In silico mining and characterization of simple sequence repeats from gilthead sea bream ( Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays
We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project (‘Marine Genomics Europe’ Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed s...
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| Published in: | Marine genomics Vol. 4; no. 2; pp. 83 - 91 |
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| Main Authors: | , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Netherlands
Elsevier B.V
01-06-2011
Elsevier |
| Subjects: | |
| Online Access: | Get full text |
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| Summary: | We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project (‘Marine Genomics Europe’ Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (
Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95
kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.
EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs.
► We screened for simple sequence repeats (SSRs) found in EST development project. ► EST-SSRs were used as template for primer design. ► 206 pairs of primers were investigated for cross-species amplification in sixteen teleost fish. ► The characteristics of 63 EST-SSR loci were studied in a wild gilthead sea bream population. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1874-7787 1876-7478 |
| DOI: | 10.1016/j.margen.2011.01.003 |