Research Article

Development and characterization of novel SSR markers in Siniperca kneri Garman

Published: March 24, 2014
Genet. Mol. Res. 13 (3) : 7593-7606 DOI: https://doi.org/10.4238/2014.March.24.18
Cite this Article:
(2014). Development and characterization of novel SSR markers in Siniperca kneri Garman. Genet. Mol. Res. 13(3): gmr3598. https://doi.org/10.4238/2014.March.24.18
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Abstract

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. The average allele number per locus was 5.1 (range: 2-8) for transcriptome-derived SSRs and 3.8 (range: 2-5) for genomic SSRs. The average observed and expected heterozygosities were 0.666 (range: 0.000-1.000) and 0.692 (range: 0.230-0.857) for transcriptome-derived SSRs, respectively. These values were 0.380 (range: 0.000-1.000) and 0.527 (range: 0.201-0.799) for genomic SSRs, respectively. The average polymorphic information content was 0.638 (range: 0.215-0.824) for transcriptome-derived SSRs and 0.477 (range: 0.183-0.752) for genomic SSRs. Seven of these loci exhibited departure from Hardy-Weinberg equilibrium after sequential Bonferroni’s correction for multiple tests, and no significant deviation was observed for the linkage disequilibrium. These developed and characterized markers are anticipated to be useful for studies on population genetics, conservation genetics, and the fishery management of this species.

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. The average allele number per locus was 5.1 (range: 2-8) for transcriptome-derived SSRs and 3.8 (range: 2-5) for genomic SSRs. The average observed and expected heterozygosities were 0.666 (range: 0.000-1.000) and 0.692 (range: 0.230-0.857) for transcriptome-derived SSRs, respectively. These values were 0.380 (range: 0.000-1.000) and 0.527 (range: 0.201-0.799) for genomic SSRs, respectively. The average polymorphic information content was 0.638 (range: 0.215-0.824) for transcriptome-derived SSRs and 0.477 (range: 0.183-0.752) for genomic SSRs. Seven of these loci exhibited departure from Hardy-Weinberg equilibrium after sequential Bonferroni’s correction for multiple tests, and no significant deviation was observed for the linkage disequilibrium. These developed and characterized markers are anticipated to be useful for studies on population genetics, conservation genetics, and the fishery management of this species.