Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua

Authors

  • J. Carlsson,

    Corresponding author
    1. School of Biology and Environmental Science, UCD Science Education and Research Centre – West, University College Dublin, Dublin 4, Ireland
    • Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • D. T. Gauthier,

    1. Department of Biological Sciences, Norfolk, VA, U.S.A.
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  • J. E. L. Carlsson,

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • J. P. Coughlan,

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • E. Dillane,

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • R. D. Fitzgerald,

    1. Carna Research Station, Ryan Institute, National University of Ireland, Galway, Ireland
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  • U. Keating,

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • P. McGinnity,

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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  • L. Mirimin,

    1. Carna Research Station, Ryan Institute, National University of Ireland, Galway, Ireland
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  • T. F. Cross

    1. Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Cork, Ireland
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Author to whom correspondence should be addressed. Tel.: +353 1 716 2197; email: jens.carlsson@ucd.ie

Abstract

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

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