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Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing

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Abstract

Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy–Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.

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Acknowledgments

This research was supported by Golden Seed Project (No. 213004-04-3-SB530), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS); and funded by Soonchunhyang University Research Fund.

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Authors and Affiliations

  1. East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea

    Keun-Sik Kim & Choong Hwan Noh

  2. Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea

    Shin-Joo Moon, Seung-Hee Han & In-Chul Bang

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  1. Keun-Sik Kim
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  2. Choong Hwan Noh
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Correspondence to In-Chul Bang.

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Kim, KS., Noh, C.H., Moon, SJ. et al. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing. Mol Biol Rep 43, 541–548 (2016). https://doi.org/10.1007/s11033-016-3980-4

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