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• Liang, X
• Huang, W
• Cao, L
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• Huang, W
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• Liang, X
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Int. J. Mol. Sci. 2012, 13(8), 9534-9544; doi:10.3390/ijms13089534

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

Chunmei Qu, Xufang Liang* , Wei Huang and Liang Cao

College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China

* Author to whom correspondence should be addressed.

Received: 9 July 2012; in revised form: 24 July 2012 / Accepted: 24 July 2012 / Published: 30 July 2012

(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

Download PDF Full-Text [194 KB, uploaded 30 July 2012 13:58 CEST]

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

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