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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88734Full metadata record
| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| 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 | - |
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| 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.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 | - |
| Appears in Collections: | 全球農業科技與基因體科學碩士學位學程 | |
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| ntu-111-2.pdf Access limited in NTU ip range | 12.01 MB | Adobe PDF | View/Open |
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