Detection of SNPs between Tainung 67 and Nipponbare Rice Cultivars

單核苷酸多型性(Single Nucleotide Polymorphisms, SNPs)被視為基因體內數量最多的變異型態。我們探用台灣優良品種台農67幼穗發育期的6千筆以上基因表現標籤(Expressed Sequence Tag, EST)為材料，估算台農67與國際水稻基因體計畫所用品種日本晴(Nipponbare)之間的多型性。估計得到台農67與日本晴間的單核苷酸多型性頻度約為0.3-0.4%，而大部分的核苷酸增減則發生在基因不轉譯的5端及3端。在鹼基置換部分，3端不轉譯區域及第三密碼子位置的異類鹼基互換較同類者多，而5端不轉譯區域及第一密碼子位置的情況相反。同時也計算同類置換與非同意置換計算演化距離。由於單核苷酸多型性通常比一般傳統分子標記之密度較高，對於像台農67及日本晴這樣的近源品種，偵測其單核苷酸多型性並依此設計分子標記將有助於進一步對遺傳圖譜或基因定位研究探討。

關鍵字

基因表現標籤；日本晴；水稻註解計畫資料庫；水稻；單核苷酸多型性；台農67

並列摘要

Single nucleotide polymorphisms (SNPs) are known as the most detectable variations among related genomes. We estimated the SNPs between Tainung 67 (TNG67), an elite cultivar of rice (Oryza sativa) in Taiwan, and Nipponbare, the cultivar used for rice genome sequencing by the international consortium. More than 6,000 expressed sequence tag (EST) sequences from developing panicles of TNG67 were compared with the annotated gene sequences of Nipponbare. The estimated SNP rate is about 0.3% to 0.4% between the two cultivars, with most of the insertions or deletions (indels) occurring on the 5' or 3' untranslated regions (UTRs). The rate of transition substitutions on the 3' UTR and the third codon positions is higher than that of transversions but lower on 5' UTR and first codon positions. The synonymous (Ks) and non-synonymous (Ka) substitution distances are also calculated, and most of the Ka/Ks ratios are less than 1. Because the SNP density is higher than that of other traditional markers, detection of SNPs in this report with subsequent development of markers will allow genetic mapping and positional cloning between TNG67 and Nipponbare.

並列關鍵字

Expressed sequence tag EST ； Nipponbare ； RAP-DB ； Rice ； Single-nucleotide polymorphisms SNP ； TNG67

國際替代計量

Detection of SNPs between Tainung 67 and Nipponbare Rice Cultivars

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