Skip to main content
SpringerLink
Log in

Identification, Inheritance, and Variation of Microsatellite Markers in the Black Scallop Mimachlamys varia

  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

Five polymorphic microsatellite loci were identified in the black scallop Mimachlamys varia after construction of a genomic library enriched for (GT)n. To examine the transmission pattern of microsatellite alleles, several families were created and genotypes scored for three loci. The expected Mendelian ratios were found in 12 of 14 segregations examined. Unexpected segregations may be explained by a genotyping error (allelic dropout), given that when a specific allele was treated as dominant, the phenotypic ratios conformed to Mendelian expectations. The five loci were also examined in two samples from the Spanish coast. The two localities displayed similar mean values for the number of alleles per locus (7.2–8.4), allelic richness (7.2–7.9), and observed (0.389–0.484) and expected heterozygosity (0.545–0.618). Significant Hardy–Weinberg deviations were observed at three loci, with heterozygote deficiency occurring in all cases. Global multilocus θ value and allele frequencies at one locus revealed significant differentiation between the two localities.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • An HS, Park JY, Lee YG, Lee DS, Lee C (2005) Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis). Mol Ecol Notes 5:806–808

    Article  CAS  Google Scholar 

  • Arias A, Freire R, Méndez J, Insua A (2009) Intron characterization and their potential as molecular markers for population studies in the scallops Aequipecten opercularis and Mimachlamys varia. Hereditas 142:46–57

    Article  Google Scholar 

  • Arias A, Freire R, Méndez J, Insua A (2010) Isolation and characterization of microsatellite markers in the queen scallop Aequipecten opercularis and their application to a population genetic study. Aquat Living Resour 23:199–207

    Article  CAS  Google Scholar 

  • Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165

    Article  PubMed  Google Scholar 

  • Beaumont AR, Beveridge CM (1984) Electrophoretic survey of genetic variation in Pecten maximus, Chlamys opercularis, Chlamys varia and Chlamys distorta from the Irish Sea. Mar Biol 81:299–306

    Article  CAS  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) Genetix 4.05, logiciel sous Windows pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France). Available from http://www.genetix.univ-montp2.fr/genetix/genetix.htm

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  PubMed  CAS  Google Scholar 

  • Benzie JAH, Smith-Keune C (2006) Microsatellite variation in Australian and Indonesian pearl oyster Pinctada maxima populations. Mar Ecol Prog Ser 314:197–211

    Article  CAS  Google Scholar 

  • Billote N, Lagoda PJL, Risterucci AM, Baurens FC (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288

    Google Scholar 

  • Brookfield JF (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455

    PubMed  CAS  Google Scholar 

  • Chambers GK, MacAvoy ES (2000) Microsatellites: consensus and controversy. Comp Biochem Physiol B 126:455–476

    Article  PubMed  CAS  Google Scholar 

  • Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  PubMed  CAS  Google Scholar 

  • Chistiakov DA, Hellemans B, Volckaert FAM (2006) Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255:1–29

    Article  CAS  Google Scholar 

  • Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques 20:758–760

    PubMed  CAS  Google Scholar 

  • Elfstrom CM, Smith CT, Jones KC, Seeb JE (2005) Characterization of 16 polymorphic microsatellite loci in weathervane scallop Patinopecten caurinus. Mol Ecol Notes 5:514–516

    Article  CAS  Google Scholar 

  • Fernández-Moreno M, Arias-Pérez A, Freire R, Méndez J (2008) Genetic analysis of Aequipecten opercularis and Mimachlamys varia (Bivalvia: Pectinidae) in several Atlantic and Mediterranean localities, revealed by mitochondrial PCR-RFLPs: a preliminary study. Aquac Res 39:474–481

    Article  Google Scholar 

  • Fernández-Tajes J, Méndez J (2007) Identification of the razor clam species Ensis arcuatus, E. siliqua, E. directus, E. macha, and Solen marginatus using PCR-RFLP analysis of the 5S rDNA region. J Agric Food Chem 55:7278–7282

    Article  PubMed  Google Scholar 

  • Gosling EM, Burnell GM (1988) Evidence for selective mortality in Chlamys varia (L) transplant experiments. J Mar Biol Assoc UK 68:251–258

    Article  Google Scholar 

  • Goudet J (2001) Fstat, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Institut d’Ecologie, Université de Lausanne, Dorigny, Switzerland. Available from http://www2.unil.ch/popgen/softwares/fstat.htm

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hedgecock D, Li G, Hubert S, Bucklin K, Ribes V (2004) Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas. J Shellfish Res 23:379–385

    Google Scholar 

  • Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638

    PubMed  CAS  Google Scholar 

  • Hui M, Bao Z, Zhan A, Hu X, Lu W, Chang D, Hu J (2006) Ten polymorphic dinucleotide microsatellite markers of the noble scallop Chlamys nobilis. Mol Ecol Notes 6:1033–1035

    Article  CAS  Google Scholar 

  • Iglesias P, Louro A, Román G (2008) How does reproduction and recruitment patterns match? The case of Chlamys varia in Ría de Betanzos-Sada, NW Spain. 2nd Mollusc Physiology Conference. September 1–4, Brest, France. Book of abstracts, p 119

  • Jeffery KJ, Keller LF, Arcese P, Bruford MW (2001) The development of microsatellite loci in the song sparrow, Melospiza melodia (Aves) and genotyping errors associated with good quality DNA. Mol Ecol Notes 1:11–13

    Article  CAS  Google Scholar 

  • Launey S, Hedgecock D (2001) High genetic load in the Pacific oyster Crassostrea gigas. Genetics 159:255–265

    PubMed  CAS  Google Scholar 

  • Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465

    Article  PubMed  CAS  Google Scholar 

  • Louis EJ, Dempster ER (1987) An exact test for Hardy–Weinberg and multiple alleles. Biometrics 43:805–811

    Article  PubMed  CAS  Google Scholar 

  • Louro A, Roche DL, Campos MJ, Román G (2003) Hatchery rearing of the black scallop, Chlamys varia (L.). J Shellfish Res 22:95–99

    Google Scholar 

  • Mathers NF (1975) Environmental variability at the phosphoglucose isomerase locus in the genus Chlamys. Biochem Syst Ecol 3:123–127

    Article  Google Scholar 

  • McGoldrick DJ, Hedgecock D, English LJ, Baoprasertkul P, Ward RD (2000) The transmission of microsatellite alleles in Australian and North American stocks of the Pacific oyster (Crassostrea gigas): selection and null alleles. J Shellfish Res 19:779–788

    Google Scholar 

  • Meglécz E (2007) Microfamily (version 1): a computer program for detecting flanking-region similarities among different microsatellite loci. Mol Ecol Notes 7:18–20

    Article  Google Scholar 

  • Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation. Proc Natl Acad Sci USA 100:4334–4339

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    PubMed  CAS  Google Scholar 

  • Raymond M, Rousset F (1995) Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Reece KS, Ribeiro WL, Gaffney PM, Carnegie RB, Allen SK Jr (2004) Microsatellite marker development and analysis in the eastern oyster (Crassostrea virginica): confirmation of null alleles and non-Mendelian segregation ratios. J Hered 95:346–352

    Article  PubMed  CAS  Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  Google Scholar 

  • Ríos C, Sanz S, Saavedra C, Pena JB (2002) Allozyme variation in populations of scallops, Pecten jacobaeus (L.) and P. maximus (L.) (Bivalvia: Pectinidae), across the Almeria-Oran front. J Exp Mar Biol Ecol 267:223–244

    Article  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386

    Google Scholar 

  • Sobolewska H, Beaumont AR (2005) Genetic variation at microsatellite loci in northern populations of the European flat oyster (Ostrea edulis). J Mar Biol Assoc UK 85:955–960

    Article  CAS  Google Scholar 

  • Soulsbury CD, Iossa G, Edwards KJ, Baker PJ, Harris S (2007) Allelic dropout from a high-quality DNA source. Conserv Genet 8:733–738

    Article  CAS  Google Scholar 

  • Taris N, Baron S, Sharbel TF, Sauvage C, Boudry P (2005) A combined microsatellite multiplexing and boiling DNA extraction method for high-throughput parentage analyses in the Pacific oyster (Crassostrea gigas). Aquac Res 36:516–518

    Article  CAS  Google Scholar 

  • Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MicroChecker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  • Wagner HP (1991) Review of the European Pectinidae. Vita Marina 41:1–48

    Google Scholar 

  • Watts PC, Mallanaphy WJ, McCarthy C, Beukers-Stewart BD, Mosley MWJ, Brand AR, Saccheri IJ (2005) Polymorphic microsatellite loci isolated from the great scallop, Pecten maximus (Bivalvia: Pectinidae). Mol Ecol Notes 5:902–904

    Article  CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16

    Article  PubMed  CAS  Google Scholar 

  • Zhan AB, Bao ZM, Hui M, Wang ML, Zhao HB, Lu W, Hu XL, Hu JJ (2007) Inheritance pattern of EST-SSRs in self-fertilized larvae of the bay scallop Argopecten irradians. Ann Zool Fenn 44:259–268

    Google Scholar 

Download references

Acknowledgments

We thank Dr. Ricardo Pérez and Dr. Pedro Cruz for assisting in the microsatellite genotyping, Jose García Gil for technical assistance in the laboratory, and anonymous reviewers for constructive comments. This study was supported by Ministerio de Ciencia y Tecnología of Spain through project ACU01-022-C2-2.

Author information

Authors and Affiliations

  1. Departamento de Biología Celular y Molecular, Universidade da Coruña, A Zapateira s/n, 15071, A Coruña, Spain

    Alberto Arias, Ruth Freire, Josefina Méndez & Ana Insua

  2. Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, A Coruña, Spain

    Juan Pablo De La Roche & Guillermo Román

Authors
  1. Alberto Arias
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ruth Freire
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Juan Pablo De La Roche
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guillermo Román
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Josefina Méndez
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ana Insua
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ana Insua.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Arias, A., Freire, R., De La Roche, J.P. et al. Identification, Inheritance, and Variation of Microsatellite Markers in the Black Scallop Mimachlamys varia . Biochem Genet 49, 139–152 (2011). https://doi.org/10.1007/s10528-010-9394-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-010-9394-4

Keywords

Search

Navigation