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

ACTA HORTICULTURAE SINICA ›› 2008, Vol. 35 ›› Issue (7): 1069-1074.

• 研究简报 • Previous Articles Next Articles

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

YANG Su-li^1,2,MING Jun^1*,LIU Chun¹,MU Ding¹,and LI Ming-yang²

（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

Abstract

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

CLC Number:

S 682.2

YANG Su-li;MING Jun;LIU Chun;MU Ding;and LI Ming-yang. Data mining for simple sequence repeats marker development in expressed sequence tags from Lilium L. [J]. ACTA HORTICULTURAE SINICA, 2008, 35(7): 1069-1074.

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

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