Development of Rice Variety Identification System using Single Nucleotide Polymorphic Markers

• Main Authors: Chia-Lin Chou, 周佳霖
• Other Authors: 胡凱康
• Format: Others
• Language: zh-TW
• Published: 2015
• Online Access: http://ndltd.ncl.edu.tw/handle/69034013452847839778

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.