Advertisement

Conservation Genetics

, Volume 7, Issue 6, pp 971–982 | Cite as

Identification and characterization of microsatellites for striped bass from repeat-enriched libraries

  • Caird Rexroad
  • Roger Vallejo
  • Issa Coulibaly
  • Charlene Couch
  • Amber Garber
  • Mark Westerman
  • Craig Sullivan
Article

Abstract

Striped bass (Morone saxatilis) is economically important in the US due to its value as an aquaculture species and in supporting commercial and recreational fisheries, especially those off the Atlantic coast and in the Gulf of Mexico. Modern strategies for managing fishery populations and aquaculture broodstocks employ the use of molecular genetic markers to identify individuals, assign parentage, and characterize population genetic structure and levels of inbreeding and migration. As part of a collaborative effort to utilize molecular genetic technologies in striped bass breeding programs we generated microsatellite markers for use in population genetic studies, broodstock selection and management strategies, and the construction of a genetic map. We developed 345 new microsatellite markers for striped bass, a subset (n=71) of which was characterized by genotyping samples from two striped bass broodstock populations to evaluate marker polymorphism, percent heterozygosity, Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD) and utility for population genetic studies.

Keywords

breeding genetics heterozygosity microsatellite striped bass 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgments

The authors would like to acknowledge Dr Curry Woods from UMD and Dr Andy S. McGinty from NCSU for contributing broodstock samples and Roseanna Athey, Kristy Anderson, Michelle Fincham, and James Field for their technical assistance. This work was supported, in part, by a University of North Carolina Office of the President Genomic Sciences Initiative grant (RA02-06) to CVS.

References

  1. Bielawski JP, Pumo DE (1997) Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic Coast striped bass. Heredity 78(Pt 1):32–40CrossRefGoogle Scholar
  2. 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 31:24–26, 28PubMedGoogle Scholar
  3. Brown KM, Baltazar GA, Hamilton MB (2005) Reconciling nuclear microsatellite and mitochondrial marker estimates of population structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis). Heredity 94:606–615CrossRefPubMedGoogle Scholar
  4. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  5. Han K, Li L, Leclerc GM, Hays AM, Ely B (2000) Isolation and characterization ofmicrosatellite loci for striped bass (Morone saxatilis). Mar. Biotechnol., (NY), 2:405–408 Google Scholar
  6. Leclerc GM, Diaz M, Ely B (1996) Use of PCR-RFLP assays to detect genetic variation at single-copy nuclear loci in striped bass (Morone saxatilis). Mol. Mar. Biol. Biotechnol. 5:138–144PubMedGoogle Scholar
  7. Peacock M, Kirchoff V, Merideth S (2002) Identification and characterization of nine polymorphic microsatellite loci in the North American pika, Ochotono princeps. Mol. Ecol. Notes 2:360–362CrossRefGoogle Scholar
  8. Raymond M, Rousset F (1995) GENEPOP (v.1.2) A population genetics software for exact tests and ecumenicism. J. Heredity 86:248–249Google Scholar
  9. Ross K, Wang X, O’Malley KG, Gatlin DM, Gold JR (2004) Microsatellite DNA markers for parental assignment in hybrid striped bass (Morone saxatilis × Morone chrysops). Mol. Ecol. Notes 4:156–159CrossRefGoogle Scholar
  10. Roy NK, MacEda L, Wirgin I (2000) Isolation of microsatellites in striped bass Morone saxatilis (Teleostei) and their preliminary use in population identification. Mol. Ecol. 9:827–829CrossRefPubMedGoogle Scholar
  11. Rychlik W, Rhoads RE (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 17:8543–8551PubMedGoogle Scholar
  12. Sambrook J, Russell D (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.Google Scholar
  13. Schneider S, Roessli D, Excoffier L (2000) Arlequin ver. 2.000: A Software for Population Genetics Data Analysis. Genetics and Biometry Laboratory, University of Geneva, SwitzerlandGoogle Scholar
  14. Wirgin I, Grunwald C, Garte S, Mesing C (1991) Use of DNAfingerprinting in the identification and management of a striped bass population in the southeastern United States. Trans. Am. Fish. Soc. 120:273–281CrossRefGoogle Scholar
  15. Wirgin I, Maceda L, Stabile J, Mesing C (1997) An evaluation of introgression of Atlantic coast striped bass mitochondrial DNA in a Gulf of Mexico population using formalin-preserved museum collections. Mol. Ecol. 6:907–916CrossRefPubMedGoogle Scholar
  16. Wirgin I, Maceda L, Waldman J, Crittenden R (1993) Use of mitochondrial DNA polymorphisms to estimate the relative contributions of Hudson River and Chesapeake Bay striped bass stocks to the mixed fishery on the Atlantic Coast. Trans. Am. Fish. Soc. 121:669–684CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Caird Rexroad
    • 1
  • Roger Vallejo
    • 1
  • Issa Coulibaly
    • 1
  • Charlene Couch
    • 2
  • Amber Garber
    • 2
  • Mark Westerman
    • 3
  • Craig Sullivan
    • 2
  1. 1.USDA/ARS/NCCCWAKearneysvilleUSA
  2. 2.Department of ZoologyNorth Carolina State UniversityRaleighUSA
  3. 3.Kent SeaTech CorporationSan DiegoUSA

Personalised recommendations