casacuberta, J.M., and N. Santiago. 2003. Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311: 1-11. Druka, A., D. Kudrna, N. Rostoks, R. Brueggeman, D. von Wettstein, and A. Kleinhofs. 2003. Chalcone isomerase gene from rice (Oryza sativa) and barley (Hordeum vulgare): physical, genetic and mutation mapping. Gene 302: 171-8. Delseny, M., J. Salses, R. Cooke, C. Sallaud, F. Regad, P. Lagoda, E. Guiderdoni, M. Ventelon, C. Brugidou and A. Ghesquiere. 2001. Rice genomics: present and future. Plant Physiol. Biochem. 39: 323-334. Dellaporta, S.L., J. Wood, and J.B. Hicks. 1983. A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1: 19-21. Feschotte, C. 2008. Transposable elements and the evolution of regulatory networks. Nature 9: 397-405. Federoff, N.V. 1989. Maize transposable elements. In Mobile DNA, pp. 375-411. American Society for Microbiology, Washington , D. C. Feschotte, C., N. Jiang, and S.R. Wessler. 2002. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329-341. Finnegan, E.J., and K.A. Kovac. 2000. Plant DNA methyltransferases. Plant Mol. Biol. 43: 189-201. Finnegan, E.J., W.J. Peacock, and E.S. Dennis. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93: 8449-54. Feinberg A.P., B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Analytical biochemistry, Academic Press 132: 6-13. Goff, S.A., D. Ricke, T.H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, D. Hadley, D. Hutchison, C. Martin, F. Katagiri, B.M. Lange, T. Moughamer, Y. Xia, P. Budworth, J. Zhong, T. Miguel, U. Paszkowski, S. Zhang, M. Colbert, W.L. Sun, L. Chen, B. Cooper, S. Park, T.C. Wood, L. Mao, P. Quail, R. Wing, R. Dean, Y. Yu, A. Zharkikh, R. Shen, S. Sahasrabudhe, A. Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, J. Mitchell, G. Eldredge, T. Scholl, R.M. Miller, S. Bhatnagar, N. Adey, T. Rubano, N. Tusneem, R. Robinson, J. Feldhaus, T. Macalma, A. Oliphant, and S. Briggs. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. Greco, R., P.B. Ouwerkerk, R.J. D. Kam, C. Sallaud, C. Favalli, L. Colombo, E. Guiderdoni, A.H. Meijer, J.H. Hoge Dagger, and A. Pereira. 2003. Transpositional behaviour of an Ac/Ds system for reverse genetics in rice. Theor. Appl. Genet. 108: 10-24. Gierl, A., and H. Saedler. 1989. The En/Spm transposable element of Zea mays. Plant Mol. Biol. 13: 261-266. Hirochika, H., E. Guiderdoni, and G. An. 2004. Rice mutant resources for gene discovery. Plant Mol. Biol. 54: 325-334. Hori, Y., R. Fujimoto, Y. Sato, T. Nishio. 2007. A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice (Oryza sativa). Theor Appl Genet 115: 217-224. Hirochika, H., H. Okamoto, and T. Kakutani. 2000. Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12: 357-69. Harushima, Y., M. Yano, A. Shomura, M. Sato, T. Shimano, Y. Kuboki, T. Yamamoto, S.Y. Lin, B.A. Antonio, A. Parco, H. Kajiya, N. Huang, K. Yamamoto, Y. Nagamura, N. Kurata, G.S. Khush, and T. Sasaki. 1998. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494. Ito, Y., M. Eiguchi, and N. Kurata. 2004. Establishment of an enhancer trap system with Ds and GUS for functional genomics in rice. Mol. Gen. Genom. 271: 639-650. Jeddeloh, J.A., J. Bender, and E.J. Richards. 1998. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12: 1714-25. Jiang, N., C. Feschotte, X. Zhang, and S.R. Wessler. 2004. Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs). Curr. Opin. Plant Biol. 7: 115-119. Jeng, T.L., S.Y. Lin, T. H. Tseng, C.S. Wang. 2008. Screen of starch mutants from a rice mutation pool of Tainung 67 rice variety: 2. Starch biosynthetic enzyme mutants. J. Agri.&For.: 57: 111-122. Jeon J.S., N. Ryoo, T.R. Hahn, H. Walia, and Y. Nakamura. 2010. Plant Physiology and Biochemistry 48: 383-392. Jeng T.L., T.H. Tseng, C.S. Wang, C.L. Chen, J.M. Sung. 2003. Field Starch biosynthesizing enzymes in developing grains of rice cultivar Tainung 67 and its sodium azide-induced rice mutant. Crops Research 84: 261-269. Jeng, T.L., C. S. Wang, T. H. Tseng, M. T. Wu, J. M. Sung. 2009. Nucleotide polymorphisms in the waxy gene of NaN3-induced waxy rice mutants. Journal of Cereal Science 49: 112-116. Keiko, H., and Y. Hitoshi. 2009. Refunctionalization of the ancient rice 4blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter. Plant J. 57: 413-425. Kenji F., S. Hiroshi, and K. Tadahiko. 2005. Identification of an active transposon in intact rice plants. Mol. Gen. Genomics. 273: 150-157. Kidwell, M.G. and D. Lisch. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 9: 7704-7711. Kidwell, M. G. and D. Lisch. 2000. Transposable elements and host genome evolution. Trends Ecol. Evol. 15: 95-99. Konzak, C.F., M. Niknejad, I. Wickham, and E. Donaldson. 1975. Mutagenic interaction of sodium azide on mutations induced in barley seeds treated with diethyl sulfate or N-methyl N'-introsourea mutation Res. 30: 55-62. Kim C.M., H.L. Piao, S.J. Park, N.S. Chon, B.I. Je, B. Sun, S.H. Park, J.Y. Park, E.J. Lee, M.J. Kim, W.S. Chung, K.H. Lee, Y.S. Lee, J.J. Lee, Y.J. Won , G. Yi, M.H. Nam, Y.S. Cha, D.W. Yun, M.Y. Eun and C.D. Han. 2004. Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J. 39:252-263. Kolesnik, T., I. Szeverenyi, D. Bachmann, C.S. Kumar, S. Jiang, R. Ramamoorthy, M. Cai, Z.G. Ma, V. Sundaresan, and S. Ramachandran. 2004. Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J. 37: 301-14. Komatsu, M., K. Shimamoto and J. Kyozuka. 2003. Two-step regulation and continuous retrotransposition of the rice LINE type retrotransposon Karma. Plant Cell 15: 1934-1944. Kikuchi S., K. Satoh , T. Nagata, N. Kawagashira, K. Doi, N. Kishimoto, J. Yazaki, M. Ishikawa, and H. Yamada. 2003. Collection, mapping, and annotation of over 28000 cDNA clones from japonica rice. Science 301: 376-379. Kunze, R., and C.F. Weil. 2002. The hAT and CACTA super families of plant transposons. In Mobile DNA II, pp. 565-610. American Society for Microbiology, Washington , D. C. Li, W.C. 1988. Mutagenic effects of ethylmethanesulfonate (EMS), Sodium-azide (SA) and combining both chemical treatments in soybean seeds. J. Agriculture Forestry 37: 107-112. Liu, B., and J.F. Wendel. 2000. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43: 874-80. McCarty, D. R. 1986. A simple method for extraction of DNA from maize tissue. Maize Genet. Crop Newsl. 60: 61. Mohd, R. W. and S. Khan. 2006. Estimates of genetic variability in mutated populations and the scope of selection for yield attributes in Vigna radiata (L.) Wilczek. Egyptian J. of Biol. 8: 1-6. Nakazaki, T., Y. Okumoto, A. Horibata, S. Yamahira, M. Teraishi, H. Nishida, H. Inoue and T. Tanisaka. 2003. Mobilization of a transposon in the rice genome. Nature 421: 170-172. Olsen, O., X. Wang, and D. von Wettstein. 1993. Sodium azide mutagenesis: preferential generation of A.T-->G.C transitions in the barley Ant18 gene. Proc. Natl. Acad. Sci. USA 90: 8043-8047. Rossi, M., P.G. Araujo, and M.V. Sluys. 2001. Survey of transposable elements in sugarcane expressed sequence tags (ESTs). Genet. Mol. Biol. 24: 147-154. Ramachandran, S. and V. Sundaresan. 2001. Transposons as tools for function genomics. Plant Physiol. Biochem. 39: 243-252. Sun M.M., S.E. Abdula, H.J. Lee, Y.C. Cho, L.Z. Han, H.J. Koh and Y.G.Cho. 2011. Molecular aspect of good eating quality formation in Japonica rice. PloS. one 6: 183-185. Stokes, T.L., B.N. Kunkel and E.J. Richards. 2002. Epigenetic variation in Arabidopsis disease resistance. Genes Dev. 16: 171–182. Song, W., Z.Z. Liu, J.T. Chen, L.Y. Zhu, Y.Q. Huang, and S.M. Chi. 2003. Application of induced mutation technology on plant breeding. J. Agricu. University Hebei. 26: 116-119. Shan, X. Z. Liu, Z. Dong, Y. Wang, Y. Chen, X. Lin, L. Long, F. Han, Y. Dong, and B. Liu. 2005. Mobilization of the active MITE transposons mPing and Pong in Rice by introgression from wild rice(Zizania latifolia Griseb). 22: 976-990. Singh, R.B., R.S.N. Pillai, and H. Kumar. 1981. Induced translocations in Safflower. Corp Sci. 21: 811-815. Till, B.J., J. Cooper, T.H. Tai, P. Colowit, E.A. Greene, S. Henikoff, and L. Comai. 2007. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 7: 19. Tsugane, K., M. Maekawa, K. Takagi, H. Takahara, Q. Qian, C. H. Eun and S. Iida. 2006. An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice. Plant J. 45: 46-57. Vicient, C.M., R. Kalendar, and A.H. Schulman. 2001. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res. 11: 2041-2049. Wilson, T.E., L.M. Topper, and P.L. Palmbos. 2003. Non-homologous end-joining: bacteria join the chromosome breakdance. TRENDS in Biochemical Sciences 28: 62-66. Wang, C.S., T.H. Tseng, and C.Y. Lin. 2002. Rice biotech research at the Taiwan Agricu. Res. Institute. APBN. 6: 950-956. Wu, J.L., C. Wu, C. Lei, M. Baraoidan, A. Bordeos, M.R. Madamba, M. Ramos-Pamplona, R. Mauleon, A. Portugal, V.J. Ulat, R. Bruskiewich, G. Wang, J. Leach, G. Khush, and H. Leung. 2005. Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol. Biol. 59: 85-97. Yu, J., S. Hu, J. Wang, G.K. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, M. Cao, J. Liu, J. Sun, J. Tang, Y. Chen, X. Huang, W. Lin, C. Ye, W. Tong, L. Cong, J. Geng, Y. Han, L. Li, W. Li, G. Hu, J. Li, Z. Liu, Q. Qi, T. Li, X. Wang, H. Lu, T. Wu, M. Zhu, P. Ni, H. Han, W. Dong, X. Ren, X. Feng, P. Cui, X. Li, H. Wang, X. Xu, W. Zhai, Z. Xu, J. Zhang, S. He, J. Xu, K. Zhang, X. Zheng, J. Dong, W. Zeng, L. Tao, J. Ye, J. Tan, X. Chen, J. He, D. Liu, W. Tian, C. Tian, H. Xia, Q. Bao, G. Li, H. Gao, T. Cao, W. Zhao, P. Li, W. Chen, Y. Zhang, J. Hu, S. Liu, J. Yang, G. Zhang, Y. Xiong, Z. Li, L. Mao, C. Zhou, Z. Zhu, R. Chen, B. Hao, W. Zheng, S. Chen, W. Guo, M. Tao, L. Zhu, L. Yuan, and H. Yang. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92. Yang, G., F. Zhang, C.N. Hancock, and S.R. Wessler. 2007. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104: 10962–10967. Zhang, X., C. Feschotte, Q. Zhang, N. Jiang, W.B. Eggleston, and S.R. Wessler. 2001. P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl. Acad. Sci. USA 98: 12572-12577. Zhou, C., Y. Yang, and A.Y. Jong. 1990. Mini-prep in ten minutes. Biotechniques 8: 172-173.
摘要: 
中文摘要

轉位子為一群大量存在於植物基因組中,會隨機在基因組中移動的基因序列,目前可以利用插入突變的方式,確認影響植株外表型的基因。轉位子Pong為DNA轉位子,其轉位方式為剪下-貼上(cut-paste),也就是Pong在基因組的轉位不會造成拷貝數的改變。疊氮化鈉(sodium azide, SA)為使水稻突變的一種有效誘變劑,水稻品種TNG67經由疊氮化鈉誘變後的M14子代中,有多個帶有特殊性狀的突變品系,其中SA0419的米粒呈現糯性(waxy)。利用南方墨點法分析台農67及SA0419,發現台農 67中的轉位子Pong有五個拷貝,而SA0419只有三個拷貝,並且在條帶的大小也發生改變。確定了各突變體基因組中Pong的拷貝數後,為瞭解Pong是否插入基因導致突變體的外表型產生改變,本論文利用基因組步行(genomic walking),自轉位子內向外擴增側邊序列,由轉位子二側的TIR(terminal inverted repeat)區域至ORF(open reading frame)區域設計引子Pong 4R及Pong 11F,擴增轉位子兩個側邊序列,結果發現,Pong的插入位置主要位在第二及第十一對染色體。突變體SA0419發現轉位子Pong插入WAX2, putative, expressed(LOC_Os02g08230)及UDP-glucoronosyl and UDP-glucosyl transferase domain containing protein, expressed (LOC_Os11g27370)基因,以下稱為Waxy2及UDPG-T基因。在糯性突變體SA0419,發現轉位子Pong插入可能影響澱粉生合成之基因,如Waxy2及UDPG-T基因,這二個基因可能會影造成直鏈澱粉及支鏈澱粉間比例的改變,使得SA0419的穀粒產生糯性外表型。在台農67及SA0419間進行南方墨點法分析轉位子Pong的插入位置,並在台農67及SA0419的F2分離族群以及台農67的SA突變庫中進行去殼糙米的透明度及碘液染色確認糯性外表型,以探討突變體是否因轉位子Pong的插入造成外表型的改變。而在台農67突變庫中利用Waxy2及UDPG-T這二個轉位子插入基因所設計的SCAR(sequence characterized amplified region)標誌引子進行PCR,發現可以準確的篩選出具有糯性外表型的突變品系,所以轉位子插入基因的SCAR標誌引子也可作為功能性分子標誌使用。未來希望可以藉由這樣的方式,發展以轉位子標定基因(transposon tagging)的系統。

Abstract

Transposon is a DNA sequence that can change its position randomly within the genome and a large number is present in plant. Insertion mutation can alter the plant phenotype hence is one of the methods used to determine the corresponding gene responsible for the phenotype. The Pong transposon is a DNA transposon that transpose through cut-and-paste mechanism and its copy number does not change in the genome. Sodium azide (SA) is an effective mutagen that can cause mutation in rice. Rice variety TNG67 was treated with sodium azide, in M14 generation, there are a number of mutant plants with specific characteristics. In this population, SA0419 was found to have waxy grain. By using Southern blot, Pong transposon is found in TNG67 and SA0419 where TNG67 has three copies while SA0419 has three copy number and changes in the band size. In order to determine whether the insertion of Pong transposon can affect the phenotype in mutant lines, genomic walking was used. At the transposon insertion site, the terminal inverted region (TIR) and open reading frame at the two sides of the transposon were used to design primer Pong 4R and Pong 11F to amplify the outward sequence at the both ends. The result found that transposon insertions are concentrated in chromosome number 2 and 11. In mutant SA0419, transposon inserts into WAX2, putative, expressed (LOC_Os02g08230) and UDP-glucoronosyl and UDP-glucosyl transferase domain containing protein, expressed (LOC_Os11g27370), also known as Waxy2 and UDPG-T gene. These two genes are responsible for starch biosynthesis, the mutation caused by transposon affects the ratio of amylose and amylopectin, caused the SA0419 to produce waxy grain. Southern blot was carried out for TNG67 and SA0419 to determine the transposon insertion site. In the F2 segregating population of TNG67/SA0419 and TNG67 SA mutant, the waxy phenotype was determine by grain transparency and iodine test. In the TNG67 mutant pool, the Sequence Characterized Amplified Region primer was designed from the transposon inserted Waxy 2 and UDPG-T genes to carry out polymerase chain reaction (PCR). These primer sets can effectively select waxy phenotype from the mutant lines, so they can be considered as functional markers. In the future, this method can be used to develop transposon tagging system.
URI: http://hdl.handle.net/11455/89497
其他識別: U0005-0502201406122300
Rights: 同意授權瀏覽/列印電子全文服務,2019-02-06起公開。
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