Development and characterization of microsatellite markers for an endangered species,Epinephelus bruneus, to establish a conservation program

Abstract

Kelp grouper (Epinephelus bruneus Bloch 1793) is a commercially important fish in Korea. In recent years, the catch of kelp grouper in the coastal waters of Korea has significantly declined. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. In this study, we isolated and characterized 12 microsatellite loci using an enrichment method based on magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. All loci were readily amplified and contained TG/CA denucleotide repeats. To characterize each locus, 30 individuals from a natural E. bruneus population in the coastal waters of Jeju Island, Korea, were genotyped. All loci except three, KEm118, KEm154, and KEm219, were polymorphic, with an average of 8.1 alleles per locus (range 2Á18). The mean observed and expected heterozygosities were 0.47 (range 0.19Á1.00) and 0.61 (range 0.29Á0.92), respectively. A significant deviation from Hardy-Weinberg equilibrium was observed at three loci (KEm134, KEm184, and KEm283). These findings will be useful for effective monitoring and management of genetic variation of kelp grouper as well as for the implementation of a fisheries conservation program.

Genetic differences between broodstock and offspring of seven-band grouper in a hatchery

“…Microsatellite (MS) DNA markers or short tandem repeats (STRs) are well-known hypervariable genetic markers that exhibit remarkable discriminatory capacities when used to evaluate genetic diversity in many marine species (An et al 2012aBlanco Gonzalez et al 2012;Kim et al 2013). This study was to genetically characterize the broodstock and offspring of a hatchery facility located in Geomundo, Korea, to determine whether the current management strategy reduces genetic variation in E. septemfasciatus.…”

High-throughput simple sequence repeat (SSR) markers development for the kelp grouper (<i>Epinephelus bruneus</i>) and cross-species amplifications for Epinephelinae species

“…Results indicate that we successfully developed new SSR markers for E. bruneus. However, it should be noted that the number of E. bruneus sequences currently available in the NCBI database is still limited (twelve SSR loci are available) [14].…”

“…Prior to our study, twelve SSR markers had been developed in E. bruneus using the traditional method [14], and they reported on development of di-nucleotide markers. Di-nucleotide SSR markers, while providing powerful discrimination, do not provide high-precision genotyping needed for comparative multi-locus profiling.…”

“…Relatively large numbers of SSR markers have been recently developed and characterized for grouper species e.g., Plectropomus maculatus [8], E. lanceolatus [9,10], E. fuscoguttatus [11], Mycteroperca tigris [12], Cromileptes altivelis [13]. However, there has been only one published research study on the SSR primers for E. bruneus in which dinucleotide markers are developed [14]. Although dinucleotide SSR markers are powerful tools for parentage analyses and gene mapping, analyses are frequently complicated by the presence of stutter bands caused by polymerase slippage during PCR amplification.…”

Comparison of genetic diversity between wild-caught broodstock and hatchery-produced offspring populations of the vulnerable Korean kelp grouper (Epinephelus bruneus) by microsatellites

“…Among the available genetic markers, microsatellite DNA markers or short tandem repeats (STRs) are well-known hypervariable genetic markers that have been successfully used in genetic monitoring of the changes between wild and hatchery populations in many marine species (An et al, 2012b;Han et al, 2012;Kim et al, 2013). Recently, microsatellite DNA markers for E. bruneus have been isolated and characterized (An et al, 2012a;Kang et al, 2013); however, there have been no reports regarding their use in analysis of the extent of genetic divergence between wild-caught broodstock and hatchery-produced offspring of Korean kelp grouper in hatcheries, although great efforts are devoted to sustainable mass fry production.…”