Chinese Journal of Oceanology and Limnology Vol. 28 No. 1, P. 46-54, 2010 DOI: 10.1007/s00343-010-9233-9 Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)* LI Qi (李琪) ** , SHU Jing (束婧), ZHAO Cui (赵翠), LIU Shikai (刘士凯), KONG Lingfeng (孔令锋), ZHENG Xiaodong (郑小东) † Fisheries College, Ocean University of China, Qingdao 266003, China Received Oct. 30, 2008; revision accepted Apr. 5, 2009 © Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag Berlin Heidelberg 2010 Abstract Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone (Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences, after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2–17, with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922, respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families, with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai, together with the high rate of transportability across Haliotis species, make this set of EST-SSR markers an important tool for comparative mapping, marker-assisted selection, and evolutionary studies, not only in the Pacific abalone, but also in related species. Keyword: Haliotis discus hannai; expressed sequence tag; EST; microsatellite; Pacific abalone; simple sequence repeats 1 INTRODUCTION The use of microsatellites (simple sequence repeats; SSRs) as genetic markers has become widespread, and has served as an invaluable tool for various genetic studies. They have been employed extensively for fishery animals in population genetic studies, parentage analysis, and genetic linkage mapping. The advantages of microsatellite loci include codominant alleles, high allelic diversity at the loci, extensive genome coverage (present in both coding and noncoding regions), and the ability to determine genotypes from small samples of tissue using polymerase chain reaction (PCR) (Zane et al., 2002). Despite these advantages, the isolation and characterization of such markers via traditional methods (i.e., the screening of size-fractionated genomic DNA libraries) are costly and time consuming (Squirrell et al., 2003). Over the past decade, there has been a tremendous increase in the availability of DNA sequence data from a wide variety of taxa, including a wealth of expressed sequence tags (ESTs). Using certain computer programs, the sequence data for ESTs can be downloaded from GenBank and scanned for the identification of microsatellites, which are typically referred to as EST-SSRs or genic microsatellites. Thus, the use of such databases for marker development can be relatively easy and inexpensive, and appears to be a promising alternative to the development of traditional genomic SSRs following standard methods. To date, EST-SSRs have been developed in some important aquaculture species (Ng et al., 2005; Serapion et al., 2004; Perez et al., 2005). In addition to requiring less time and money to develop, EST-SSRs have a number of intrinsic advantages over genomic SSRs. One advantage is that EST-SSRs are directly associated with a coding gene, and so might be useful ∗ Supported by the National High Technology Research and Development Program of China (863 Program) (No. 2007AA09Z433) and the Cultivation Fund of the Key Scientific and Technical Innovation Project Ministry of Education of China (No. 707041) ∗∗ Corresponding author: qili66@ouc.edu.cn