SHORT COMMUNICATION Expressed sequence tag-derived microsatellite markers for the zhikong scallop (Chlamys farreri) and their utility in two other scallop species Cui Zhao & Qi Li Fisheries College, Ocean University of China, Qingdao, China Correspondence: Q Li, Fisheries College, Ocean University of China, Qingdao 266003, China. E-mail: qili66@mail.ouc.edu.cn The zhikong scallop, Chlamys farreri (Jones et Preston), a native species to China, has a wide distribution along the coast of northern China, Korea, Japan and eastern Russia.This species is one of the most important cul- tured molluscs in China, with an annual production of over 500 000 tonnes (Guo, Ford & Zhang 1999). In re- cent years, however, intensive aquaculture of this spe- cies has resulted in serious problems such as retarded growth and increased mortality. Mass mortality of this species occurred frequently in many farming areas in China (Zhang & Yang 1999). The situation has not yet changed and large-scale death of the farmed C. farreri has become a major constraint for the development of the scallop culture. To genetically improve the scallop, a selective breeding programme was initiated in China in 2001, and a preliminary linkage map has been con- structed for C. farreri using ampli¢ed fragment length polymorphism (AFLP) markers (Li, Xiang, Liu, Zhang, Dong & Zhang 2005). Microsatellites (or simple sequence repeats, SSRs) are ubiquitous in eukaryotic genomes and consist of tandem repeats of one to six nucleotides.Variation in microsatellite length occurs primarily due to slipped- strand mispairing during DNA replication, and mu- tations of this sort occur at a much higher frequency than do point mutations and insertions/deletions (Katti, Ranjekar & Gupta 2001; Li, Korol, Fahima, Beiles & Nevo 2002). The £anking regions of microsa- tellite loci are relatively conserved, so primers can be developed easily for a simple polymerase chain reac- tion (PCR) ampli¢cation to screen for polymorphism on agarose or acrylamide gels, depending on the dif- ference in size between the alleles. They are charac- terized by their hypervariability and co-dominance. Compared with AFLP markers, microsatellites are ideal molecular markers for mapping due to the high levels of polymorphism and transferability across dif- ferent strains (Scott, Eggler, Seaton, Rossetto, Ablett, Lee & Henry 2000; Rossetto, McNally & Henry 2002). However, the development of microsatellite markers has traditionally been limited by the time-consum- ing and labour-intensive requirement to construct, enrich and sequence genomic libraries (Edwards, Barker, Daly, Jones & Karp 1996). To date, o20 geno- mic microsatellites have been identi¢ed in C. farreri (Zhan, Bao,Yao,Wang, Hui & Hu 2006). Recently, a new alternative source of microsatel- lites has been utilized. Over the past decade, there has been a tremendous increase in the availability of DNA sequences from a wide variety of species, includ- ing a wealth of expressed sequence tags (ESTs) that are typically unedited, automatically processed, single- pass sequences produced from cDNAs (Pashley, Ellis, McCauley & Burke 2006). The EST databases are being examined for their microsatellite-containing se- quences, and these microsatellites are being used as markers in various studies. A large number of EST-de- rived microsatellite markers (EST^SSRs) have been suc- cessfully developed from public sequence database in many species, such as bay scallop (Roberts, Romano & Gerlach 2005), eastern oyster (Wang & Guo 2007), Paci- ¢c oyster (Yu & Li 2007a) and blue mussel (Yu & Li 2007b). As a new kind of molecular marker, EST^SSR markers have many intrinsic advantages over genomic Aquaculture Research, 2008, 39, 557^560 doi: 10.1111/j.1365-2109.2008.01908.x r 2008 The Authors Journal Compilation r 2008 Blackwell Publishing Ltd 557