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Journal of Heredity Advance Access published online on January 30, 2008
Journal of Heredity, doi:10.1093/jhered/esm124
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Exploiting EST Databases for the Development and Characterization of EST–SSRs in the Pacific Oyster (Crassostrea gigas)

Hong Yu, and Qi Li

From the Department of Aquaculture, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, China

Address correspondence to Dr Qi Li at the address above, or e-mail: qili66{at}mail.ouc.edu.cn.

A total of 147 microsatellite-containing expressed sequence tags (ESTs) (3.63%) were detected from 4053 ESTs of the Pacific oyster (Crassostrea gigas) in GenBank. The average density of simple sequence repeats (SSRs) was 1 per 8.25 kb of EST after redundancy elimination. Dinucleotide repeat motifs appeared to be the most abundant type. Sixteen new polymorphic EST–SSRs were developed. The number of alleles per locus varied from 3 to 12, with an average of 5.9 alleles per locus. Marker transferability was tested on 2 other Crassostrea species, and 14 loci gave successful amplifications in both species. Twenty EST–SSRs were tested on 3 families of C. gigas for examination of inheritance mode of EST–SSRs. Thirty-five tests of segregation ratios revealed 5 significant departures from expected Mendelian ratios, 4 of which confirmed Mendelian expectations when accounting for the presence of null alleles. Null alleles were detected at 3 loci (15.0%) of the 20 loci, and the frequency of null alleles at EST–SSRs was lower than that in genomic SSRs in C. gigas. The results obtained in this study suggest that C. gigas EST–SSRs will complement the currently available genomic SSR markers and may be useful for comparative mapping, marker-assisted selection, and evolutionary studies.

Corresponding Editor: Jill Pecon-Slattery

Received June 5, 2007
Accepted November 24, 2007


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