Development of SSR primers from EST sequences and their application in germplasm identification of Porphyra lines (Rhodophyta)

This paper reports the development of SSR markers from EST data and their utilization in germplasm identification of Porphyra. The publicly available EST (expressed sequence tag) sequences of Porphyra were searched from the Internet ( http://www.kazura.or.jp/en/plant/porphyra/EST/ ). From a total of...

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Bibliographic Details
Published in:European journal of phycology 2006-08, Vol.41 (3), p.329-336
Main Authors: Sun, Jianwei, Liu, Tao, Guo, Baotai, Jin, Demin, Weng, Manli, Feng, Yanbin, Xu, Pu, Duan, Delin, Wang, Bin
Format: Article
Language:English
Subjects:
cSSR
DNA fingerprint
microsatellite
Porphyra
Rhodophyta
seaweeds
simple sequence repeats (SSRs)
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Summary:This paper reports the development of SSR markers from EST data and their utilization in germplasm identification of Porphyra. The publicly available EST (expressed sequence tag) sequences of Porphyra were searched from the Internet ( http://www.kazura.or.jp/en/plant/porphyra/EST/ ). From a total of 20,779 obtained EST sequences, 391 SSRs (simple sequence repeats) were analysed with SSRIT software ( http://www.gramene.org/db/searches/ssrtool ). From those, 48 SSR primer-pairs were designed and tested by commonly used SSR reaction conditions using 22 Porphyra DNA samples as templates. Results showed that 41 SSR primer-pairs gave good amplification patterns. These were used to conduct SSR analyses of genetic diversity and variety identification of the 22 Porphyra lines. A dendrogram and the DNA fingerprints of the Porphyra lines were developed based on the obtained SSR data.
ISSN:0967-0262
1469-4433
DOI:10.1080/09670260600740906