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Development of EST-SSR Markers by Data Mining in Three Species of Shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy

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Abstract

We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.

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Acknowledgments

We are grateful to Dr. Paul Gross and the research team at Marine Genomics for their work on EST development on Litopenaeus vannamei. Without their publicly available sequences, this research could have not been accomplished. This work was carried out with financial support from the Ecuadorian Science and Technology Foundation (FUNDACYT-SENACYT) under Project PFN-084 and the Belgian Technical Cooperation (BTC). We thank S. Sonnenholzner for the facilities provided during sampling of wild animals.

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Authors and Affiliations

  1. Fundación CENAIM-ESPOL, Km. 30.5 Viá Perimetral, Campus Politécnico, Guayaquil, Ecuador

    Franklin Pérez, Juan Ortiz, Mariuxi Zhinaula, Cesar Gonzabay & Jorge Calderón

  2. Katholieke Universiteit Leuven, Laboratory of Aquatic Ecology, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium

    Filip A.M.J. Volckaert

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  1. Franklin Pérez
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  2. Juan Ortiz
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  3. Mariuxi Zhinaula
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  4. Cesar Gonzabay
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  5. Jorge Calderón
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  6. Filip A.M.J. Volckaert
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Correspondence to Franklin Pérez.

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Pérez, F., Ortiz, J., Zhinaula, M. et al. Development of EST-SSR Markers by Data Mining in Three Species of Shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar Biotechnol 7, 554–569 (2005). https://doi.org/10.1007/s10126-004-5099-1

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