Skip to main content
SpringerLink
Log in

Characterization of 95 novel microsatellite markers for Zhikong scallop Chlamys farreri using FIASCO-colony hybridization and EST database mining

  • Published:
Fisheries Science Aims and scope Submit manuscript

Abstract

In order to construct a simple sequence repeat (SSR)-based genetic linkage map and to promote molecular marker-assisted selection (MAS) in scallop breeding, the methods of Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO)-colony hybridization and expressed sequence tag (EST) database mining were modified and used to develop 95 novel microsatellite markers for Zhikong scallop. The SSR-enriched library constructed by the FIASCO method consisted of 830 clones, and 295 (35.5%) positive clones were identified after colony hybridization. One hundred and fifty clones were randomly sequenced and the results showed all clones contained at least one microsatellite. Of 91 primer pairs designed, 72 were amplified scorable polymerase chain reaction (PCR) products and 70 were polymorphic with the allele number range of 3–16 alleles/locus (average 7.0 alleles/locus). When EST database mining was performed, 66 microsatellites containing ESTs were identified from 3467 sequences deposited in GenBank. Based on cluster analysis of length and GC content of the flanking regions, 47 primer pairs were designed and 23 scorable EST SSRs were obtained. Compared with genomic SSRs developed in this study, EST SSRs showed lower genetic variability with an average of 4.2 alleles/locus. The results in the present study demonstrate that modified FIASCO-colony hybridization is an efficient and low-cost method for the isolation of large numbers of microsatellite markers for scallop species.

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

  1. Guo XM. Aquaculture in China: two decades of rapid growth. Aquacult. Mag. 2000; 26: 1–3.

    Google Scholar 

  2. Hawkins A, Duarte P, Fang J, Pascoe PL, Zhang JH, Zhang XL, Zhu MY. A functional model of responsive suspension-feeding and growth in bivalve shellfish configured and validated for the scallop Chlamys farreri during culture in China. J. Exp. Mar. Biol. Ecol. 2002; 281: 13–40.

    Article  Google Scholar 

  3. Zhan AB, Bao ZM, Yao B, Wang XL, Hui M, Hu JJ. Polymorphic microsatellite markers in the Zhikong scallop Chlamys farreri. Mol. Ecol. Notes 2006; 6: 127–129.

    Article  CAS  Google Scholar 

  4. Zhan AB, Bao ZM, Hu XL, Hui M, Wang ML, Peng W, Zhao HB, Hu JJ. Isolation and characterization of 150 novel microsatellite markers for Zhikong scallop (Chlamys farreri). Mol. Ecol. Notes 2007; 7: 1012–1022.

    Article  Google Scholar 

  5. Sato M, Kawamata K, Zaslabskaya N, Nakamura A, Ohta T, Nishikiori T, Brykov V, Nagashima K. Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study. Mar. Biotechnol. 2005; 7: 713–728.

    Article  PubMed  CAS  Google Scholar 

  6. Hubert S, Hedgecock D. Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas. Genetics 2004; 168: 351–362.

    Article  PubMed  CAS  Google Scholar 

  7. Baranski M, Loughnan S, Austin CM, Robinson N. A microsatellite linkage map of the blacklip abalone, Haliotis rubra. Anim. Genet. 2006; 37: 563–570.

    Article  PubMed  CAS  Google Scholar 

  8. Sekino M, Hara M. Linkage maps for the Pacific abalone (genus Haliotis) based on microsatellite DNA markers. Genetics 2007; 175: 945–958.

    Article  PubMed  CAS  Google Scholar 

  9. Takagi M, Chow S, Okamura T, Scholey V, Nakazawa A, Margules D, Wexler JB, Taniguchi N. Mendelian inheritance and variation of four microsatellite DNA markers in the yellow-fin tuna Thunnus albacares. Fish. Sci. 2003; 69: 1306–1308.

    Article  CAS  Google Scholar 

  10. Takagi M, Sato J, Monbayashi C, Aoki K, Tsuji T, Hatanaka H, Takahashi H, Sakai H. Evaluation of microsatellites identified in the tiger puffer Takifugu rubripes DNA database. Fish. Sci. 2003; 69: 1085–1095.

    Article  CAS  Google Scholar 

  11. Zhang LL, Bao ZM, Cheng J, Li H, Huang XT, Wang S, Zhang C, Hu JJ. Fosmid library construction and initial analysis of and sequences in Zhikong scallop (Chlamys farreri). Mar. Biotechnol. 2007; 9: 606–612.

    Article  PubMed  CAS  Google Scholar 

  12. Zhan AB, Bao ZM, Wang XL, Hu JJ. Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fish. Sci. 2005; 71: 1341–1346.

    Article  CAS  Google Scholar 

  13. Zhan AB, Hu JJ, Wang XL, Lu W, Hui M, Bao ZM. A panel of polymorphic EST-derived microsatellite loci for the bay scallop (Argopecten irradians). J. Mollus. Stud. 2006; 72: 436–438.

    Article  Google Scholar 

  14. Vos P, Hogers R, Bleeker M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995; 23: 4407–4414.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  16. Steven CR, Hill J, Masters B, Place AR. Genetic markers in blue crabs (Callinectes sapidus) I: isolation and characterization of microsatellite markers. J. Exp. Mar. Biol. Ecol. 2005; 319: 3–14.

    Article  CAS  Google Scholar 

  17. Guo SW, Thompson EA. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 1992; 48: 361–372.

    Article  PubMed  CAS  Google Scholar 

  18. Rice WR. Analyzing tables of statistical tests. Evolution 1989; 43: 223–225.

    Article  Google Scholar 

  19. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ. Analysis of SSRs derived from grape ESTs. Theor. Appl. Genet. 2000; 100: 723–726.

    Article  CAS  Google Scholar 

  20. Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S. Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor. Appl. Genet. 2003; 106: 912–922.

    PubMed  CAS  Google Scholar 

  21. Harada K, Okaura T, Giang LH, Huan NV, Iwasaki M, Nitasaka E. A novel microsatellite locus isolated from an AFLP fragment in the mangrove species Kandelia obovata (Rhizophoraceae). J. Plant Res. 2005; 118: 49–51.

    Article  PubMed  CAS  Google Scholar 

  22. Cordeiro GM, Maguire TL, Edwards KJ, Henry R. Optimisation of a micro satellite enrichment technique in Saccharum spp. Plant. Mol. Biol. Rep. 1999; 17: 225–229.

    Article  CAS  Google Scholar 

  23. Jakse J, Javornik B. High throughput isolation of microsatellites in hop (Humulus lupulus L.). Plant. Mol. Biol. Rep. 2001; 19: 217–226.

    Article  CAS  Google Scholar 

  24. Hu JJ, Nakatani M, Mizuno K, Fujimura T. Development and characterization of microsatellite markers in sweetpotato. Breed Sci. 2004; 54: 177–188.

    Article  CAS  Google Scholar 

  25. Edwards KJ, Baker JH, Daly A, Jones C, Karp A. Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 1996; 20: 758–760.

    PubMed  CAS  Google Scholar 

  26. Apte G, Gardner JP. Absence of population genetic differentiation in the New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) as assessed by allozyme variation. J. Exp. Mar. Biol. Ecol. 2001; 258: 173–194.

    Article  PubMed  Google Scholar 

  27. Li G, Hubert S, Bucklin K, Ribes V, Hedgecock D. Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Mol. Ecol. Notes 2003; 3: 228–232.

    Article  CAS  Google Scholar 

  28. Li Q, Park C, Kobayashi T, Kijima A. Inheritance of microsatellite DNA markers in the Pacific abalone Haliotis discus hannai. Mar. Biotechnol. 2003; 5: 331–338.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  30. Fraser LG, Harvey CF, Crowhurst RN, DeSilva HN. EST-derived microsatellites from Actinidia species and their potential for mapping. Theor. Appl. Genet. 2004; 108: 1010–1016.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  32. Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor. Appl. Genet. 2002; 104: 399–407.

    Article  PubMed  CAS  Google Scholar 

  33. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Parl WD, Ayres N, Cartinhour S. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryzasatica L.). Theor. Appl. Genet. 2000; 100: 713–722.

    Article  CAS  Google Scholar 

  34. Martin AP, Pardini AT, Noble LR, Jones CS. Conservation of a dinucleotide simple sequence repeat locus in sharks. Mol. Phylogenet. Evol. 2002; 23: 205–213.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Aibin Zhan

    Present address: Department of Integrative Biology, University of Guelph, NIG 2W1, Guelph, Ontario, Canada

Authors and Affiliations

  1. Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, China

    Aibin Zhan, Zhenmin Bao, Xiaoli Hu, Shi Wang, Wei Peng, Mingling Wang & Jingjie Hu

  2. Shandong Entry-Exit Inspection and Quarantine Bureau, 266001, Qingdao, China

    Chengzhu Liang & Zhiqin Yue

Authors
  1. Aibin Zhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhenmin Bao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaoli Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wei Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mingling Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jingjie Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chengzhu Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Zhiqin Yue
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jingjie Hu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhan, A., Bao, Z., Hu, X. et al. Characterization of 95 novel microsatellite markers for Zhikong scallop Chlamys farreri using FIASCO-colony hybridization and EST database mining. Fish Sci 74, 516–526 (2008). https://doi.org/10.1111/j.1444-2906.2008.01554.x

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1111/j.1444-2906.2008.01554.x

Key Words

Search

Navigation