請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88734完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 伊藤剛 | zh_TW |
| dc.contributor.advisor | Takeshi Itoh | en |
| dc.contributor.author | Phong Ngoc Hai Trieu | zh_TW |
| dc.contributor.author | Ngoc Hai Trieu Phong | en |
| dc.date.accessioned | 2023-08-15T17:34:09Z | - |
| dc.date.available | 2023-11-09 | - |
| dc.date.copyright | 2023-08-15 | - |
| dc.date.issued | 2023 | - |
| dc.date.submitted | 2023-08-07 | - |
| dc.identifier.citation | Alexander, D.H., Novembre, J. and Lange, K. (2009) ‘Fast model-based estimation of ancestry in unrelated individuals’, Genome Research, 19(9), pp. 1655–1664. Available at: https://doi.org/10.1101/gr.094052.109.
Barker, R. (1985) The rice economy of Asia / Randolph Barker, Robert W. Herdt, with Beth Rose. Washington, D.C: Resources for the Future. Barker, R. (2011) ‘The Origin and Spread of Early-Ripening Champa Rice: It’s Impact on Song Dynasty China’, Rice, 4(3), pp. 184–186. Available at: https://doi.org/10.1007/s12284-011-9079-6. Bolger, A.M., Lohse, M. and Usadel, B. (2014) ‘Trimmomatic: a flexible trimmer for Illumina sequence data’, Bioinformatics, 30(15), pp. 2114–2120. Available at: https://doi.org/10.1093/bioinformatics/btu170. Bray, F. (1994) The Rice Economies: Technology and Development in Asian Societies. Bryant, D. and Moulton, V. (2004) ‘Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks’, Molecular Biology and Evolution, 21(2), pp. 255–265. Available at: https://doi.org/10.1093/molbev/msh018. Bulliet, R. et al. (2010) The Earth and Its Peoples. Cengage Learning. ‘Các giống lúa trồng ở VN từ thời nguyên thủy đến hiện đại | Tập San Việt Học’ (no date). Available at: http://viethocjournal.com/2019/12/cac-giong-lua-trong-o-vn-tu-thoi-nguyen-thuy-den-hien-dai/ (Accessed: 3 July 2023). Chang, T.-T. and Bunting, A.H. (1976) ‘The Rice Cultures [and Discussion]’, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 275(936), pp. 143–157. Cheng, C. et al. (2003) ‘Polyphyletic Origin of Cultivated Rice: Based on the Interspersion Pattern of SINEs’, Molecular Biology and Evolution, 20(1), pp. 67–75. Available at: https://doi.org/10.1093/molbev/msg004. Choi, J.Y. et al. (2017) ‘The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice’, Molecular Biology and Evolution, 34(4), pp. 969–979. Available at: https://doi.org/10.1093/molbev/msx049. Choi, J.Y. et al. (2020) ‘Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice’, Genome Biology, 21(1), p. 21. Available at: https://doi.org/10.1186/s13059-020-1938-2. Civáň, P. et al. (2015) ‘Three geographically separate domestications of Asian rice’, Nature plants, 1, p. 15164. Available at: https://doi.org/10.1038/nplants.2015.164. Civáň, P. et al. (2019) ‘Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent’, Genome Biology and Evolution, 11(3), pp. 832–843. Available at: https://doi.org/10.1093/gbe/evz039. Collins, R.L. et al. (2020) ‘A structural variation reference for medical and population genetics’, Nature, 581(7809), pp. 444–451. Available at: https://doi.org/10.1038/s41586-020-2287-8. Cullen, L.M. (2003) A History of Japan, 1582–1941: Internal and External Worlds. Cambridge: Cambridge University Press. Available at: https://doi.org/10.1017/CBO9780511606557. Danecek, P. et al. (2021) ‘Twelve years of SAMtools and BCFtools’, GigaScience, 10(2), p. giab008. Available at: https://doi.org/10.1093/gigascience/giab008. Daniel H. Huson, D.B. (2021) ‘SplitsTree5’, Github [Preprint]. Available at: https://github.com/husonlab/splitstree5. Das, S. and Khanda, C. (2020) ‘Origin and evolution of aus type fragrant rice (Oryza sativa L.) : A review’, Oryza-An International Journal on Rice, 57, pp. 169–180. Available at: https://doi.org/10.35709/ory.2020.57.3.1. Đỗ, T.G. et al. (2017) ‘Champa Citadels: An Archaeological and Historical Study’, Asian Review of World Histories, 5(2), pp. 70–105. Available at: https://doi.org/10.1163/22879811-12340006. Dunna, V. and Roy, B. (2013) ‘Rice (Oryza sativa L.)’, in, p. 52. Ebana, K. et al. (2008) ‘Development of mini core collection of Japanese rice landrace’, Breeding Science, 58(3), pp. 281–291. Available at: https://doi.org/10.1270/jsbbs.58.281. Ewels, P. et al. (2016) ‘MultiQC: summarize analysis results for multiple tools and samples in a single report’, Bioinformatics, 32(19), pp. 3047–3048. Available at: https://doi.org/10.1093/bioinformatics/btw354. Farris, W.W. (2006) Japan’s Medieval Population: Famine, Fertility, and Warfare in a Transformative Age, Japan’s Medieval Population. University of Hawaii Press. Available at: https://doi.org/10.1515/9780824841591. Farris, W.W. (2009) ‘The Revival of Growth, 1280–1450’, in W.W. Farris (ed.) Japan to 1600: A Social and Economic History. University of Hawai’i Press, p. 0. Available at: https://doi.org/10.21313/hawaii/9780824833251.003.0006. Fujio, S. (2021) ‘Early Grain Cultivation and Starting Processes in the Japanese Archipelago’, Quaternary, 4, p. 3. Available at: https://doi.org/10.3390/quat4010003. Giang, D.T. (2016) ‘Diplomacy, Trade and Networks: Champa in the Asian Commercial Context (7th-10th Centuries)’, Moussons. Recherche en sciences humaines sur l’Asie du Sud-Est, (27), pp. 59–82. Gross, B.L. and Zhao, Z. (2014) ‘Archaeological and genetic insights into the origins of domesticated rice’, Proceedings of the National Academy of Sciences, 111(17), pp. 6190–6197. Available at: https://doi.org/10.1073/pnas.1308942110. d’Alpoim Guedes, J., Jin, G. and Bocinsky, R.K. (2015) ‘The Impact of Climate on the Spread of Rice to North-Eastern China: A New Look at the Data from Shandong Province’, PLoS ONE, 10(6), p. e0130430. Available at: https://doi.org/10.1371/journal.pone.0130430. Gutaker, R.M. et al. (2020) ‘Genomic history and ecology of the geographic spread of rice’, Nature Plants, 6(5), pp. 492–502. Available at: https://doi.org/10.1038/s41477-020-0659-6. Hall, R.B. (1934) ‘Agricultural Regions of Asia. Part VII--The Japanese Empire’, Economic Geography, 10(4), pp. 323–347. Available at: https://doi.org/10.2307/140659. Higgins, J. et al. (2021) ‘Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam’, Rice, 14, p. 52. Available at: https://doi.org/10.1186/s12284-021-00481-0. Huang, X. et al. (2012) ‘A map of rice genome variation reveals the origin of cultivated rice’, Nature, 490(7421), pp. 497–501. Available at: https://doi.org/10.1038/nature11532. Kawahara, Y. et al. (2013) ‘Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data’, Rice (New York, N.Y.), 6(1), p. 4. Available at: https://doi.org/10.1186/1939-8433-6-4. Koizumi, T., Gay, S.H. and Furuhashi, G. (2021) Reviewing Indica and Japonica rice market developments. Paris: OECD. Available at: https://doi.org/10.1787/0c500e05-en. Kozlov, A.M. et al. (2019) ‘RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference’, Bioinformatics, 35(21), pp. 4453–4455. Available at: https://doi.org/10.1093/bioinformatics/btz305. Li, H. (2013) ‘Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM’. arXiv. Available at: https://doi.org/10.48550/arXiv.1303.3997. Li, J.-Y., Wang, J. and Zeigler, R.S. (2014) ‘The 3,000 rice genomes project: new opportunities and challenges for future rice research’, GigaScience, 3(1), pp. 2047-217X-3–8. Available at: https://doi.org/10.1186/2047-217X-3-8. Liu, H., Li, Q. and Xing, Y. (2018) ‘Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion’, Genes, 9(10), p. 489. Available at: https://doi.org/10.3390/genes9100489. Lu, Y., Xu, Y. and Li, N. (2022) ‘Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies’, Rice, 15(1), p. 11. Available at: https://doi.org/10.1186/s12284-022-00556-6. Macrae, S. (2016) ‘Agricultural Strategies Amongst the Charter States of the Cham and Dai Viet A Study of the Adaptive Cycle and Spatial Resilience’, Trent University Occasional Papers in Anthropology, 18, pp. 82–104. Momoki, S. (1996) ‘A Short Introduction to Champa Studies’, 重点領域研究総合的地域研究成果報告書シリーズ : 総合的地域研究の手法確立 : 世界と地域の共存のパラダイムを求めて, 30, pp. 35–42. Moska, W. (2022) ‘Champa Kingdom towers as a tourist attraction in Vietnam. Historical, geographical and architectural aspects’, Wydawnictwo Uniwersytetu Gdańskiego, 12(4), pp. 52–64. Available at: https://doi.org/10.26881/jpgs.2022.4.06. Oikawa, T. et al. (2015) ‘The Birth of a Black Rice Gene and Its Local Spread by Introgression’, The Plant Cell, 27(9), pp. 2401–2414. Available at: https://doi.org/10.1105/tpc.15.00310. Ortiz, E.M (2019) ‘vcf2phylip v2.0’. Available at: https://doi.org/10.5281/zenodo.2540861. Peng, B. et al. (2021) ‘Detection and Analysis of Rice Quality of Yunnan Purple Rice Seed Resources’, Journal of Plant Sciences, 9(3), p. 84. Available at: https://doi.org/10.11648/j.jps.20210903.13. Picard Tools - By Broad Institute (2019). Available at: https://broadinstitute.github.io/picard/ (Accessed: 30 March 2023). Ronald A. Edwards (no date). Available at: http://www.ronaldaedwards.com/index.html (Accessed: 3 July 2023). Shaun Purcell, C.C. (2019) PLINK 1.9. Available at: https://www.cog-genomics.org/plink/1.9/data#set_missing_var_ids (Accessed: 15 June 2023). Song, S. et al. (2018) ‘Rice Genomics: over the Past Two Decades and into the Future’, Genomics, Proteomics & Bioinformatics, 16(6), pp. 397–404. Available at: https://doi.org/10.1016/j.gpb.2019.01.001. Sweeney, M.T. et al. (2007) ‘Global Dissemination of a Single Mutation Conferring White Pericarp in Rice’, PLOS Genetics, 3(8), p. e133. Available at: https://doi.org/10.1371/journal.pgen.0030133. Tamura, K., Stecher, G. and Kumar, S. (2021) ‘MEGA11: Molecular Evolutionary Genetics Analysis Version 11’, Molecular Biology and Evolution, 38(7), pp. 3022–3027. Available at: https://doi.org/10.1093/molbev/msab120. Tanaka, Nobuhiro et al. (2020) ‘Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing’, Plant and Cell Physiology, 61(12), pp. 2087–2096. Available at: https://doi.org/10.1093/pcp/pcaa125. Tanaka, N et al. (2020) ‘Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies’, Plant and Cell Physiology, 61(5), pp. 922–932. Available at: https://doi.org/10.1093/pcp/pcaa019. Việt ~ Lược Sử Tộc (2021) ‘530. ☀ Lúa chiêm và vấn đề trồng lúa của người Việt’, Lược Sử Tộc Việt, 5 May. Available at: https://luocsutocviet.com/2021/05/05/530-lua-chiem-va-van-de-trong-lua-cua-nguoi-viet/ (Accessed: 3 July 2023). Wang, W. et al. (2018) ‘Genomic variation in 3,010 diverse accessions of Asian cultivated rice’, Nature, 557(7703), pp. 43–49. Available at: https://doi.org/10.1038/s41586-018-0063-9. Wang, X. et al. (2022) ‘Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding’, Journal of Advanced Research, 42, pp. 1–16. Available at: https://doi.org/10.1016/j.jare.2022.08.004. Wickham, H. (2009) ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer. Available at: https://doi.org/10.1007/978-0-387-98141-3. Wickham, H. et al. (2019) ‘Welcome to the Tidyverse’, Journal of Open Source Software, 4(43), p. 1686. Available at: https://doi.org/10.21105/joss.01686. Wu, C.-C. et al. (2020) Impact of the early-ripening Champa rice – Are they aus? preprint. In Review. Available at: https://doi.org/10.21203/rs.3.rs-76113/v1. Yu, G. et al. (2017) ‘ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data’, Methods in Ecology and Evolution, 8(1), pp. 28–36. Available at: https://doi.org/10.1111/2041-210X.12628. Zhao, Q. et al. (2018) ‘Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice’, Nature Genetics, 50(2), pp. 278–284. Available at: https://doi.org/10.1038/s41588-018-0041-z. | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88734 | - |
| dc.description.abstract | None | zh_TW |
| dc.description.abstract | This study investigates the genetic diversity, population structure, and relationships among Japanese red rice accessions, as well as their counterparts from China and Vietnam, with a specific focus on Champa rice. The dataset included six Japanese landraces, seven Vietnamese rice varieties associated with the Champa Kingdom, and accessions from the 3K-RP and WRC collections. A substantial level of genetic diversity such as with 6,956,304 SNP variants was detected in the dataset. Population structure analysis using various methods revealed distinct clustering patterns and three major clusters were observed: Japonica, Indica, and Aus. Within Japonica group, the red rice DRR240845_Akamai was close to Chinese accessions, and DRR240846_Akamai was close to Vietnamese accessions. Among the Indica group, both red rice varieties, DRR240828_Akamai and DRR240848_Akamai, as well as the Japanese Champa rice varieties Touboshi and Karahoushi showed a closer genetic relationship to some Chinese accessions. By incorporating some more new Vietnamese accessions into the initial dataset, this study achieved a more comprehensive representation of subpopulations. Consistent results were observed across multiple analyses. However, apparent differences were found between the Vietnamese accessions and the Japanese accessions classified as Champa rice, suggesting a potential discrepancy between them. It is speculated that the rice accessions currently recognized as Champa rice might have been derived from multiple sources. Overall, this study provides valuable insights into the genetic diversity, population structure, and potential of Champa rice in modern rice research. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-08-15T17:34:09Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2023-08-15T17:34:09Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | Acknowledgment ii
Abstract iii Table of Contents iv List of Figures vi List of Tables vii Abbreviation viii Chapter 1. Introduction 1 Overview of genetic diversity in Asian rice 1 Review of whole genome sequencing and its application to genetic diversity analysis 3 Champa Rice 5 Champa Rice in Japan 9 The potential of colored rice in rice breeding 14 Research objectives 16 Chapter 2. Materials and Methods 17 2.1 Material 17 2.2 Methods 22 2.2.1 Data collection 22 2.2.2 Data processing 22 2.2.3 Analysis of population structure, and phylogenetic relationships 23 2.2.4 Extraction of gene sequences 26 Chapter 3. Results 27 Overview of sequencing and data quality control 27 Variants detection 28 Principal component analysis 29 ADMIXTURE 31 Phylogenetic tree 34 Neighbor-Net network 38 Gene phylogenetic trees 41 Expanding the dataset 44 Chapter 4. Discussion 52 Dataset 52 The SNPs detection workflow 52 Population structure 53 Potential in breeding programs and conversation of Champa rice 59 Chapter 5. Conclusion and Perspective 60 References 62 | - |
| dc.language.iso | en | - |
| dc.subject | None | zh_TW |
| dc.subject | Champa rice | en |
| dc.subject | genetic diversity | en |
| dc.subject | Japanese red rice | en |
| dc.subject | SNPs | en |
| dc.title | Genetic Diversity Analysis of Japanese Champa Rice on The Basis of Whole genome Sequence Data | zh_TW |
| dc.title | Genetic Diversity Analysis of Japanese Champa Rice on The Basis of Whole genome Sequence Data | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 111-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 董致韡;熊谷 真彦 | zh_TW |
| dc.contributor.oralexamcommittee | Chih-Wei Tung;Kumagai Masahiko | en |
| dc.subject.keyword | None, | zh_TW |
| dc.subject.keyword | Champa rice,Japanese red rice,genetic diversity,SNPs, | en |
| dc.relation.page | 66 | - |
| dc.identifier.doi | 10.6342/NTU202302533 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2023-08-08 | - |
| dc.contributor.author-college | 國際學院 | - |
| dc.contributor.author-dept | 全球農業科技與基因體科學碩士學位學程 | - |
| 顯示於系所單位： | 全球農業科技與基因體科學碩士學位學程 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-111-2.pdf 授權僅限NTU校內IP使用（校園外請利用VPN校外連線服務） | 12.01 MB | Adobe PDF |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。