Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers
碩士 === 國立臺灣大學 === 農藝學研究所 === 103 === The goal of this study is to develop a set of single nucleotide polymorphism (SNP) markers for identification of Taiwan rice varieties. At first, 130 candidate SNP were selected based on call rates, SNP types, allele positions and minor allele frequency (MAF) fro...
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ndltd-TW-103NTU054170192016-11-19T04:09:54Z http://ndltd.ncl.edu.tw/handle/69034013452847839778 Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers 開發水稻之單一核苷酸多型性品種鑑別系統 Chia-Lin Chou 周佳霖 碩士 國立臺灣大學 農藝學研究所 103 The goal of this study is to develop a set of single nucleotide polymorphism (SNP) markers for identification of Taiwan rice varieties. At first, 130 candidate SNP were selected based on call rates, SNP types, allele positions and minor allele frequency (MAF) from 35,746 SNP datasets which derived from 413 rice varieties analyzed by rice 44K SNP microarray chip. By laboratory analysis around 130 SNP and 8 genetically distinct japonica Taiwan rice varieties, we narrowed down the candidate SNP into 47 SNP loci. After genotyping 49 rice varieties with these 47 SNP markers, we found that a selected set of 10 SNP markers was capable to distinguish 1,173 pairs out of total 1,176 variety pairs except 3 pairs of closly related varieties, ‘TN16’/‘Koshihikari’, ‘TT30’/‘TT33’ and ‘TCSG1’/‘TCSG2’. The average of polymorphism information contents (PICs) is 0.402 for the selected set. We also selected 3 varieties as reference varieties that they have largest genetic distance within 49 Taiwan rice varieties and all without protect by Plant Variety Right. The reference varieties cover 100% of the alleles of 49 rice varieties used in this study. 胡凱康 2015 學位論文 ; thesis 59 zh-TW |
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碩士 === 國立臺灣大學 === 農藝學研究所 === 103 === The goal of this study is to develop a set of single nucleotide polymorphism (SNP) markers for identification of Taiwan rice varieties. At first, 130 candidate SNP were selected based on call rates, SNP types, allele positions and minor allele frequency (MAF) from 35,746 SNP datasets which derived from 413 rice varieties analyzed by rice 44K SNP microarray chip. By laboratory analysis around 130 SNP and 8 genetically distinct japonica Taiwan rice varieties, we narrowed down the candidate SNP into 47 SNP loci. After genotyping 49 rice varieties with these 47 SNP markers, we found that a selected set of 10 SNP markers was capable to distinguish 1,173 pairs out of total 1,176 variety pairs except 3 pairs of closly related varieties, ‘TN16’/‘Koshihikari’, ‘TT30’/‘TT33’ and ‘TCSG1’/‘TCSG2’. The average of polymorphism information contents (PICs) is 0.402 for the selected set. We also selected 3 varieties as reference varieties that they have largest genetic distance within 49 Taiwan rice varieties and all without protect by Plant Variety Right. The reference varieties cover 100% of the alleles of 49 rice varieties used in this study.
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author2 |
胡凱康 |
author_facet |
胡凱康 Chia-Lin Chou 周佳霖 |
author |
Chia-Lin Chou 周佳霖 |
spellingShingle |
Chia-Lin Chou 周佳霖 Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
author_sort |
Chia-Lin Chou |
title |
Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
title_short |
Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
title_full |
Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
title_fullStr |
Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
title_full_unstemmed |
Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers |
title_sort |
development of rice variety identification system using single nucleotide polymorphic markers |
publishDate |
2015 |
url |
http://ndltd.ncl.edu.tw/handle/69034013452847839778 |
work_keys_str_mv |
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1718395051644551168 |