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Int. J. Mol. Sci. 2012, 13(8), 9534-9544; doi:10.3390/ijms13089534

Isolation and Characterization of 46 Novel Polymorphic EST-Simple Sequence Repeats (SSR) Markers in Two Sinipercine Fishes (Siniperca) and Cross-Species Amplification

College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
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Received: 9 July 2012 / Revised: 24 July 2012 / Accepted: 24 July 2012 / Published: 30 July 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract

With the development of next generation sequencing technologies, transcriptome level sequence collections are emerging as prominent resources for the discovery of gene-based molecular markers. In this study, we described the isolation and characterization of 46 novel polymorphic microsatellite loci for Siniperca chuatsi and Siniperca scherzeri from the transcriptome of their F1 interspecies hybrids. Forty-three of these loci were polymorphic in S. chuatsi, and 20 were polymorphic in S. scherzeri. In S. chuatsi, the number of alleles per locus ranged from 2 to 8, and the observed and expected heterozygosities varied from 0.13 to 1.00 and from 0.33 to 0.85, respectively. In S. scherzeri, the number of alleles per locus ranged from 3 to 9, and the observed and expected heterozygosities varied from 0.19 to 1.00 and from 0.28 to 0.88, respectively. We also evaluated the cross-amplification of 46 polymorphic loci in four species of sinipercine fishes: Siniperca kneri, Siniperca undulata, Siniperca obscura, and Coreoperca whiteheadi. The interspecies cross-amplification rate was very high, totaling 94% of the 184 locus/taxon combinations tested. These markers will be a valuable resource for population genetic studies in sinipercine fishes.
Keywords: Siniperca chuatsi; Siniperca scherzeri; EST-SSRs; transcriptome; cross-species amplification Siniperca chuatsi; Siniperca scherzeri; EST-SSRs; transcriptome; cross-species amplification
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Qu, C.; Liang, X.; Huang, W.; Cao, L. Isolation and Characterization of 46 Novel Polymorphic EST-Simple Sequence Repeats (SSR) Markers in Two Sinipercine Fishes (Siniperca) and Cross-Species Amplification. Int. J. Mol. Sci. 2012, 13, 9534-9544.

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