Marine Biotechnology

, Volume 6, Issue 1, pp 26–36 | Cite as

AFLP-Based Genetic Linkage Maps of the Pacific Oyster Crassostrea gigas Thunberg

  • Li Li
  • Ximing Guo


Amplified fragment length polymorphisms (AFLPs) were used for genome mapping in the Pacific oyster Crassostrea gigas Thunberg. Seventeen selected primer combinations produced 1106 peaks, of which 384 (34.7%) were polymorphic in a backcross family. Among the polymorphic markers, 349 were segregating through either the female or the male parent. Chi-square analysis indicated that 255 (73.1%) of the markers segregated in a Mendelian ratio, and 94 (26.9%) showed significant (P < 0.05) segregation distortion. Separate genetic linkage maps were constructed for the female and male parents. The female framework map consisted of 119 markers in 11 linkage groups, spanning 1030.7 cM, with an average interval of 9.5 cM per marker. The male map contained 96 markers in 10 linkage groups, covering 758.4 cM, with 8.8 cM per marker. The estimated genome length of the Pacific oyster was 1258 cM for the female and 933 cM for the male, and the observed coverage was 82.0% for the female map and 81.3% for the male map. Most distorted markers were deficient for homozygotes and closely linked to each other on the genetic map, suggesting the presence of major recessive deleterious genes in the Pacific oyster.


linkage mapping genetic map AFLP genome oyster Crassostrea gigas 



We thank Mr. Gregory DeBrosse for care of experimental animals and Dr. Ziniu Yu for technical assistance with AFLP analysis. This work is conducted at Rutgers University and partly supported by grants from the New Jersey Commission on Science and Technology (00-2042-007-20) and Sea Grant (OD-9915 and ODRP-29). Li Li is a visiting student from IOCAS and partly supported by China’s Natural Science Foundation (Grant 39825121). This is publication IMCS-2003-27 and NJSG-03-39.


  1. Agresti, J.J., Seki, S., Cnaaani, A., Poompuang, S., Hallerman, E.M., Umiel, N., Hulada, G., Gall, G.A.E., May, B. 2000Breeding new strains of tilapia: development of an artificial center of origin and linkage map based on AFLP and microsatellite loci.Aquaculture1854356CrossRefGoogle Scholar
  2. Ahmed, M., Sparks, A.K. 1967A preliminary study of chromosomes of two species of oyster (Ostrea lurida and Crassostrea gigas).J Fish Res Bd Can2421552159Google Scholar
  3. Bert, P.F., Charmet, G., Sourdille, P., Hayward, M.D. 1999A high-density molecular map for ryegrass (Lolium perenne).Theoret Appl Genet99445452CrossRefGoogle Scholar
  4. Castiglioni, P., Pozzi, C., Heun, M., Terzi, V., Muller, K.J., Rohde, W., Salmini, F. 1998An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley.Genetics14920392056PubMedGoogle Scholar
  5. Castiglioni, P., Ajmone-Marsan, P., Wijk, R.V., Motto, M. 1999AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution.Theoret Appl Genet99425431CrossRefGoogle Scholar
  6. Cervera, M.-T., Storme, V., Ivens, B., Gusmao, J., Liu, B.H., Hostyn, V., Slycken, J.V., Montagu, M.V., Boerjan, W. 2001Dense genetic linkage map of three populus species (Populus deltoides, P. nigra, and P. trichocarpa) based on AFLP and microsatellite markers.Genetics158787809PubMedGoogle Scholar
  7. Chakravarti, A., Lasher, L.K., Reefer, J.E. 1991A maximum likelihood for estimating genome length using genetic linkage data.Genetics128175182PubMedGoogle Scholar
  8. Collins, A., Teague, J., Keats, B.J.B., Morton, N.E. 1996Linkage map integration.Genomics36157162Google Scholar
  9. Fishman, L., Kelly, A.J., Morgan, E., Willis, J.H. 2001A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions.Genetics15917011716Google Scholar
  10. Foltz, D.W. 1986Segregation and linkage studies of allozyme loci in pair crosses of the oyster Crassostrea virginica. Biochem Genet24941956PubMedGoogle Scholar
  11. Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., Talbot, W.S. 1999A genetic linkage map for zebrafish comparative analysis and localization of genes and expressed sequences.Genome Res9334347PubMedGoogle Scholar
  12. Gaffney, P.M. (2002) Associations between Microsatellites and repetetive elements in bivalve genomes. Presented at The International Conference on the Status of Plant, Animal and Microbe Genomes X, January 12–16, San Diego, Ca.Google Scholar
  13. Grewe, P.M., Krueger, C.C., Aquadro, C.F., Bermingham, E., Kincaid, H.L., May, B. 1993Mitochondrial DNA variation among lake trout (Salvelinus namaycush) strains stocked into Lake Ontario.Can J Fish Aquat Sci5023972403Google Scholar
  14. Guo, X., Allen, S.K. 1996Complete interference and nonrandom distribution of meiotic crossover in a mollusk, Mulinia lateralis.Biol Bull191145148PubMedGoogle Scholar
  15. Haanstra, J., Wye, C., Verbakel, H., Meijer-Dekens, F., Berg, P., Odinot, P., Heusden, A.W., Tanksley, S., Lindhout, P.L., Peleman, J. 1999An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations.Theoret Appl Genet99254271CrossRefGoogle Scholar
  16. Hedgecock, D., Hubert, S., Li, G., Bucklin, K. 2002A genetic linkage map of 100 microsatellite markers for the Pacific oyster Crassostrea gigas [abstract].J Shellfish Res21381Google Scholar
  17. Hu, Y.P., Foltz, D.W. 1996Genetics of scnDNA polymorphisms in controlled crosses.Mol Mar Biol Biotechnol5123129PubMedGoogle Scholar
  18. Hulbert, S.H., Ilott, T.W., Legg, E.J., Lincoln, S.E., Lander, E.S., Michelmore, R.W. 1988Genetic analysis of the fungus, Bremia lactucae using restriction fragment length polymorphisms.Genetics120947958PubMedGoogle Scholar
  19. Kelly, P.D., Chu, F., Woods, L.G., Ngo-Hazelett, P., Cardozo, T., Huang, H., Kimm, F., Liao, L., Yang, Y., Zhou, Y., Johnson, S.L., Abagyan, R., Schier, A.F., Posttlethwait, J.H., Talbot, W.S. 2000Genetic linkage mapping of zebrafish genes and ESTs.Genome Res10558567Google Scholar
  20. Kocher, T.D., Lee, W., Sobolewska, H., Penman, D., McAndrew, B. 1998A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus).Genetics14812251232Google Scholar
  21. Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newburg, L. 1987MAPMAKER, an interactive computer package for constructing primary genetic linkage map of experimental and natural populations.Genomics1174180PubMedGoogle Scholar
  22. Launey, S., Hedgecock, D. 2001High genetic load in the Pacific oyster Crassostrea gigas. Genetics159155165Google Scholar
  23. Liu, Z., Nichols, A., Li, P., Dunham, R.A. 1998Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their F1, F2 and backcross hybrids.Mol Gen Genet258260268CrossRefPubMedGoogle Scholar
  24. Liu, Z., Li, P., Kucuktas, H., Nichols, A., Tan, G., Zheng, X., Argue, B.J., Dunham, R.A. 1999Development of amplified fragment length polymorphism (AFLP) markers suitable for genetic linkage mapping of catfish.Trans Am Fish Soc128317327Google Scholar
  25. Liu, Z., Karsi, A., Li, P., Cao, D., Dunhum, R.A. .An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family.Genetics..Google Scholar
  26. McGoldrick, D.J., Hedgecock, D. 1997Fixation, segregation and linkage of allozyme loci in inbred families of the Pacific oyster Crassostrea gigas (Thunberg): implications for the causes of inbreeding depression.Genetics146321334Google Scholar
  27. Meksen, K., Ruben, E., Hyten, D., Triwitayakorn, K., Lightfoot, D.A. 2001Conversion of AFLP bands into high-throughput DNA markers.Mol Genet Genomics265207214PubMedGoogle Scholar
  28. Moore, S.S., Whan, V., Davis, G.P., Byrne, K., Hetzel, D.J.S., Preston, N. 1999The development and application of genetic markers for the kuruma prawn Penaeus japonicus.Aquaculture1731932CrossRefGoogle Scholar
  29. Nandi, S., Subudhi, P.K., Senadhira, D., Manigbs, N.L., Sen-Mandi, S., Huang, N. 1997Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping.Mol Gen Genet25518PubMedGoogle Scholar
  30. Naruse, K., Fukamachi, S., Mitani, H., Kondo, M., Matauoka, T., Kondo, S., Hanamura, N., Morita, Y., Hasegawa, K., Nishgaki, R., Shimada, A., Wada, H., Kusakabe, T., Suzuki, N., Kinoshita, M., Kanamori, A., Trerado, T., Kimura, H., Nonaka, M., Shima, A. 2000A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution.Genetics15417731795PubMedGoogle Scholar
  31. Neff, M.W., Broman, K.W., Mellersh, C.S., Ray, K., Acland, G.M., Aguirre, G.D., Ziegle, J.S., Ostrander, E.A., Rine, J. 1999A second-generation genetic linkage map of the domestic dog, Canis familiaries. Genetics151803820PubMedGoogle Scholar
  32. Negi, M.S., Devic, M., Delseny, M., Lakshmikumaran, M. 2000Identification of AFLP fragments linked to seed coat colour in Brassica juncea and conversation to a SCAR marker for rapid selection.Theor Appl Genet101146152CrossRefGoogle Scholar
  33. NIH/CEPH Collaborative Mapping Group.1992A comprehensive genetic linkage map of the human genome.Science2586786PubMedGoogle Scholar
  34. Nikaido, A., Yoshimaru, H., Tsumura, Y., Suyama, Y., Murai, M., Nagaasaka, K. 1999Segregation distortion for AFLP markers in Cryptomeria japonica. Genes Genet Syst745559CrossRefGoogle Scholar
  35. Ott, J. 1991Analysis of Human Genetic Linkage.Johns Hopkins University Press.Baltimore, MD.Google Scholar
  36. Postlethwait, J.H., Johnson, S.L., Midson, C.N., Talbot, W.S., Gates, M., Ballinger, E.W., Africa, D., Andrews, R., Carl, T., Risen, J.S., Horne, S., Kimmel, C.B., Hutchinson, M., Johnson, M., Rodriguez, A. 1994A genetic linkage map for the zebrafish.Science264699703PubMedGoogle Scholar
  37. Qi, X., Lindhout, P. 1997Development of AFLP markers in barley.Mol Gen Genet254330336CrossRefPubMedGoogle Scholar
  38. Qi, X., Stam, P., Lindhout, P. 1998Use of locus-specific markers to construct a high-density molecular map in barley.Theoret Appl Genet96376395CrossRefGoogle Scholar
  39. Reece, K.S., Morrison, C.L., Ribeiro, W.L., Gaffney, P.M., and Allen, S.K. (2002). Microsatellite markers for the eastern oyster Crassostrea viginica: linkage mapping and genetic monitoring for restoration projects. Presented at The International Conference on the Status of Plant, Animal and Microbe Genome X, January 12–16, San Diego, Ca.Google Scholar
  40. Sakamoto, T., Danzmann, R.G., Gharbi, K., Howard, P. 2000A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates.Genetics15513311345PubMedGoogle Scholar
  41. Singer, A., Perlman, H., Yan, Y., Walker, C., Corleyp-Smith, G., Brandhorst, B., Postlethwait, J. 2002Sex-specific recombination rates in zebrafish (Danio rerio).Genetics160649657Google Scholar
  42. Sybenga, J. 1996Recombination and chiasmata: a few intriguing discrepancies.Genome39473495Google Scholar
  43. Voorrips, R.E. 2001Mapchart Version 2.0: Windows software for the graphical presentation of linkage maps and QTLs.Plant Research InternationalWageningen, The NetherlandsGoogle Scholar
  44. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M. 1995AFLP: a new technique for DNA fingerprinting.Nucleic Acids Res2344074414PubMedGoogle Scholar
  45. Waugh, R., Bonar, N., Baird, E., Thomas, B., Graner, A., Haypes, P., Powell, W. 1997Homology of AFLP products in three mapping population of barley.Mol Gen Genet255311321PubMedGoogle Scholar
  46. Wilson, K., Li, Y., Whan, V., Lehnert, S., Byrne, K., Moore, S., Pongsomboon, S., Tassanakajon, A., Rosenberg, G., Ballment, E., Fayazi, Z., Swan, J., Kenway, M., Benzie, J. 2002Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism.Aquaculture204297309CrossRefGoogle Scholar
  47. Young, W.P., Wheeler, P.A., Coryell, V.H., Keim, P., Thorgaard, G.H. 1998A detailed linkage map of rainbow trout produced using doubled haploids.Genetics148113Google Scholar
  48. Yu, Z., Guo, X. 2002A basic AFLP linkage map for the eastern oyster, Crassostrea virginica Gmelin [abstract].J Shellfish Res21382Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  1. 1.Haskin Shellfish Research LaboratoryInstitute of Coastal and Marine Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349USA
  2. 2.Experimental Marine Biology LaboratoryInstitute of Oceanology, Chinese Academy of Science, 7 Nanhai Road, Qingdao, Shandong 266071P.R.C.
  3. 3.The Graduate School of Chinese Academy of Sciences, Beijing 100039P.R.C.

Personalised recommendations