Skip to main content
SpringerLink
Log in

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

  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1

Similar content being viewed by others

References

  • J.J. Agresti S. Seki A. Cnaaani S. Poompuang E.M. Hallerman N. Umiel G. Hulada G.A.E. Gall B. May (2000) ArticleTitleBreeding new strains of tilapia: development of an artificial center of origin and linkage map based on AFLP and microsatellite loci. Aquaculture 185 43–56 Occurrence Handle10.1016/S0044-8486(99)00335-X Occurrence Handle1:CAS:528:DC%2BD3cXitlKrtbc%3D

    Article  CAS  Google Scholar 

  • M. Ahmed A.K. Sparks (1967) ArticleTitleA preliminary study of chromosomes of two species of oyster (Ostrea lurida and Crassostrea gigas). J Fish Res Bd Can 24 IssueID10 2155–2159

    Google Scholar 

  • P.F. Bert G. Charmet P. Sourdille M.D. Hayward (1999) ArticleTitleA high-density molecular map for ryegrass (Lolium perenne). Theoret Appl Genet 99 445–452 Occurrence Handle10.1007/s001220051256 Occurrence Handle1:CAS:528:DyaK1MXmsVKksr0%3D

    Article  CAS  Google Scholar 

  • P. Castiglioni C. Pozzi M. Heun V. Terzi K.J. Muller W. Rohde F. Salmini (1998) ArticleTitleAn AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genetics 149 2039–2056 Occurrence Handle1:CAS:528:DyaK1cXlsFegsrw%3D Occurrence Handle9691056

    CAS  PubMed  Google Scholar 

  • P. Castiglioni P. Ajmone-Marsan R.V. Wijk M. Motto (1999) ArticleTitleAFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theoret Appl Genet 99 425–431 Occurrence Handle10.1007/s001220051253 Occurrence Handle1:CAS:528:DyaK1MXmsVKksr8%3D

    Article  CAS  Google Scholar 

  • M.-T. Cervera V. Storme B. Ivens J. Gusmao B.H. Liu V. Hostyn J.V. Slycken M.V. Montagu W. Boerjan (2001) ArticleTitleDense genetic linkage map of three populus species (Populus deltoides, P. nigra, and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158 787–809 Occurrence Handle1:CAS:528:DC%2BD3MXltFSisLc%3D Occurrence Handle11404342

    CAS  PubMed  Google Scholar 

  • A. Chakravarti L.K. Lasher J.E. Reefer (1991) ArticleTitleA maximum likelihood for estimating genome length using genetic linkage data. Genetics 128 175–182 Occurrence Handle1:STN:280:By6B1crjvFA%3D Occurrence Handle2060775

    CAS  PubMed  Google Scholar 

  • A. Collins J. Teague B.J.B. Keats N.E. Morton (1996) ArticleTitleLinkage map integration. Genomics 36 157–162

    Google Scholar 

  • L. Fishman A.J. Kelly E. Morgan J.H. Willis (2001) ArticleTitleA genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 159 1701–1716

    Google Scholar 

  • D.W. Foltz (1986) ArticleTitleSegregation and linkage studies of allozyme loci in pair crosses of the oyster Crassostrea virginica. Biochem Genet 24 941–956 Occurrence Handle1:CAS:528:DyaL2sXmsVGltQ%3D%3D Occurrence Handle3800871

    CAS  PubMed  Google Scholar 

  • M.A. Gates L. Kim E.S. Egan T. Cardozo H.I. Sirotkin S.T. Dougan D. Lashkari R. Abagyan A.F. Schier W.S. Talbot (1999) ArticleTitleA genetic linkage map for zebrafish comparative analysis and localization of genes and expressed sequences. Genome Res 9 334–347 Occurrence Handle1:CAS:528:DyaK1MXivVOrtrY%3D Occurrence Handle10207156

    CAS  PubMed  Google Scholar 

  • 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.

  • P.M. Grewe C.C. Krueger C.F. Aquadro E. Bermingham H.L. Kincaid B. May (1993) ArticleTitleMitochondrial DNA variation among lake trout (Salvelinus namaycush) strains stocked into Lake Ontario. Can J Fish Aquat Sci 50 2397–2403

    Google Scholar 

  • X. Guo S.K. Allen (1996) ArticleTitleComplete interference and nonrandom distribution of meiotic crossover in a mollusk, Mulinia lateralis. Biol Bull 191 IssueID2 145–148 Occurrence Handle1:STN:280:ByiD2szpvFU%3D Occurrence Handle8916540

    CAS  PubMed  Google Scholar 

  • J. Haanstra C. Wye H. Verbakel F. Meijer-Dekens P. Berg P. Odinot A.W. Heusden S. Tanksley P.L. Lindhout J. Peleman (1999) ArticleTitleAn integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations. Theoret Appl Genet 99 254–271 Occurrence Handle10.1007/s001220051231 Occurrence Handle1:CAS:528:DyaK1MXlvFGltbw%3D

    Article  CAS  Google Scholar 

  • D. Hedgecock S. Hubert G. Li K. Bucklin (2002) ArticleTitleA genetic linkage map of 100 microsatellite markers for the Pacific oyster Crassostrea gigas [abstract]. J Shellfish Res 21 IssueID1 381

    Google Scholar 

  • Y.P. Hu D.W. Foltz (1996) ArticleTitleGenetics of scnDNA polymorphisms in controlled crosses. Mol Mar Biol Biotechnol 5 IssueID2 123–129 Occurrence Handle1:CAS:528:DyaK28XjtlOntLk%3D Occurrence Handle8680525

    CAS  PubMed  Google Scholar 

  • S.H. Hulbert T.W. Ilott E.J. Legg S.E. Lincoln E.S. Lander R.W. Michelmore (1988) ArticleTitleGenetic analysis of the fungus, Bremia lactucae using restriction fragment length polymorphisms. Genetics 120 947–958 Occurrence Handle1:STN:280:BiaC3sjptlI%3D Occurrence Handle2906309

    CAS  PubMed  Google Scholar 

  • P.D. Kelly F. Chu L.G. Woods P. Ngo-Hazelett T. Cardozo H. Huang F. Kimm L. Liao Y. Yang Y. Zhou S.L. Johnson R. Abagyan A.F. Schier J.H. Posttlethwait W.S. Talbot (2000) ArticleTitleGenetic linkage mapping of zebrafish genes and ESTs. Genome Res 10 558–567

    Google Scholar 

  • T.D. Kocher W. Lee H. Sobolewska D. Penman B. McAndrew (1998) ArticleTitleA genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics 148 1225–1232

    Google Scholar 

  • E.S. Lander P. Green J. Abrahamson A. Barlow M.J. Daly S.E. Lincoln L. Newburg (1987) ArticleTitleMAPMAKER, an interactive computer package for constructing primary genetic linkage map of experimental and natural populations. Genomics 1 174–180 Occurrence Handle1:CAS:528:DyaL1cXhsVCksrk%3D Occurrence Handle3692487

    CAS  PubMed  Google Scholar 

  • S. Launey D. Hedgecock (2001) ArticleTitleHigh genetic load in the Pacific oyster Crassostrea gigas. Genetics 159 155–165

    Google Scholar 

  • Z. Liu A. Nichols P. Li R.A. Dunham (1998) ArticleTitleInheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their F1, F2 and backcross hybrids. Mol Gen Genet 258 260–268 Occurrence Handle10.1007/s004380050730 Occurrence Handle1:CAS:528:DyaK1cXjvFGiurs%3D Occurrence Handle9645432

    Article  CAS  PubMed  Google Scholar 

  • Z. Liu P. Li H. Kucuktas A. Nichols G. Tan X. Zheng B.J. Argue R.A. Dunham (1999) ArticleTitleDevelopment of amplified fragment length polymorphism (AFLP) markers suitable for genetic linkage mapping of catfish. Trans Am Fish Soc 128 317–327 Occurrence Handle1:CAS:528:DyaK1MXktlegsrY%3D

    CAS  Google Scholar 

  • Z. Liu A. Karsi P. Li D. Cao R.A. Dunhum (.) ArticleTitleAn AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. Genetics . .

    Google Scholar 

  • D.J. McGoldrick D. Hedgecock (1997) ArticleTitleFixation, segregation and linkage of allozyme loci in inbred families of the Pacific oyster Crassostrea gigas (Thunberg): implications for the causes of inbreeding depression. Genetics 146 321–334

    Google Scholar 

  • K. Meksen E. Ruben D. Hyten K. Triwitayakorn D.A. Lightfoot (2001) ArticleTitleConversion of AFLP bands into high-throughput DNA markers. Mol Genet Genomics 265 207–214 Occurrence Handle1:STN:280:DC%2BD3M3nsFCmtA%3D%3D Occurrence Handle11361330

    CAS  PubMed  Google Scholar 

  • S.S. Moore V. Whan G.P. Davis K. Byrne D.J.S. Hetzel N. Preston (1999) ArticleTitleThe development and application of genetic markers for the kuruma prawn Penaeus japonicus. Aquaculture 173 19–32 Occurrence Handle10.1016/S0044-8486(98)00461-X Occurrence Handle1:CAS:528:DyaK1MXhvVGhsL4%3D

    Article  CAS  Google Scholar 

  • S. Nandi P.K. Subudhi D. Senadhira N.L. Manigbs S. Sen-Mandi N. Huang (1997) ArticleTitleMapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet 255 1–8 Occurrence Handle1:CAS:528:DyaK2sXkvVWnurk%3D Occurrence Handle9230893

    CAS  PubMed  Google Scholar 

  • K. Naruse S. Fukamachi H. Mitani M. Kondo T. Matauoka S. Kondo N. Hanamura Y. Morita K. Hasegawa R. Nishgaki A. Shimada H. Wada T. Kusakabe N. Suzuki M. Kinoshita A. Kanamori T. Trerado H. Kimura M. Nonaka A. Shima (2000) ArticleTitleA detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics 154 1773–1795 Occurrence Handle10747068

    PubMed  Google Scholar 

  • M.W. Neff K.W. Broman C.S. Mellersh K. Ray G.M. Acland G.D. Aguirre J.S. Ziegle E.A. Ostrander J. Rine (1999) ArticleTitleA second-generation genetic linkage map of the domestic dog, Canis familiaries. Genetics 151 803–820 Occurrence Handle1:CAS:528:DyaK1MXhtlCgs7k%3D Occurrence Handle9927471

    CAS  PubMed  Google Scholar 

  • M.S. Negi M. Devic M. Delseny M. Lakshmikumaran (2000) ArticleTitleIdentification of AFLP fragments linked to seed coat colour in Brassica juncea and conversation to a SCAR marker for rapid selection. Theor Appl Genet 101 146–152 Occurrence Handle10.1007/s001220051463 Occurrence Handle1:CAS:528:DC%2BD3cXlvVyksLo%3D

    Article  CAS  Google Scholar 

  • InstitutionalAuthorNameNIH/CEPH Collaborative Mapping Group. (1992) ArticleTitleA comprehensive genetic linkage map of the human genome. Science 258 67–86 Occurrence Handle1439770

    PubMed  Google Scholar 

  • A. Nikaido H. Yoshimaru Y. Tsumura Y. Suyama M. Murai K. Nagaasaka (1999) ArticleTitleSegregation distortion for AFLP markers in Cryptomeria japonica. Genes Genet Syst 74 55–59 Occurrence Handle10.1266/ggs.74.55 Occurrence Handle1:CAS:528:DyaK1MXms12itrY%3D

    Article  CAS  Google Scholar 

  • J. Ott (1991) Analysis of Human Genetic Linkage. Johns Hopkins University Press. Baltimore, MD.

    Google Scholar 

  • J.H. Postlethwait S.L. Johnson C.N. Midson W.S. Talbot M. Gates E.W. Ballinger D. Africa R. Andrews T. Carl J.S. Risen S. Horne C.B. Kimmel M. Hutchinson M. Johnson A. Rodriguez (1994) ArticleTitleA genetic linkage map for the zebrafish. Science 264 699–703 Occurrence Handle1:CAS:528:DyaK2cXktVagsLo%3D Occurrence Handle8171321

    CAS  PubMed  Google Scholar 

  • X. Qi P. Lindhout (1997) ArticleTitleDevelopment of AFLP markers in barley. Mol Gen Genet 254 330–336 Occurrence Handle10.1007/s004380050423 Occurrence Handle1:CAS:528:DyaK2sXjsFOhs7o%3D Occurrence Handle9150268

    Article  CAS  PubMed  Google Scholar 

  • X. Qi P. Stam P. Lindhout (1998) ArticleTitleUse of locus-specific markers to construct a high-density molecular map in barley. Theoret Appl Genet 96 376–395 Occurrence Handle10.1007/s001220050752 Occurrence Handle1:CAS:528:DyaK1cXivVWls7w%3D

    Article  CAS  Google Scholar 

  • 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 

  • T. Sakamoto R.G. Danzmann K. Gharbi P. Howard (2000) ArticleTitleA microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 155 1331–1345 Occurrence Handle1:CAS:528:DC%2BD3cXlsFSku7Y%3D Occurrence Handle10880492

    CAS  PubMed  Google Scholar 

  • A. Singer H. Perlman Y. Yan C. Walker G. Corleyp-Smith B. Brandhorst J. Postlethwait (2002) ArticleTitleSex-specific recombination rates in zebrafish (Danio rerio). Genetics 160 649–657

    Google Scholar 

  • J. Sybenga (1996) ArticleTitleRecombination and chiasmata: a few intriguing discrepancies. Genome 39 473–495 Occurrence Handle1:CAS:528:DyaK28Xktlekurg%3D

    CAS  Google Scholar 

  • R.E. Voorrips (2001) Mapchart Version 2.0: Windows software for the graphical presentation of linkage maps and QTLs. Plant Research International Wageningen, The Netherlands

    Google Scholar 

  • P. Vos R. Hogers M. Bleeker M. Reijans T. Lee M. Hornes A. Frijters J. Pot J. Peleman M. Kuiper M. Zabeau (1995) ArticleTitleAFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23 4407–4414 Occurrence Handle1:CAS:528:DyaK2MXpslensbo%3D Occurrence Handle7501463

    CAS  PubMed  Google Scholar 

  • R. Waugh N. Bonar E. Baird B. Thomas A. Graner P. Haypes W. Powell (1997) ArticleTitleHomology of AFLP products in three mapping population of barley. Mol Gen Genet 255 311–321 Occurrence Handle1:CAS:528:DyaK2sXlsFeqsrs%3D Occurrence Handle9268022

    CAS  PubMed  Google Scholar 

  • K. Wilson Y. Li V. Whan S. Lehnert K. Byrne S. Moore S. Pongsomboon A. Tassanakajon G. Rosenberg E. Ballment Z. Fayazi J. Swan M. Kenway J. Benzie (2002) ArticleTitleGenetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture 204 297–309 Occurrence Handle10.1016/S0044-8486(01)00842-0 Occurrence Handle1:CAS:528:DC%2BD38XmsFSmtA%3D%3D

    Article  CAS  Google Scholar 

  • W.P. Young P.A. Wheeler V.H. Coryell P. Keim G.H. Thorgaard (1998) ArticleTitleA detailed linkage map of rainbow trout produced using doubled haploids. Genetics 148 1–13

    Google Scholar 

  • Z. Yu X. Guo (2002) ArticleTitleA basic AFLP linkage map for the eastern oyster, Crassostrea virginica Gmelin [abstract]. J Shellfish Res 21 IssueID1 382

    Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Haskin Shellfish Research Laboratory, Institute of Coastal and Marine Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA

    Li Li & Ximing Guo

  2. Experimental Marine Biology Laboratory, Institute of Oceanology, Chinese Academy of Science, 7 Nanhai Road, Qingdao, Shandong 266071, P.R.C.

    Li Li

  3. The Graduate School of Chinese Academy of Sciences, Beijing 100039, P.R.C.

    Li Li

Authors
  1. Li Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ximing Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ximing Guo.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, L., Guo, X. AFLP-Based Genetic Linkage Maps of the Pacific Oyster Crassostrea gigas Thunberg . Mar. Biotechnol. 6, 26–36 (2004). https://doi.org/10.1007/s10126-003-0001-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-003-0001-0

Keywords

Search

Navigation