园艺学报 ›› 2008, Vol. 35 ›› Issue (7): 1069-1074.

• 研究简报 • 上一篇    下一篇


杨素丽1,2;明 军1*;刘 春1;穆 鼎1;李名扬2   

  1. (1中国农业科学院蔬菜花卉研究所,北京 100081; 2西南大学园艺园林学院,重庆 400715 )
  • 收稿日期:2008-03-25 修回日期:2008-05-23 出版日期:2008-07-25 发布日期:2008-07-25
  • 通讯作者: 明 军

Data mining for simple sequence repeats marker development in expressed sequence tags from Lilium L.

YANG Su-li1,2,MING Jun1*,LIU Chun1,MU Ding1,and LI Ming-yang2

  1. 1Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Beijing 100081,China;2College of Horticulture and Landscape,Southwest University,Chongqing 400715,China)
  • Received:2008-03-25 Revised:2008-05-23 Online:2008-07-25 Published:2008-07-25
  • Contact: MING Jun

摘要: 依据已知的百合EST(expressed sequence tags)序列信息,开发新的SSR(simple sequence repeats)标记,在NCBI的EST数据库1 688 EST中检索到98条含有101个SSR的序列, SSR的检出率为5.98%,其中三核苷酸重复类型占主导地位,出现频率为2.84%。EST-SSR的重复基元共搜索到47种,其中三核苷酸重复基元类型最为丰富,大约占重复基元类型总数的一半。利用部分EST-SSRs序列共设计23对SSR引物, 以铁炮百合‘Snow Queen' DNA为模板,对引物进行筛选,其中18对引物有扩增产物,占所设计引物总数的78.26%;进一步用这些引物在5个杂种系列13个百合品种进行多态性测试,显示多态性的引物占可扩增引物的66.7%。本研究结果证明了基于百合EST信息建立SSR标记是一种有效而又可行的方法。

关键词: 百合, EST, SSR, 引物设计

Abstract: The growing availability of EST sequences from Lilium L. provides a potential valuable source of new SSR markers. In this study, 101 SSR-ESTs from 1688 ESTs in the National Center for Biotechnology Information (NCBI) database, representing 5.98% of the total number of ESTs were identified .Among them, the trinucleotide repeat is the dominant type with repeat motifs being the most common, accounting for 2.84% of ESTs. 47 kinds of repeat motifs were mined out from all SSRs. 23 SSR primers were designed to sequence flanking SSRs, the primer pairs designed were screened against genomic DNA of‘Snow Queen’from which most EST-SSRs were derived, and 18 primer pairs showed the amplification, accounting for 78.26% of total primers. Then the primers showing amplification were subjected to PCR for DNA from 13 Lilium L. cultivars of 5 hybridism series and 12 primer pairs showed polymorphisms, accounting for 66.7% of primers available. Results prove that it is an effective and feasible approach to develop SSR markers based on ESTs in Lilium L.

Key words: Lilium L., EST(expressed sequence tags), SSR (simple sequence repeats), primer design