Development of novel EST-SSR markers in common carp by data mining from public EST sequences

Aquaculture

Volumn 271, Issue 1-4, 2007, Pages 558-574

  Wang, Dan ^a,b   Liao, Xiaolin ^a,b   Cheng, Lei ^a,b   Yu, Xiaomu ^a   Tong, Jingou ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Cross species amplification; Cyprinus carpio; Data mining; EST SSRs; Expressed sequence tag (EST); Polymorphism

Indexed keywords

ALLELE; CYPRINID; DATA MINING; DATABASE; GENOME; HETEROZYGOSITY; POLYMORPHISM; POPULATION GENETICS;

CARASSIUS; CARASSIUS AURATUS; CYPRINIDAE; CYPRINUS CARPIO; HYPOPHTHALMICHTHYS MOLITRIX; HYPOPHTHALMICHTHYS NOBILIS; PISCES;

EID: 34548230410     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2007.06.001     Document Type: Article

References (29)

1. Aljanabi S.M., and Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25 (1997) 4692-4693
2. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (1999) 573-580
3. Chen C.X., Zhou P., Choi Y.A., Huang S., and Gmitter F.G. Mining and characterizing microsatellites from citrus ESTs. Theor. Appl. Genet. 112 (2006) 1248-1257
4. Chen S.L., Liu Y.G., Xu M.Y., and Li J. Isolation and characterization of polymorphic microsatellite loci from an EST-library of red sea bream (Chrysophrys major) and cross-species amplification. Mol. Ecol. Notes 5 (2005) 215-217
5. Cho Y.G., Ishii T., Temnykh S., Chen X., Lipovich L., McCouch S.R., Park W.D., Ayres N., and Cartinhour S. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100 (2000) 713-722
6. Cordeiro G.M., Casu R., McIntyre C.L., Manners J.M., and Henry R.J. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci. 160 (2001) 1115-1123
7. David L., Rajasekaran P., Fang J., Hillel J., and Lavi U. Polymorphism in ornamental and common carp strains (Cyprinus carpio L.) as revealed by AFLP analysis and a new set of microsatellite marker. Mol. Genet. Genomics 266 (2001) 353-362
8. Edwards Y.J., Elgar G., Clark M.S., and Bishop M.J. The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses. J. Mol. Biol. 278 (1998) 843-854
9. Guo S.W., and Thompson E.A. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48 (1992) 361-372
10. Gupta P.K., and Varshney R.K. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113 (2000) 163-185
11. Kantety R.V., Rota M.L., Matthews D.E., and Sorrells M.E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48 (2002) 501-510
12. Liao X.L., Yu X.M., and Tong J.G. Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers. Hydrobiologia 568 (2006) 445-453
13. Liu Z.J., and Cordes J.F. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238 (2004) 1-37
14. Maneeruttanarungroj C., Pongsomboon S., Wuthisuthimethavee S., Klinbunga S., Wilson K.J., Swan J., Li Y., Whan V., Chu K.H., Li C.P., Tong J., Glenn K., Rothschild M., Jerry D., and Tassanakajon A. Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon). Anim. Genet. 37 (2006) 363-368.
15. Neff B.D., and Gross M.R. Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 55 (2001) 1717-1733
16. Nonneman D., and Waldbieser G.C. Isolation and enrichment of abundant microsatellites from a channel catfish (Ictalurus punctatus) brain cDNA library. Anim. Biotechnol. 16 (2005) 103-116
17. Pérez F., Ortiz J., Zhinaula M., Gonzabay C., Calderón J., and Volckaert F.A.M.J. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar. Biotechnol. 7 (2005) 554-569
18. Rexroad III C.E., Rodriguez M.F., Coulibaly I., Gharbi K., Danzmann R.G., Dekoning J., Phillips R., and Palti Y. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 6 (2005) 54
19. Schneider S., Roessli D., and Excoffier L. Arlequin: a software for population genetics data analysis, version 2.000 (2000), Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland
20. Serapion J., Kucuktas H., Feng J.N., and Liu Z.J. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar. Biotechnol. 6 (2004) 364-377
21. Stallings R.L., Ford A.F., Nelson D., Torney D.C., Hildebrand C.E., and Moyzis R.K. Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics 10 (1991) 807-815
22. Sun X.W., and Liang L.Q. A genetic linkage map of common carp (Cyprinus carpio L.) and mapping of a locus associated with cold tolerance. Aquaculture 238 (2004) 165-172
23. Tong J., Lehnert S.A., Byrne K., Kwan H.S., and Chu K.H. Development of polymorphic EST markers in Penaeus monodon: applications in Penaeid genetics. Aquaculture 208 (2002) 69-79
24. Tong J., Yu X., and Liao X. Characterization of a highly conserved microsatellite marker with utility potentials in cyprinid fishes. J. Appl. Ichthyol. 21 (2005) 232-235
25. Wang H.X., Li F.H., and Xiang J.H. Polymorphic EST-SSR markers and their mode of inheritance in Fenneropenaeus chinensis. Aquaculture 249 (2005) 107-114
26. Wohlfarth G. In: Mason I.L. (Ed). Common carp, in evolution of domesticated animals (1984), Longman, London
27. Yeh, F.C., Yang, R.C., Boyle, T., 1999. POPGENE, Version 1.3.1: microsoft windows-based freeware for population genetic analysis. Available at (www.ualberta.ca/~fyeh). University of Alberta and the Centre for International Forestry Research.
28. Yue G.H., Ho M.Y., Orban L., and Komen J. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp. Aquaculture 234 (2004) 85-98
29. Zhan A.B., Bao Z.M., Wang X.L., and Hu J.J. Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fish. Sci. 71 (2005) 1341-1346