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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 陳凱儀 | |
dc.contributor.author | Tzu-Yun Huang | en |
dc.contributor.author | 黃子芸 | zh_TW |
dc.date.accessioned | 2021-06-17T04:37:10Z | - |
dc.date.available | 2020-08-09 | |
dc.date.copyright | 2018-08-09 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-08-08 | |
dc.identifier.citation | 林志忠, 楊遠波. (2009). 原生民俗植物-臺灣藜. 農業世界 307(3):15-17.
高驥. (2016). 應用雙限制酶切位點標定法定位番椒稔性恢復基因. 碩士論文.國立台灣大學農藝學系.台北,台灣. 黃子芸, and 陳振義. (2014). 臺灣藜品系蒐集及品種選育評估. 臺東區農業改良場103年試驗研究推廣成果研討會專刊, 91-101. Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., and Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet, 17(2), 81-92. Ba, H., Jia, B., Wang, G., Yang, Y., Kedem, G., and Li, C. (2017). Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing. G3 (Bethesda), 7(9), 3169-3176. Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3(10), e3376. Baxter, S. W., Davey, J. W., Johnston, J. S., Shelton, A. M., Heckel, D. G., Jiggins, C. D., et al. (2011). Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One, 6(4), e19315. Bhargava, A., Shukla, S., and Ohri, D. (2007). Genome size variation in some cultivated and wild species ofChenopodium(Chenopodiaceae). Caryologia, 60(3), 245-250. Bhargava, A., Shukla, S., and Ohri, D. (2006). Chenopodium quinoa—An Indian perspective. Industrial Crops and Products, 23(1), 73-87. Burford Reiskind, M. O., Coyle, K., Daniels, H. V., Labadie, P., Reiskind, M. H., Roberts, N. B., et al. (2016). Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa. Mol Ecol Resour, 16(6), 1303-1314. Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., and Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Mol Ecol, 22(11), 3124-3140. Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., and Postlethwait, J. H. (2011). Stacks: building and genotyping Loci de novo from short-read sequences. G3 (Bethesda), 1(3), 171-182. Christensen, S. A., Pratt, D. B., Pratt, C., Nelson, P. T., Stevens, M. R., Jellen, E. N., et al. (2007). Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant Genetic Resources: Characterization and Utilization, 5(02), 82-95. Costa Tártara, S. M., Manifesto, M. M., Bramardi, S. J., and Bertero, H. D. (2012). Genetic structure in cultivated quinoa (Chenopodium quinoa Willd.), a reflection of landscape structure in Northwest Argentina. Conservation Genetics, 13(4), 1027-1038. Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., and Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet, 12(7), 499-510. del Castillo, C., Winkel, T., Mahy, G., and Bizoux, J.-P. (2006). Genetic structure of quinoa (Chenopodium quinoa Willd.) from the Bolivian altiplano as revealed by RAPD markers. Genetic Resources and Crop Evolution, 54(4), 897-905. Dierickx, E. G., Shultz, A. J., Sato, F., Hiraoka, T., and Edwards, S. V. (2015). Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using dou ble digest RADseq: implications for conservation. Evol Appl, 8(7), 662-678. Earl, D. A., and vonHoldt, B. M. (2011). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361. Eaton, D. A. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, 30(13), 1844-1849. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 32(5), 1792-1797. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460-2461. Evanno, G., Regnaut, S., and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 14(8), 2611-2620. Fuentes, F. F., Martinez, E. A., Hinrichsen, P. V., Jellen, E. N., and Maughan, P. J. (2009). Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers. Conservation Genetics, 10(2), 369-377. Fulton, T. M., Chunwongse, J., and Tanksley, S. D. (1995). Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biology Reporter, 13(3), 207-209. Huang, H., and Knowles, L. L. (2016). Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences. Syst Biol, 65(3), 357-365. Jarvis, D. E., Ho, Y. S., Lightfoot, D. J., Schmockel, S. M., Li, B., Borm, T. J., et al. (2017). The genome of Chenopodium quinoa. Nature, 542(7641), 307-312. Mason, S. L., Stevens, M. R., Jellen, E. N., Bonifacio, A., Fairbanks, D. J., Coleman, C. E., et al. (2005). Development and Use of Microsatellite Markers for Germplasm Characterization in Quinoa ( Willd.). Crop Science, 45(4), 1618. Mastretta-Yanes, A., Arrigo, N., Alvarez, N., Jorgensen, T. H., Pinero, D., and Emerson, B. C. (2015). Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Mol Ecol Resour, 15(1), 28-41. Paris, J. R., Stevens, J. R., Catchen, J. M., and Johnston, S. (2017). Lost in parameter space: a road map for stacks. Methods in Ecology and Evolution, 8(10), 1360-1373. Parlevliet, J. E. (2006). How to maintain improved cultivars. Euphytica, 153(3), 353-362. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., and Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One, 7(5), e37135. Pritchard, J. K., Wen, X., and Falush, D. (2010). Documentation for STRUCTURE software: version 2.3. University of Chicago, Chicago, IL. Puritz, J. B., Hollenbeck, C. M., and Gold, J. R. (2014). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2, e431. Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Booth, A., et al. (2005). Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics, 274(5), 515-527. Rubin, B. E., Ree, R. H., and Moreau, C. S. (2012). Inferring phylogenies from RAD sequence data. PLoS One, 7(4), e33394. Shih, K. M., Chang, C. T., Chung, J. D., Chiang, Y. C., and Hwang, S. Y. (2018). Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana). Front Plant Sci, 9, 92. Yagi, M., Shirasawa, K., Waki, T., Kume, T., Isobe, S., Tanase, K., et al. (2016). Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (Dianthus caryophyllus L.). Plant Molecular Biology Reporter, 35(1), 110-117. Zhou, X., Xia, Y., Ren, X., Chen, Y., Huang, L., Huang, S., et al. (2014). Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics, 15(1), 351. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/70751 | - |
dc.description.abstract | 臺灣藜 (Chenopodium formosanum Koidz.) 為臺東縣重要特色雜糧作物,現有栽培種原多為原住民族部落流傳下來之地方品系,因年代久遠,品系多混雜,且相關之遺傳與育種等研究甚少。為了解種原遺傳背景及提升品種改良效率,本研究以臺東區農業改良場自2009年於臺東縣、花蓮縣及屏東縣等地蒐集的39個種原為材料,為探討臺灣藜與其他藜屬種原之關係,再加入藜麥 (Chenopodium quinoa Willd.) 種原及Chenopodium berlandieri nuttaliae種原共2個種原,總計41個種原作為試驗材料。研究方法使用雙限制酶切位點標定法 (double digest Restriction Associated DNA sequencing, ddRAD) 建立定序圖書庫,次世代定序 (Next generation sequencing, NGS) 採用Illumina HiSeq平台,定序結果以Stacks軟體進行分析,篩選出1,046個具多型性的基因座供後續族群結構、主成分分析及集群分析。種原代號98T011因定序量不足,排除於後續的分析。族群結構分析以STRUCTURE軟體進行,40個種原在K=2時,ΔK呈最高峰值,顯示K=2為最佳次族群分群數;臺灣藜種原在K=3時,ΔK呈最高峰值,顯示K=3為最佳次族群分群數。主成分分析及集群分析以R軟體進行分析,40個種原分析結果,將臺灣藜種原與其他藜屬種原 (藜麥及C. berlandieri nuttaliae) 分為兩群;臺灣藜種原分析結果則依蒐集地區分為兩大群,株型直立、黑色籽實之98T020種原的遺傳背景與其他種原差異較大,另成一群,本結果明確臺灣藜與國外藜麥之親緣關係,並可提供未來臺灣藜育種利用與種原保存策略之參考。 | zh_TW |
dc.description.abstract | Djulis (Chenopodium formosanum Koidz.) is an important specialty cereal crop in Taitung. Current cultivars are almost local lines conserved by aboriginal tribes. Due to the traditional djulis cultivation habit is remote from now, local lines are mixed by multiple lines, and the related genetics and breeding studies are also deficient. In order to understand the genetic background among djulis germplasms and improve the breeding efficiency, this study used 39 djulis accessions collected in Taitung, Hualien, and Pingtung by Taitung District Agricultural Research and Extension Station in 2009. And 2 Chenopodium genus but different species accessions from NPGRC. In total 41 accessions as the material, to understand the relationship between djulis and other Chenopodium genus.
We used double-digest RAD sequencing to build the library, and Illumina HiSeq platform for Next generation sequencing. Data was analyzed by Stacks software, resulting 1,046 polymorphic loci for genetic structure analysis, principal coordinate anlysis and cluster analysis. The sequencing quantity of 98T011 accession was not enough and was excluded from the following analysis. Genetic structure analysis was analyzed by STRUCTURE software. When K=2, 40 accessions had the maximum ΔK, indicated that K=2 was the best cluster number of subpopulation. When K=3, djulis accessions had the maximum ΔK, indicated that K=3 was the best cluster number of subpopulation. Principal coordinate anlysis and cluster analysis were analyzed by R software, the result of the 40 accessions showed that the djulis and the accessions from NPGRC were clearly divided into two groups. As for the result within the djulis accessions, djulis accessions were divided into two groups according to the region they had been collected. The genetic background of the accessions 98T020 was different from other accessions, and was classified to another groups. The result of this study confirm the relationship between djulis and quinoa, and providing the strategy for djulis breeding and germplasm conservation. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T04:37:10Z (GMT). No. of bitstreams: 1 ntu-107-R02621106-1.pdf: 2329705 bytes, checksum: e841a3ac5121a71638fce5c327a0000e (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | 口試委員會審定書 i
致謝 ii 中文摘要 iii Abstract iv 目 錄 vi 圖目錄 viii 表目錄 ix 第一章 前言 1 第二章 前人研究 2 第一節 藜麥簡介及相關遺傳歧異度研究 2 第二節 RAD及ddRAD定序技術介紹 3 第三節 RAD-seq定序資料分析方法介紹 4 第三章 材料及方法 6 第一節 試驗材料 6 第二節 基因體大小測定 10 第三節 ddRAD定序圖書庫的建構 10 1. Genomic DNA的萃取與定量 10 2. 限制酶切割 11 3. P1、P2 adapter連接酶反應 11 4. DNA 片段篩選 11 5. ddRAD定序圖書庫備製 12 第四節 ddRAD定序資料處理 12 第五節 族群結構分析 13 第四章 結果 15 第一節 基因體大小測定 15 第二節 ddRAD定序結果與SNP分子標記篩選 17 第三節 40個藜屬種原的族群結構 19 第四節 臺灣藜種原的族群結構 25 第五節 40個藜屬種原及臺灣藜種原之親緣關係 32 第五章 討論 35 第一節 ddRAD定序資料品質探討及缺值處理 35 第二節 Stacks軟體de novo分析流程參數設定 36 第三節 藜屬族群結構 38 第六章 結論 40 參考文獻 41 附錄 45 | |
dc.language.iso | zh-TW | |
dc.title | 應用雙限制酶切位點標定法進行臺灣藜種原遺傳歧異度分析 | zh_TW |
dc.title | The Analysis of Genetic Diversity of Djulis (Chenopodium formosanum Koidz.) Using Double Digest RADseq | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 胡凱康,邱春火,陳虹諺 | |
dc.subject.keyword | 臺灣藜,藜麥,種原,雙限制?切位點標定法,遺傳歧異度, | zh_TW |
dc.subject.keyword | djulis,quinoa,accession,ddRAD,genetic diversity, | en |
dc.relation.page | 48 | |
dc.identifier.doi | 10.6342/NTU201802704 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2018-08-08 | |
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 |
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