A preliminary genetic map of Zhikong scallop (Chlamys farreri Jones et Preston 1904) Lingling Wang 1,2 , Linsheng Song 1 ,Yaqing Chang 3 ,Wei Xu 1,2 , Duojiao Ni 1,2 & Ximing Guo 4 1 Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China 2 Graduate School, Chinese Academy of Sciences, Beijing, China 3 Dalian Fisheries College, Dalian, China 4 Haskin Shell¢sh Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, USA Correspondence: Dr L Song, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China. E-mail: lshsong@ms.qdio.ac.cn Abstract Zhikong scallop ( Chlamys farreri Jones et Preston 1904) is one of the most important aquaculture spe- cies in China. The development of a genetic linkage map would provide a powerful tool for the genetic im- provement of this species. Ampli¢ed fragment length polymorphism (AFLP) is a PCR-based technique that has proven to be powerful in genome ¢ngerprinting and mapping, and population analysis. Genetic maps of C. farreri were constructed using AFLP markers and a full-sib family with 60 progeny. Atotal of 503 segregating AFLP markers were obtained, with 472 following the Mendelian segregation ratio of 1:1 and 31markers showing signi¢cant ( Po0.05) segregation distortion. The male map contained 166 informative AFLP markers in 23 linkage groups covering 2468 cM. The average distance between markers was 14.9cM. The female genetic map consisted of 198 markers in 25 linkage groups spanning 3130 cM with an average inter-marker spacing of 15.8 cM. DNA polymorphisms that segregated in a 3:1 ratio as well as the AFLP markers that were heterozygous in both parents were included to construct combined linkage genetic map. Five shared linkage groups, ran- ging from 61.1 to 162.5 cM, were identi¢ed between the male and female maps, covering 431cM. Ampli- ¢ed fragment length polymorphism markers ap- peared to be evenly distributed within the linkage groups. Although preliminary, these maps provide a starting point for the mapping of the functional genes and quantitative trait loci in C. farreri . Keywords: Chlamys farreri , genetic map, AFLP, scallop, aquaculture Introduction Zhikong scallop ( Chlamys farreri Jones et Preston 1904) is one of the most important aquaculture spe- cies in China. It accounts for about 75^80% of the to- tal scallop production from Chinese aquaculture, which amounted to 1 million tonnes in 1996 (Guo, Ford & Zhang1999). Severe summer mortalities have caused a 37% decline in scallop production in1998, probably because of diseases and degradation in stock quality (Wang & Xiang 1999; Song, Li & Li 2002). As a native species, C. farreri culture in China is exclusively based on natural seed. With the rapid development of scallop aquaculture, the natural re- source of C. farreri has been stressed, and the devel- opment of selective breeding strategies to enhancing growth performance and disease resistance is ur- gently needed. From a practical viewpoint, genetic maps would provide the basis for the detection of quantitative trait loci (QTLs) a¡ecting economically importance traits such as growth and disease resis- tance. Knowledge of linkage between markers and QTL alleles can be used in marker-assisted breeding programmes for the genetic improvement of C. farreri . Ampli¢ed fragment length polymorphism (AFLP) is a PCR-based technique that has proven to be powerful in genome ¢ngerprinting and mapping, and population analysis (Vos, Hogers, Bleeker, Rei- jans, Van De Lee, Hornes, Frijters, Pot, Peleman & Zabeau 1995). In AFLP analysis, a large number of markers are generated per reaction, providing more e⁄cient detection of variation than randomly ampli- ¢ed polymorphic DNAs (RAPDs) or restriction frag- ment length polymorphisms. The assay e⁄ciency index of AFLPs was ¢ve to10 times higher than that Aquaculture Research, 2005, 36, 643^653 doi: 10.1111/j.1365-2109.2005.01268.x r 2005 Blackwell Publishing Ltd 643