Exploiting EST Databases for the Development and Characterization of EST-SSRs in the Pacific Oyster (Crassostrea gigas)
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...
| Published in: | Journal of Heredity |
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| Main Authors: | , |
| Format: | Text |
| Language: | English |
| Published: |
Oxford University Press
2008
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| Subjects: | |
| Online Access: | http://jhered.oxfordjournals.org/cgi/content/short/99/2/208 https://doi.org/10.1093/jhered/esm124 |
| Summary: | 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. |
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