Abstract
A total of 1479 recombinant clones were obtained from a Sau3A-digested genomic library of Penaeus (Litopenaeus) vannamei and used for probe hybridization. Of the 251 clones that tested positive to one or more of the probes and were sequenced, 173 (69%) contained 573 simple sequence repeats, or microsatellites, with 3 or more repeats. The frequency of microsatellites with 3, 5, and 10 or more repeats was 1 in 0.94 kb, 1 in 2.78 kb, and 1 in 5.94 kb, respectively. To increase the number of polymorphic markers for mapping, 136 primer sets that flanked microsatellites containing single or multiple motifs with 3 or more repeats were designed and tested. Of the 136 primers, 93 (68.0%) were polymorphic in cultured shrimp, with polymorphism information content (PIC) values ranging from 0.195 to 0.873, and observed heterozygosities ranging from 10% to 100%. These markers are being used along with other markers to construct a linkage map for P. vannamei.
Similar content being viewed by others
References
A. Alcivar-Warren Z. Xu D. Meehan Y. Fan L. Song (2002) Shrimp genomics: development of a genetic map to identify QTLs responsible for economically important traits in Litopenaeus vannamei. N. Shimizu T. Aoki I. Hirono F. Takashima (Eds) Aquatic Genomics: Steps Toward a Great Future. Springer-Verlag Tokyo, Japan 61–72
B.J. Argue A. Alcivar-Warren (1999) Genetics and breeding applied to the penaeid shrimp farming industry. R.A. Bullis G.D. Pruder (Eds) Controlled and Biosecure Production Systems: Preliminary Proceedings of a Special Session on Evolution and Integration of Shrimp and Chicken Models Oceanic Institute Honolulu, Hawaii 29–54
F.M. Ausubel R. Brent R.E. Kingston D.D. Moore J.G. Seidman J.A. Smith K. Struhl (2002) Current Protocols in Molecular Biology. John Wiley and Sons, Inc. Waltham, Mass
J. Bagshaw M. Bucholt (1997) ArticleTitleA novel satellite/microsatellites combination in the genome of the marine shrimp, Penaeus vannamei. Gene 184 211–214 Occurrence Handle1:CAS:528:DyaK28XnsFSls7g%3D Occurrence Handle9031630
J.D. Baldwin A.L. Bass B.W. Bowen W.H. Clark (1998) ArticleTitleMolecular phylogeny and biogeography of the marine shrimp Penaeus. Mol Phylogenet Evol 10 399–407 Occurrence Handle1:CAS:528:DyaK1MXhtlKmtL0%3D Occurrence Handle10051392
A.O. Ball S. Leonards R.W. Chapman (1998) ArticleTitleCharacterization of (GT)n microsatellites from native white shrimp (Penaeus setiferus). Mol Ecol 7 1251–1253 Occurrence Handle1:CAS:528:DyaK1cXmtFOitr4%3D Occurrence Handle9734081
J.S. Beckmann J.P. Weber (1992) ArticleTitleSurvey of human and rat microsatellites. Genetics 12 627–631 Occurrence Handle1:CAS:528:DyaK38Xlt1Glt7k%3D
D. Botstein R.P. White M. Skolnick R.W. Davis (1980) ArticleTitleConstruction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Anim Genet 32 314–331 Occurrence Handle1:CAS:528:DyaL3cXkvFamtbc%3D
A.L. Brooker D. Cook P. Bentzen J.M. Wright R.W. Doyle (1994) ArticleTitleOrganization of microsatellites differs between mammals and cold-water teleost fishes. Can J Fish Aquat Sci 51 1959–1966
A.L. Brooker J.A.H. Benzie D. Blair (2000) ArticleTitlePopulation structure of the giant tiger prawn Penaeus monodon in Australian waters determined using microsatellites markers. Mar Biol 136 149–157
W.H. Carr K.T. Fjalestad D. Godin J. Swingle J.N. Sweeney T. Gjedrem (1997) Genetic variation in weight and survival in a population of specific pathogen-free shrimp, Penaeus vannamei. T.W. Flegel I.H. MacRae (Eds) Diseases in Asian Aquaculture III. Fish Health Section, Asian Fisheries Society Manila, Philippines 265–271
R.P.M.A. Crooijmans V.A.F. Bierbooms J. Komen J.J. Van de Poel M.A.M. Groenen (1997) ArticleTitleMicrosatellite markers in common carp (Cyprinus carpio P.). Anim Genet 28 129–134 Occurrence Handle1:CAS:528:DyaK2sXjs1Cgt7k%3D
A. Estoup P. Presa F. Krieg D. Vaiman R. Guyomard (1993a) ArticleTitle(CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout). Heredity 71 488–496 Occurrence Handle1:CAS:528:DyaK2cXitFejtLc%3D
A. Estoup M. Solignac M. Harry J.M. Cornut (1993b) ArticleTitleCharacterization of GT and CT microsatellites in two insect species: Apis mellifera and Bombus terrestris. Nucleic Acids Res 21 1427–1431 Occurrence Handle1:CAS:528:DyaK3sXit1Ohtr8%3D
Garcia, D.K., and Alcivar-Warren, A. (1996) Identification and organization of microsatellites in Penaeus vannamei shrimp. Proceedings of the XXVth International Conference on Animal Genetics, Tours, France, July, 2125, 1996, Abstract C061, 113.
D.K. Garcia M.A. Faggart L. Rhoades J.A. Wyban W. Carr K.M. Ebert J.N. Sweeney A. Alcivar-Warren (1994) ArticleTitleGenetic diversity of cultured Penaeus vannamei shrimp using three molecular genetic techniques. Mol Mar Biol Biotechnol 3 270–280 Occurrence Handle1:CAS:528:DyaK2MXjt12gtL0%3D Occurrence Handle7881514
D.K. Garcia A.K. Dhar A. Alcivar-Warren (1996) ArticleTitleMolecular analysis of a RAPD marker (B20) reveals two microsatellites and differential mRNA expression. Mol Mar Biol Biotechnol 5 71–83 Occurrence Handle8869519
C.M. Hearne S. Ghosh J.A. Todd (1992) ArticleTitleMicrosatellites for linkage analysis of genetic traits. Trends Genet 8 288–294 Occurrence Handle1:CAS:528:DyaK38Xls1Crur0%3D Occurrence Handle1509520
D.V. Lightner R.M. Redman B.T. Poulus L.M. Nuna J.L. Mari K.W. Hasson (1997) ArticleTitleRisk of spread of penaeid shrimp viruses in the Americas by the international movement of live and frozen shrimp. Rev Sci Tech Off Int Epiz 16 146–160 Occurrence Handle1:STN:280:ByiH28bmslc%3D
J.M. Lotz C.L. Browdy W.H. Carr P.P. Frelier D.V. Lightner (1995) USMSFP suggested procedures and guidelines for assuring the specific pathogen status of shrimp broodstock and seed. C.L. Browdy J.S. Hopkins (Eds) Swimming Through Troubled Waters (Proceedings of the Special Session on Shrimp Farming) World Aquaculture Society Baton Rouge, La.
S.K. McConnell P. O'Reilly L. Hamilton J.M. Wright P. Bentzen (1995) ArticleTitlePolymorphic microsatellites loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Can J Fish Aquat Sci 52 1863–1872 Occurrence Handle1:CAS:528:DyaK28XmvV2gug%3D%3D
S.S. Moore V.A. 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
Y. Naciri Y. Vigouroux J. Dallas E. Desmarais C. Delsert F. Bonhomme (1995) ArticleTitleIdentification and inheritance of (GA/TC)n and (AC/GT)n repeats in European flat oyster Ostrea edulis (L.). Mol Mar Biol Biotechnol 4 83–89 Occurrence Handle1:CAS:528:DyaK2MXmvVKnsbY%3D Occurrence Handle7749469
R.L. Naylor R.J. Goldburg J.H. Primavera N. Kautsky M.C.M. Beveridge J. Clay C. Folke J. Lubchenco H. Mooney M. Troell (2000) ArticleTitleEffect of aquaculture on world fish supplies. Nature 405 1017–1024 Occurrence Handle10.1038/35016500 Occurrence Handle1:CAS:528:DC%2BD3cXkvFKlsrg%3D Occurrence Handle10890435
M. Nei (1987) Molecular Evolutionary Genetics. Columbia University Press New York, N.Y. 176–207
G. Orti D.E. Pearse J.C. Avise (1997) ArticleTitlePhylogenetic assessment of length variation at a microsatellite locus. Proc Natl Acad Sci USA 94 10745–10749 Occurrence Handle1:CAS:528:DyaK2sXmtlekt7k%3D Occurrence Handle9380705
A. Ozaki T. Sakamoto S. Khoo K. Nakamura M.R. Coimbra T. Akutsu N. Okamoto (2000) ArticleTitleQuantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Mol Genet Genom 265 23–31
J.M. Pemberton J. Slate D.R. Bancroft J.A. Barrett (1995) ArticleTitleNonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4 249–252 Occurrence Handle1:STN:280:ByqB2Mzkslw%3D Occurrence Handle7735527
S. Rozen H.J. Skaletsky (2000) Primer 3 on the WWW for general users and for biologist programmers. S. Krawtz S. Misener (Eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press Totowa, N.I. 365–386
M.D. Schug K.A. Wetterstrand M.S. Gaudette R.H. Lim C.M. Hutter C.F. Aquadro (1998) ArticleTitleThe distribution and frequency of microsatellites loci in Drosophila melanogaster. Mol Ecol 7 57–70 Occurrence Handle1:CAS:528:DyaK1cXhtFSqu7w%3D Occurrence Handle9465417
A. Slettan I. Olsaker O. Lie (1993) ArticleTitleIsolation and characterization of variable (GT)n repetitive sequences from Atlantic salmon, Salmo salar L. Anim Genet 24 195–197 Occurrence Handle1:CAS:528:DyaK3sXltlGqt7o%3D
R.L. Stallings A.F. Ford D. Nelson D.C. Torney C.E. Hildebrand R.K. Moyzis (1991) ArticleTitleEvolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics 10 807–815 Occurrence Handle1:CAS:528:DyaK3MXlslKns7c%3D Occurrence Handle1909685
J.E. Strassman K. Barefield C.R. Solis C.R. Hughes D.C. Queller (1997) ArticleTitleTrinucleotide microsatellites loci for a social wasp, Polistes. Mol Ecol 6 97–100 Occurrence Handle9004523
A. Tassanakajon A. Tiptawonnukul P. Supungul V. Rhimphanitchayakit D. Cook P. Jarayabhand S. Klinbunga V. Boonsaeng (1998) ArticleTitleIsolation and characterization of microsatellites markers in the black tiger prawn Penaeus monodon. Mol Mar Biol Biotechnol 7 55–61 Occurrence Handle1:CAS:528:DyaK1cXjtVGqsrY%3D
D. Tautz (1989) ArticleTitleHypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17 6468–6471
P.A. Thoren R.J. Paxton A. Estoup (1995) ArticleTitleUnusually high frequency of (CT)n and (GT)n microsatellites loci in a yellowjacket wasp, Vespula rufa (P.) (Hymenoptera: Vespidae). Insect Mol Biol 4 141–148 Occurrence Handle8589840
V. Vonau M. Ohresser N. Bierne C. Delsert I. Beuzart E. Bedier F. Bonhomme (1999) ArticleTitleThree polymorphic microsatellites in the shrimp Penaeus stylirostris. Anim Genet 30 234–235
J.L. Weber (1990) ArticleTitleInformativeness of human (dC-dA)n (dG-dT)n polymorphisms. Genomics 7 524–530 Occurrence Handle1974878
G.M. Wolfus D.K. Garcia A. Alcivar-Warren (1997) ArticleTitleApplication of the microsatellites technique for analyzing genetic diversity in shrimp breeding programs. Aquaculture 152 35–47 Occurrence Handle10.1016/S0044-8486(96)01527-X Occurrence Handle1:CAS:528:DyaK2sXjslKntL8%3D
J.M. Wright P. Bentzen (1994) ArticleTitleMicrosatellites: genetic markers for the future. Rev Fish Biol Fish 4 384–388
Z. Xu A.K. Dhar J. Wyrzykoswki A. Alcivar-Warren (1999) ArticleTitleIdentification of abundant and informative microsatellites from shrimp (Penaeus monodon) genome. Anim Genet 30 1–17 Occurrence Handle10.1046/j.1365-2052.1999.00377.x Occurrence Handle1:CAS:528:DyaK1MXhsVyqtrc%3D Occurrence Handle10050277
Acknowledgements
Thanks to Steve Arce, Brad Argue, Fernanda Calderon, William Carr, Shaun Moss, Monica Traub, and Jim Sweeney, from the Oceanic Institute, Honolulu, Hawaii, for access to shrimp tissue samples, Kelly Johnson for assistance with plasmid DNA isolation, and Kireina Bell for editing the cloned sequences. This work was supported by the U.S. Department of Agriculture, through a grant (#95-388-1424) to the USMSFP. Partial support was received from the Department of Environmental and Population Health at Tufts University School of Veterinary Medicine.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Meehan, D., Xu, Z., Zuniga, G. et al. High Frequency and Large Number of Polymorphic Microsatellites in Cultured Shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda] . Mar. Biotechnol. 5, 311–330 (2003). https://doi.org/10.1007/s10126-002-0092-z
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10126-002-0092-z