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.
Highlights
Mandarin fish (Siniperca chuatsi), an economically important species in China, has a relatively high market value, and is wide cultured throughout the country [1,2]
Forty-three of these loci were polymorphic in S. chuatsi, and 20 were polymorphic in S. scherzeri
Five loci (Sin134 in S. chuatsi, Sin118, Sin122, Sin158 and Sin159 in S. scherzeri) showed significant deviation from the Hardy-Weinberg equilibrium (HWE) after Bonferroni correction, which may be due to the small sample size (n = 32) or the excess of heterozygotes
Summary
Mandarin fish (Siniperca chuatsi), an economically important species in China, has a relatively high market value, and is wide cultured throughout the country [1,2]. It has a fast growth rate, but is susceptible to diseases. Microsatellites or simple sequence repeats (SSRs) have become a useful tool to assess genetic diversity and develop molecular breeding techniques in fish due to their co-dominance, ubiquitous distribution within genomes, high reproducibility, and transferability across species [5,6]. We test the transferability of these markers in other four species of sinipercine fishes: Siniperca kneri, Siniperca undulata, Siniperca obscura, and Coreoperca whiteheadi
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