Characterization of EST–SSRs from Cryptomeria japonica

Simple sequence repeat (SSR) markers were developed for Cryptomeria japonica from 55,530 expressed sequence tags (ESTs). Of the 219 designed primer pairs, 176 showed clear PCR amplification products and 27 of these revealed polymorphisms in six individuals sampled at sites across Japan. When these 2...

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Bibliographic Details
Published in:Conservation genetics resources 2009-12, Vol.1 (1), p.373-376
Main Authors: Moriguchi, Yoshinari, Ueno, Saneyoshi, Ujino-Ihara, Tokuko, Futamura, Norihiro, Matsumoto, Asako, Shinohara, Kenji, Tsumura, Yoshihiko
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Biodiversity
Biomedical and Life Sciences
Conservation Biology/Ecology
Cryptomeria japonica
Ecology
Evolutionary Biology
Expressed sequence tags
Gene mapping
Genetic diversity
Life Sciences
Plant Genetics and Genomics
Population genetics
Technical Note
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Summary:Simple sequence repeat (SSR) markers were developed for Cryptomeria japonica from 55,530 expressed sequence tags (ESTs). Of the 219 designed primer pairs, 176 showed clear PCR amplification products and 27 of these revealed polymorphisms in six individuals sampled at sites across Japan. When these 27 loci were examined in 48 individuals from a single population, the number of alleles and the Polymorphism Information Content (PIC) ranged from 2 to 17 and 0.09 to 0.86, respectively. The average PIC value obtained from EST–SSR markers (0.40) was lower than that from genomic SSR markers (0.67 and 0.62). We observed a significant departure from Hardy–Weinberg equilibrium in five of the 27 loci. These EST–SSR markers will be useful for the evaluation of genetic variation in C. japonica and for genetic mapping.
ISSN:1877-7252
1877-7260
DOI:10.1007/s12686-009-9086-8