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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 胡凱康 | |
dc.contributor.author | Yu-Shan Ko | en |
dc.contributor.author | 柯宇珊 | zh_TW |
dc.date.accessioned | 2021-06-16T05:35:03Z | - |
dc.date.available | 2016-08-15 | |
dc.date.copyright | 2014-08-17 | |
dc.date.issued | 2014 | |
dc.date.submitted | 2014-08-13 | |
dc.identifier.citation | 林美瑄 (2001) 臺灣種子繁殖檢查制度。兩岸種苗科技研討會專刊,頁31-35
吳東鴻 (2006) 水稻於良種繁殖制度下之遺傳變異(未出版之碩士論文)。國立臺灣大學。臺北市 張心怡 (2009) 開發適用於鑑別不同地理來源水稻品種之SSR DNA分子標誌(未出版之碩士論文)。國立臺灣大學。臺北市 行政院農業委員會農糧署統計室 (2014) 臺灣地區稻作種植、收穫面積及產量。2014年6月26日取自http://www.afa.gov.tw/Public/GrainStatistics/20144241424285334.pdf Ali, M.L., J.F. Rajewski, P.S. Baenziger, K.S. Gill, K.M. Eskridge, and I. Dweikat. 2008. Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Mol. Breeding 21: 497–509. Anderson, J.A., G. A. Churchill, J. E. Autrique, S. D. Tanksley, and M. E. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181–186. Belaj, A., Z. Satovic, G. Cipriani, L. Baldoni, R. Testolin, L. Rallo, and I. Trujillo. 2003. Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736–744. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucl. Acids Res. 27: 573–580. Beukelaer, H.D., P. Smýkal, G.F. Davenport, and V. Fack. 2012. Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search. BMC Bioinformatics 13: 312–331. Bhargava, A., and F.F. Fuentes. 2010. Mutational Dynamics of Microsatellites. Mol. Biotechnol. 44: 250–266. Bonow, S., E.V.R. Von Pinho, M.G.C. Vieira, and B. Vosman. 2009. Microsatellite Markers in and around Rice Genes: Applications in Variety Identification and DUS Testing. Crop Sci. 49: 880–886. Brownstein, M.J., J.D. Carpten, and J.R. Smith. 1996. Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. BioTechniques 20: 1004–1006, 1008–1010. Camlin, M.S. 2003. Plant cultivar identification and registration - The role for molecular techniques. Acta Hort. 625:37–47. Caramante, M., G. Corrado, L.M. Monti, and R. Rao. 2011. Simple sequence repeats are able to trace tomato cultivars in tomato food chains. Food Control 22: 549–554. Cho, Y.G., T. Ishii, S. Temnykh, X. Chen, L. Lipovich, S.R. McCouch, W.D. Park, N. Ayres, and S. Cartinhour. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100: 713–722. Cieslarová, J., P. Hanáček, E. Fialová, M. Hýbl, and P. Smýkal. 2011. Estimation of pea (Pisum sativum L.) microsatellite mutation rate based on pedigree and single-seed descent analyses. J. Appl. Genetics 52: 391–401. Collard, B.C.Y., A. Das, P.S. Virk, and D.J. Mackill. 2007. Evaluation of “quick and dirty” DNA extraction methods for marker-assisted selection in rice (Oryza sativa L.). Plant Breeding 126: 47–50. Gelfand, Y., A. Rodriguez, and G. Benson. 2007. TRDB—The Tandem Repeats Database. Nucl. Acids Res. 35: 80–87. Glenn, T.C. 2006. Directly tagging PCR primers with fluorescent dyes. Retrieved June 26, 2014, from http://itd.unair.ac.id/files/ABI/Directly%20Tagging%20PCR%20primers%20with%20fluorescent%20dyes%20for%20use%20in%20genotyping.pdf Goodman, M.C., and C.W. Stuber. 1983. Races of maize. VI. Isozyme variation among races of maize in Bolivia. Maydica 28:169–187. Gower, J.C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325–338. Hayden, M.J., T.M. Nguyen, A. Waterman, and K.J. Chalmers. 2008. Multiplex-Ready PCR: A new method for multiplexed SSR and SNP genotyping. BMC Genomics 9: 80–91. Heckenberger, M., M. Bohn, J.S. Ziegle, L.K. Joe, J.D. Hauser, M. Hutton, and A.E. Melchinger. 2002. Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. Mol. Breeding 10: 181–191. Hill, C.R., D.L. Duewer, M.C. Kline, C.J. Sprecher, R.S. McLaren, D.R. Rabbach, B.E. Krenke, M.G. Ensenberger, P.M. Fulmer, D.R. Storts, and J.M. Butler. 2011. Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 Systems. Forensic Sci. Int-Gen. 5: 269–275. Holleley, C.E., and P.G. Geerts. 2009. Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. BioTechniques 46: 511–517. Jain, S., R.K. Jain, and S.R. McCouch. 2004. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor. Appl. Genet. 109: 965–977. Jobes, D.V., D.L. Hurley, and L.B. Thien. 1995. Plant DNA Isolation: A Method to Efficiently Remove Polyphenolics, Polysaccharides, and RNA. Taxon 44: 379–386. Kwon, Y.-S., Y.-H. Oh, S.-I. Yi, H.-Y. Kim, J.-M. An, S.-G. Yang, S.-H. Ok, and J.-S. Shin. 2010. Informative SSR markers for commercial variety discrimination in watermelon (Citrullus lanatus). Genes Genom. 32: 115–122. Lin, H.-Y., Y.-P. Wu, A.-L. Hour, S.-W. Ho, F.-J. Wei, Y.-I. C.Hsing, and Y.-R. Lin. 2012. Genetic diversity of rice germplasm used in Taiwan breeding programs. Bot. Stud. 53: 363–376. McCouch, S.R., L. Teytelman, Y. Xu, K.B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, I. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware, and L. Stein. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199–207. Meglécz, E., C. Costedoat, V. Dubut, A. Gilles, T. Malausa, N. Pech, and J.-F. Martin. 2010. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26: 403–404. Nguyen, T.V., T.T.B. Doan, A.E. Leo, C.M. Bui, P.W.J. Taylor, and R. Ford. 2012. Application of Microsatellite Markers to Fingerprint and Determine the Representational Diversity within a Recently Established Elite Maize Inbred Line Breeding Program. J. Agr. Sci. 4: 258–266. Reif, J.C., A.E. Melchinger, and M. Frisch. 2005. Genetical and Mathematical Properties of Similarity and Dissimilarity Coefficients Applied in Plant Breeding and Seed Bank Management. Crop Sci. 45: 1–7. Röder, M. S., K. Wendehake, V. Korzun, G. M. N. Bredemeijer, D. Laborie, L. Bertrand, P. Isaac, S. Rendell, J. Jackson, R. J. Cooke, B. Vosman, and M. W. Ganal. 2002. Construction and analysis of a microsatellite-based database of European wheat varieties. Theor. Appl. Genet. 106:67–73. Rossi, L., G. Bindler, H. Pijnenburg, P.G. Isaac, I. Giraud-Henry, M. Mahe, C. Orvain, and F. Gadani. 2001. Potential of molecular marker analysis for variety identification in processed tobacco. Plant Var. Seeds 14: 89–101. Schoske, R., P.M. Vallone, C.M. Ruitberg, and J.M. Butler. 2003. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal. Bioanal. Chem. 375: 333–343. Singh, N., D.R. Choudhury, A.K. Singh, S. Kumar, K. Srinivasan, R.K. Tyagi, N.K. Singh, and R. Singh. 2013. Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties. PLoS ONE 8: e84136. Smýkal, P., J. Horáček, R. Dostálová, and M. Hýbl. 2008. Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers. J. Appl. Genet. 49: 155–166. Tantasawat, P., J. Trongchuen, T. Prajongjai, W. Seehalak, and Y. Jittayasothorn. 2010. Variety identification and comparative analysis of genetic diversity in yardlong bean (Vigna unguiculata spp. sesquipedalis) using morphological characters, SSR and ISSR analysis. Sci. Horitic-Amsterdam 124: 204–216. Thachuk, C., J. Crossa, J. Franco, S. Dreisigacker, M. Warburton, and G.F. Davenport. 2009. Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. BMC Bioinformatics 10: 243–255. Thomson, M.J., E.M. Septiningsih, F. Suwardjo, T.J. Santoso, T.S. Silitonga, and S.R. McCouch. 2007. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114: 559–568. Thuillet, A.-C., D. Bru, J. David, P. Roumet, S. Santoni, P. Sourdille, and T. Bataillon. 2002. Direct Estimation of Mutation Rate for 10 Microsatellite Loci in Durum Wheat, Triticum turgidum (L.) Thell. ssp durum desf. Mol. Biol. Evol. 19: 122–125. Tommasini, L., J. Batley, G. M. Arnold, R. J. Cooke, P. Donini, D. Lee, J. R. Law, C. Lowe, C. Moule, M. Trick, and K. J. Edwards. 2003. The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor. Appl. Genet. 106:1091–1101. Treuren, R. van, H. Kemp, G. Ernsting, B. Jongejans, H. Houtman, and L. Visser. 2010. Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genet. Resour. Crop. Evol. 57: 853–865. Tucker, V.C., A.J. Kirkham, and A.J. Hopwood. 2012. Forensic validation of the PowerPlex® ESI 16 STR Multiplex and comparison of performance with AmpFlSTR® SGM Plus®. Int. J. Legal. Med. 126: 345–356. UPOV-BMT. 2007. Guidelines For DNA-profiling: Molecular Marker Selection and Database Construction (“BMT Guidelines”), Geneva. UPOV. 1991. Act of 1991. International Union for the Protection of New Variety of Plants, Geneva, Switzerland. Vigourous, Y., J. S. Jaqueth, Y. Matsuoka, O. S. Smith, W. D. Beavis, J. Stephen, C. Smith, and J. Doebley. 2002. Rate and pattern of mutation at microsatellite loci in maize. Mol. Biol. Evol. 19:1251–1260. Waits, L.P., G. Luikart, and P. Taberlet. 2001. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10: 249–256. Wright, S. 1978. Evolution and the Genetics of Populations. Vol. IV. The Univ. of Chicago Press. Yada, B., P. Tukamuhabwa, B. Wanjala, D.-J. Kim, R.A. Skilton, A. Alajo, and R.O.M. Mwanga. 2010. Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers. HortScience 45: 225–230. Yoon, M.S., Q.J. Song, I.Y. Choi, J.E. Specht, D.L. Hyten, and P.B. Cregan. 2007. BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification. Theor. Appl. Genet. 114: 885–899. You, F.M., N. Huo, Y.Q. Gu, M. Luo, Y. Ma, D. Hane, G.R. Lazo, J. Dvorak, and O.D. Anderson. 2008. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9: 253–265. Ys, K., L. Jm, Y. Gb, Y. Si, K. Km, S. Eh, B. Km, P. Ek, S. Ih, and K. Bd. 2005. Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol. Cells 19: 428–435. Yu, Z., L. Li-Qiong, L. Huan, B. Jie, Y. Man-Ye, M. Chen, C. Ying-Fan, Q. Xiao-Lin, and C. Fang. 2002. RAPD markers in diversity detection and variety identification of Tibetan hulless barley. Plant Mol. Biol. Rep. 20: 369–377. Zhao, W., Chung, J.-W., Ma, K.-H., Kim, T.-S., Kim, S.-M., Shin, D.-I., Kim, C.-H., Koo, H.-M., and Park, Y.-J. 2009. Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers. Genes & Genom. 31: 283–292. Zhao, K., C.-W. Tung, G.C. Eizenga, M.H. Wright, M.L. Ali, A.H. Price, G.J. Norton, M.R. Islam, A. Reynolds, J. Mezey, A.M. McClung, C.D. Bustamante, and S.R. McCouch. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2: 467–456. Zhu, Y.-F., G.-C. Qin, J. Hu, Y. Wang, J.-C. Wang, and S.-J. Zhu. 2012. Fingerprinting and variety identification of rice (Oryza sativa L.) based on simple sequence repeat markers. Retrieved June 26, 2014, from http://search.informit.com.au/documentSummary;dn=673478355361391;res=IELHSS. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/56563 | - |
dc.description.abstract | 水稻 (Oryza sativa L.) 為臺灣地區重要的糧食作物,本研究針對水稻提供一套有效的品種純化與品種鑑別工具,以提升國內種苗純度。本研究篩選重複單位為4鹼基對的SSR分子標誌,所建立的套件包含12個SSR分子標誌,分散於12對染色體上。以4種螢光分別標定由3組分子量不同標誌所組成的次群,全部12組SSR分子標誌可於單次的多重PCR反應 (Multiplex PCR) 同步增幅,並於單次的多重毛細管電泳 (Multiplex capillary electrophoresis) 完成基因型分析。分析315個水稻種原得到12組SSR分子標誌的PIC值範圍為0.49至0.84,期望相符率 (Probability of identity) 為1.91x10-7。與以3鹼基為重複單位的SSR分子標誌相較,此套件的痕跡條帶高度明顯降低,整體螢光訊號強弱相當對平均,並未隨標誌分子量增高而有漸次遞減的情形。雖然在水稻種原具有高度的鑑別率,但由於臺灣地區稉稻品種間的高度親緣關係,此套件有18組無法區別的兩兩臺灣品種組合。本套件以12個臺灣水稻品種建立標準品種,可涵蓋53個臺灣品種96.2%的對偶基因型。 | zh_TW |
dc.description.abstract | Rice (Oryza sativa L.) is the most important food crop in Taiwan. The goal of this study is to develop a set of simple sequence repeat (SSR) markers for rice variety identification. By screening SSRs with four-nucleotide repeat units from the published rice whole genome sequence, we have successfully developed a set of 12 SSR markers that are distributed over the 12 rice chromosomes. The complete set of 12 SSR markers are arranged into 4 non-overlapping groups that are labeled with 4 different fluorophores and may be combined into a multiplex-PCR reaction and analyzed concurrently with multiplex capillary electrophoresis. A total of 315 varieties from a wide geographical area were evaluated with these 12 SSR markers, polymorphism information contents (PICs) of the markers ranged from 0.49 to 0.84. The probability of identity (PID) value for this set is 1.91x10-7. Compared with SSR markers with three-nucleotide repeat units, the set of markers developed in the study have significantly lower stutter ratio and more uniform signal strength. These 12 selected markers having high discriminatory power allow to discriminate all of Taiwan rice varieties except 18 unresolved pairs of Taiwan rice varieties with high kinship. We have also selected 12 Taiwan rice varieties as the reference varieties, which effectively cover 96.2% of the alleles of 53 Taiwan rice varieties. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T05:35:03Z (GMT). No. of bitstreams: 1 ntu-103-R01621109-1.pdf: 2960066 bytes, checksum: 5b80707c1d495a497610ffa29e053f0d (MD5) Previous issue date: 2014 | en |
dc.description.tableofcontents | 目錄
目錄 i 致謝 iii 圖目錄 iv 表目錄 v 中文摘要 vi Abstract vii 第一章 前言 1 第二章 文獻探討 4 第三章 材料與方法 9 一、植物材料 9 二、水稻DNA萃取、定量與品質檢定 9 三、SSR分子標誌設計 10 四、篩選SSR分子標誌 11 五、SSR聚合酶連鎖反應 12 六、毛細管電泳分析 12 七、定序分析 13 八、多型性訊息提供量 14 九、期望相符率 14 十、遺傳距離 15 十一、主成分分析 15 十二、架構水稻品種鑑別套件 15 十三、建立標準品種 16 第四章 結果與討論 17 一、SSR分子標誌篩選結果 17 二、SSR分子標誌缺值處理 23 三、水稻品種鑑別套件 28 四、引子交互作用與上拉問題改善 32 五、分子標誌多型性與鑑別力評估 37 六、無法區別之臺灣品種 43 七、標準品種 46 第五章 結論 47 參考文獻 48 附錄 53 附錄 1、參試水稻材料 53 附錄 2、定序引子序列 62 附錄 3、第一階段篩選結果摘要 63 附錄 4、第二階段篩選結果摘要 66 附錄 5、水稻品種權案件彙整 68 附錄 6、建立標準品種R程式碼 69 附錄 7、標準品種與對偶基因型 70 | |
dc.language.iso | zh-TW | |
dc.title | 以簡單重複序列開發水稻品種鑑別系統 | zh_TW |
dc.title | Development of an Identification System for Rice Varieties Based on Simple Sequence Repeats | en |
dc.type | Thesis | |
dc.date.schoolyear | 102-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 林彥蓉,陳凱儀,董致韡 | |
dc.subject.keyword | 品種檢查,簡單重複序列,遺傳純度, | zh_TW |
dc.subject.keyword | variety testing,simple sequence repeats,genetic purity, | en |
dc.relation.page | 70 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2014-08-13 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 農藝學研究所 | zh_TW |
顯示於系所單位: | 農藝學系 |
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