臺灣稉型水稻品種隨機型SNP分子標誌資料庫的建構

The Construction of Random-Type SNP Molecular Marker Database for Taiwanese Japonica Rice Varieties

陳榮坤(R. K. Chen) ； 蔡孟勳(M. H. Tsai) ； 陳凱儀(K. Y. Chen)

《臺南區農業改良場研究彙報》 61期 (2013/06) Pp. 15-28

摘要

本研究針對臺灣稉型水稻品種進行隨機型SNP分子標誌資料庫的初步開發，以應用於遺傳歧異度分析、品種鑑定、數量性狀基因座定位，及分子標誌輔助選拔等多功能使用。為開發臺灣稉型水稻之SNP分子標誌，首先比對九個臺灣稉稻品種重新定序的基因體組資料，並參考日本農業生物資源研究所（NIAS）針對日本稉稻品種所開發的隨機型SNP分子標誌，由其中挑選144個均勻散佈於水稻基因體組的SNP位點，再自臺灣各稻作育種改良場所收集共460個品種（系），包括各改良場所已育成之品種、及雜交育種通常使用的優良親本，以Illumina BeadXpress平臺鑑定該460個品種的基因型。結果共成功開發123個在稉稻品種間具有多形性之SNP分子標誌，成功率達85％；並依據研究結果，提出後續SNP分子標誌開發的策略與方法。

關鍵字

單一核苷酸多型性 ； 分子標誌 ； 稉稻

並列摘要

The objective of this project is to develop polymorphic SNP markers for Taiwanese japonica rice varieties. We expect these SNP markers can be used not only for identification of rice varieties, but also for QTL mapping as well as assistance of rice breeding. The strategy to develop SNP markers was as below: The SNP sites based on the shot-gun sequencing data of 9 Taiwanese japonica rice varieties was identified first. Then approximately equally spaced SNP sites (approximately 3 Mb per site) from the identified SNP pools was selected, including those SNPs developed by NIAS in Japan. The genotyping panel includes 460 rice varieties and elite breeding lines. We totally picked 144 SNPs (34 from NIAS) for genotyping on those 460 varieties using Illumina BeadXpress platform. The results showed that 123 SNP markers were successfully genotyped and the successful rate is approximately 85%.

並列關鍵字

Polymorphic SNP ； Molecular Marker ； Japonica Rice