《植物生理学报》 2009, 45(1): 23-27

甘薯EST 资源的SSR 信息分析

黄立飞, 房伯平*, 陈景益, 张雄坚, 罗忠霞

广东省农业科学院作物研究所, 广州510640

通信作者：房伯平；E-mail: bpfang01@163.com；Tel: 020-85514 242)

摘　要：

从 NCBI 公共数据库下载获得 22 371 条甘薯 EST 序列, 去除低质量的和冗余的序列后, 得到总长为 5.09×103 kb 的9 204 条唯一序列。从这些序列中搜索到总共 436 个 SSR 位点, 平均相距 11.68 kb 出现一个 SSR。这些 SSR 的出现频率和平均长度分别为 4.4% 和 24.28 bp。在 2~6 bp 的重复基元中, 六核苷酸重复基元出现频率最高(30.96%), 其次是三核苷酸重复基元(29.59%)和二核苷酸重复基元(24.54%)。出现最多的重复基元是 AG/CT (16.28%), 其次是 AAG/CTT (11.01%)。

关键词：甘薯; EST-SSR; 基元

收稿：2008-09-26   修定：2008-11-11

资助：国家高技术研究发展计划(“863” 计划) (2006AA100107)、国家科技基础条件平台项目(2005DKA2100205)、广东省自然科学基金项目(8151064001000033)、广东省科技计划项目(2008B020200003)。

Analysis of SSR Information in EST Resource of Sweet Potato [Ipomoea batatas (L.) Lam]

HUANG Li-Fei, FANG Bo-Ping*, CHEN Jing-Yi, ZHANG Xiong-Jian, LUO Zhong-Xia

Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China

Corresponding author: FANG Bo-Ping; E-mail: bpfang01@163.com; Tel: 020-85514 242)

Abstract:

In this study, 22 371 ESTs of sweet potato (Ipomoea batatas) in the database of NCBI were downloaded and some redundants or with low qualities were removed, finally 9 204 unique sequences with total length about 5.09×10³ kb were obtained. In total, 436 SSRs (4.4%) containing unique sequences were identified. The overall average length of SSRs was 24.28 bp. This was equivalent to 1 SSR per 11.68 kb EST sequence. About 30.96% of the SSRs was hexanucleotides, 29.59% was trinucleotides, 24.54% was dinucleotides, and the remaining 14.91% consisted of tetra- and pentanucleotides. Among the identified SSRs, AG/CT was the most frequent (16.28%) followed by AAG/CTT at 11.01%.

Key words: sweet potato; EST-SSR; motifs