Genetic Linkage Map of the Eastern Oyster Crassostrea virginica Gmelin ZINIU YU 1,2 AND XIMING GUO 1, * 1 Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey 08349; and 2 Mariculture Research Laboratory, College of Fisheries, Ocean University of Qingdao, Qingdao 266003, People’s Republic of China Abstract. Amplified fragment length polymorphisms (AFLPs), along with some microsatellite and Type I mark- ers, were used for linkage analysis in Crassostrea virginica Gmelin, the eastern oyster. Seventeen AFLP primer com- binations were selected for linkage analysis with two par- ents and their 81 progeny. The 17 primer combinations produced 396 polymorphic markers, and 282 of them were segregating in the two parents. Chi-square analysis indi- cated that 259 (91.8%) markers segregated in Mendelian ratio, while the other 23 (8.2%) showed significant (P  0.05) segregation distortion, primarily for homozygote de- ficiency and probably due to deleterious recessive genes. Moderately dense linkage maps were constructed using 158 and 133 segregating markers (including a few microsatellite and Type I markers) from male and female parents, respec- tively. The male framework map consisted of 114 markers in 12 linkage groups, covering 647 cM. The female map had 84 markers in 12 linkage groups with a length of 904 cM. The estimated genome length was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and female map when all linked markers were considered. Genetic maps observed in this study are longer than the cytogenetic map, possibly because of low marker density. Introduction The past decade has brought tremendous advances in genomics. Complete genome sequences are now available for many organisms including several eukaryotes such as Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. The list of completed genomes is rapidly growing, and representative organisms of most taxa are now subjects of intensive genomic analysis. Mollusca, the sec- ond largest phylum of invertebrates, has received little at- tention. The number of available markers remains small and inadequate for genomic-wide mapping analysis, and no genetic linkage map has been published for any species. Understanding the genome of molluscs is important for comparative and evolutionary genomics, as well as for genetic improvement of cultured species. Crassostrea virginica Gmelin, the eastern oyster, is one of the best-understood molluscs. It is a marine bivalve that occurs naturally along the Atlantic coast of North America (Galtsoff, 1964); it is easily cultured and widely available. It has a haploid number of 10 chromosomes (Longwell and Stiles, 1967), one of the lowest among molluscs, making it an ideal model mollusc for genetic and genomic analysis. The eastern oyster is also a species of economic signifi- cance, supporting major fishery and aquaculture industries in North America, so studies of its genome would be im- portant for genetic improvement of this species. The devel- opment of genetic linkage maps is particularly useful for the mapping of quantitative trait loci (QTLs) and for marker- assisted selection (MAS) (Lander and Botstein, 1989; Cho et al., 1994). Genetic linkage maps have been developed for almost all major aquaculturally important species, including tilapia, rainbow trout, catfish, oysters, and shrimps (Kocher et al., 1998; Young et al., 1998; Sakamoto et al., 2000; Waldbieser et al., 2001; Hubert et al., 2002; Li and Guo, 2002; Moore et al., 1999; Wilson et al., 2002). Two preliminary linkage maps were recently constructed for the Pacific oyster (Crassostrea gigas): one with micro- satellites (Hubert et al., 2002) and one with RAPD and AFLP markers (Li and Guo, 2002). However, details of the two maps have not been published. As for the eastern * To whom correspondence should be addressed: E-mail: xguo@ hsrl.rutgers.edu Reference: Biol. Bull. 204: 327–338. (June 2003) © 2003 Marine Biological Laboratory 327