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

Authors

  • Aibin ZHAN,

    1. Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, and
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      Present address: Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.

  • Zhenmin BAO,

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

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

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

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

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

    Corresponding author
    1. Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, and
      * Tel: 86-532-8203-1969.
      Fax: 86-532-8203-1969. Email: hujingjie@ouc.edu.cn
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      Present address: Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.

  • Chengzhu LIANG,

    1. Shandong Entry–Exit Inspection and Quarantine Bureau, Qingdao, 266001, China
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  • Zhiqin YUE

    1. Shandong Entry–Exit Inspection and Quarantine Bureau, Qingdao, 266001, China
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* Tel: 86-532-8203-1969.
Fax: 86-532-8203-1969. Email: hujingjie@ouc.edu.cn

Abstract

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.

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