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Development of EST-SSR markers for Taxus cuspidata from publicly available transcriptome sequences

Author:
Ueno, Saneyoshi, Wen, Yafeng, Tsumura, Yoshihiko
Source:
Biochemical systematics and ecology 2015 v.63 pp. 20-26
ISSN:
0305-1978
Subject:
Taxus cuspidata, alleles, databases, genetic variation, heterozygosity, microsatellite repeats, polymerase chain reaction, transcriptome, trees
Abstract:
Simple sequence repeats (SSRs) from a public database were surveyed to identify potential EST-SSR markers for Taxus cuspidata. A total of 5.4 gigabase pairs of RNA-sequencing data were downloaded and assembled into 179,687 contigs, 7404 (4.1%) of which contained SSR sequences. One hundred and fifty PCR primer pairs were designed for SSRs with repeat numbers ≥9 and screened for variation in 18 T. cuspidata trees. Eighty markers showed length variation, with numbers of alleles and expected heterozygosity ranging from 2 to 11 and 0.056 to 0.907, respectively. These EST-SSR markers are expected to be useful for studying the genetic diversity and conservation of Taxus genetic resources.
Agid:
5360338