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González P, Dettleff P, Valenzuela C, Estrada JM, Valdés JA, Meneses C, Molina A. Evaluating the genetic structure of wild and commercial red cusk-eel (Genypterus chilensis) populations through the development of novel microsatellite markers from a reference transcriptome. Mol Biol Rep 2019; 46:5875-5882. [PMID: 31598817 DOI: 10.1007/s11033-019-05021-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/03/2019] [Indexed: 11/30/2022]
Abstract
The red cusk-eel (Genypterus chilensis) is a native Chilean species with a high-value market, with the potential to diversify Chilean aquaculture. The objective of this study was to develop a set of microsatellite markers, estimate genetic parameters, determine population differentiation, and identify the population structure of wild and commercial populations of G. chilensis. We discovered 6427 microsatellites markers from RNA-seq data, of which 54.9%, 20.2% and 16.8% were di-, tri-, and tetranucleotides, respectively. We used 12 of these markers to genotype two sets of broodstock, one group from commercial fish, and one group from wild fish from the Coquimbo Region of G. chilensis. We estimate the genetic parameters of the markers, selecting ten polymorphic markers (PIC > 0.5). We observed differences in the inbreeding coefficient among populations, with high values of inbreeding in one broodstock set and lower values in the other groups. The evaluation of population differentiation using Fst showed small (0.0195) to large (0.1888) genetic differentiation between the groups. The structure analysis showed that commercial and wild groups were formed by three clusters, without relevant evidence of admixture process, suggesting that groups evaluated in this study are formed of at least three subpopulations of G. chilensis, which could be explained by the low or lack of migration suggested for this species. This is the first study that identifies a high number of molecular markers in G. chilensis, providing relevant information of the genetic structure of commercial and wild population of this species.
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Affiliation(s)
- Pamela González
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Phillip Dettleff
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Cristián Valenzuela
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Juan Manuel Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan Antonio Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile.
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
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An HS, Cho JK, Kim KM, Son MH, Park JY, Myeong JI, An CM. Genetic characterization of four hatchery populations of the seven-band grouper (Epinephelus septemfasciatus) using microsatellite markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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An HS, Nam MM, Myeong JI, An CM. Genetic diversity and differentiation of the Korean starry flounder (Platichthys stellatus) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis. Mol Biol Rep 2014; 41:7281-92. [PMID: 25064574 DOI: 10.1007/s11033-014-3614-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
Abstract
The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy-Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.
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An HS, Kang HW, Han HS, Park JY, Myeong JI, An CM. Population genetic structure of the tongue sole (Cynoglossus semilaevis) in Korea based on multiplex PCR assays with 12 polymorphic microsatellite markers. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0190-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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An HS, Lee JW, Kim HY, Kim JB, Chang DS, Park JY, Myeong JI, An CM. Genetic differences between wild and hatchery populations of Korean spotted sea bass (Lateolabrax maculatus) inferred from microsatellite markers. Genes Genomics 2013; 35:671-80. [DOI: 10.1007/s13258-013-0135-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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An HS, Byun SG, Kim YC, Lee JW, Myeong JI. Wild and hatchery populations of Korean starry flounder (Platichthys stellatus) compared using microsatellite DNA markers. Int J Mol Sci 2011; 12:9189-202. [PMID: 22272127 DOI: 10.3390/ijms12129189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022] Open
Abstract
Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity.
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