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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

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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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Acknowledgements

This study was supported by CONICYT/FONDAP [Grant Number 15110027] awarded to Juan Antonio Valdés and Alfredo Molina, and CONICYT FONDECYT Postdoctorado [Grant Number 3180283] awarded to Phillip Dettleff.

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Authors and Affiliations

  1. Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile

    Pamela González, Phillip Dettleff, Cristián Valenzuela, Juan Antonio Valdés & Alfredo Molina

  2. Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile

    Pamela González, Phillip Dettleff, Cristián Valenzuela, Juan Antonio Valdés & Alfredo Molina

  3. Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile

    Juan Manuel Estrada

  4. Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile

    Claudio Meneses

  5. FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile

    Claudio Meneses

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  1. Pamela González
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  2. Phillip Dettleff
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  7. Alfredo Molina
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Correspondence to Alfredo Molina.

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The authors declare that there are no financial or non-financial conflict of interest.

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The procedures with animals in this study were according to animal welfare procedures of the National Commission for Scientific and Technological Research (CONICYT) of the Chilean government and approved by the bioethical committees of the Universidad Andres Bello (Approbation Number 0072018).

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González, P., Dettleff, P., Valenzuela, C. et al. 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 46, 5875–5882 (2019). https://doi.org/10.1007/s11033-019-05021-0

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