Abstract
Our research on slimy sculpins (Cottus cognatus), a benthic, freshwater fish, requires highly polymorphic genetic markers, and microsatellite loci developed for other Cottus species were insufficient for our needs. We therefore developed 13 polymorphic microsatellite loci from C. cognatus libraries enriched for tri- and tetranucleotide repeats. These loci had 2–22 alleles and observed heterozygosities ranging from 0.36 to 0.86 in a sample of 47 individuals from one population. There was no evidence of linkage disequilibrium; however, one locus had a putative null allele. Twelve loci also worked for mottled sculpin (Cottus bairdi) but only eight were polymorphic in a sample of seven individuals.
References
Adams SB, Schmetterling DA (2007) Freshwater sculpins: phylogenetics to ecology. Trans Am Fish Soc 136:1736–1741
Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF (2001) M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. BioTechniques 31:25–28
Englbrecht CC, Largiader CR, Hanfling B, Tautz D (1999) Isolation and characterization of polymorphic microsatellite loci in the European bullhead Cottus gobio L. (Osteichthyes) and their applicability to related taxa. Mol Ecol 8:1957–1969
Englbrecht CC, Freyhof J, Nolte A, Rassmann K, Schliewen U, Tautz D (2000) Phylogeography of the bullhead Cottus gobio (pisces: Teleostei: Cottidae) suggests a pre-Pleistocene origin of the major central European populations. Mol Ecol 9:709–722
Fiumera AC, Porter BA, Grossman GD, Avise JC (2002) Intensive genetic assessment of the mating system and reproductive success in a semi-closed population of the mottled sculpin, Cottus bairdi. Mol Ecol 11:2367–2377
Glenn TC, Schable NA (2005) Isolation microsatellite DNA loci. Methods Enzymol 395:202–222
Kalinowski ST (2006) HW-QUICKCHECK: an easy-to-use computer program for checking genotypes for agreement with Hardy–Weinberg expectations. Mol Ecol Notes 6:974–979
Meyer KA, Schill DJ, Campbell MR, Kozfkay CC (2008) Distribution, abundance, and genetic population structure of Wood River sculpin, Cottus leiopomus. West N Am Nat 68:508–520
Nolte AW, Stemshorn KC, Tautz D (2005) Direct cloning of microsatellite loci from Cottus gobio through a simplified enrichment procedure. Mol Ecol Notes 5:628–636
Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misnener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386
Sweigart A (2009) Sculpin hybrid zones: natural laboratories for the early stages of speciation. Mol Ecol 18:2547–2548
Acknowledgments
This work is the result of research sponsored by the Minnesota Sea Grant Research Program supported by the NOAA office of Sea Grant, United States Department of Commerce, under grant No. R/F33-09. The U.S. Government is authorized to reproduce and distribute reprints for government purposes, not withstanding any copyright notation that may appear hereon. This paper is journal reprint No. 565 of the Minnesota Sea Grant College Program.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fujishin, L.M., Keith Barker, F., Huff, D.D. et al. Isolation of 13 polymorphic microsatellite loci for slimy sculpin (Cottus cognatus). Conservation Genet Resour 1, 429 (2009). https://doi.org/10.1007/s12686-009-9099-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12686-009-9099-3