Development of EST-SSRs by an efficient FIASCO-based strategy: A case study in rare minnow (gobiocyrpis rarus)

Animal Biotechnology

Volumn 18, Issue 3, 2007, Pages 143-152

  Cheng, L ^b   Liao, X ^b   Yu, X ^a   Tong, J ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b NONE

Author keywords

cDNA library; Expressed sequence tag; FIASCO; Fish; Microsatellite

Indexed keywords

BIOMARKERS; DNA; GENETIC ENGINEERING;

EXPRESSED SEQUENCE TAGS (EST); GENETIC ANALYSIS; GOBIOCYPRIS RARUS; MICROSATELLITES;

FISH;

CYPRINIDAE; GOBIOCYPRIS RARUS;

COMPLEMENTARY DNA; MICROSATELLITE DNA;

ALLELE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; CYPRINIFORMES; EXPRESSED SEQUENCE TAG; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ALLELES; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; CYPRINIDAE; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; VARIATION (GENETICS);

EID: 34547298884     PISSN: 10495398     EISSN: 15322378     Source Type: Journal    
DOI: 10.1080/10495390601054980     Document Type: Article

References (25)

1. Tautz D, Trick M, Dover GA. Cryptic simplicity in DNA is a major source of genetic variation. Nature 1986; 322(6080):652-656.
2. Liu Z, Cordes JF. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 2004; 238(1-4): 1-37.
3. Adams MD, Kelley JM, Gocayne JD, Dubnick MP, Mihael H, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, Mccombie WR, Venter JC. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 1991; 252(5013):1651-1656.
4. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: Features and applications. Trends in Biotechnology 2005; 23(1):48-55.
5. Serapion J, Kucuktas H, Feng J, Liu Z. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Marine Biotechnology 2004; 6(4):364-377.
6. Yue GH, Ho MY, Orban L, Komen J. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp. Aquaculture 2004; 234(1-4): 85-98.
7. Coulibaly I, Gharbi K, Danzmann RG, Yao J, Rexroad CE. Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags. Animal Genetics 2005; 36(4):309-315.
8. Wang H, Li F, Xiang J. Polymorphic EST-SSR markers and their mode of inheritance in Fenneropenaeus chinensis. Aquaculture 2005; 249(1-4): 107-114.
9. Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: A review. Molecular Ecology 2002; 11(1): 1-16.
10. Zhou YX, Cheng SP, Hu W, Song MJ. A new toxicity test organism-Gobiocypris rarus. Zoology Research 1995; 16:59-63.
11. Cao W, Wang J. Rare minnow: A new laboratory animal in China. Laboratory Animal Science and Management 2003; 20(suppl.):96-99.
12. Zhu B, Liao X, Shao Z, Rosenthal H, Chang J. Isolation and characterization of microsatellites in Chinese sturgeon, Acipenser sinensis. Molecular Ecology Notes 2005; 5(4):888-892.
13. Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research 1999; 27(2):573-580.
14. Rozen S, Skaletsky H. Bioinformatics Methods and Protocols: Methods in Molecular Biology; Humana Press, Totowa, NJ, 2000; 365-386.
15. Tong J, Yu X, Liao X. Characterization of a highly conserved microsatellite marker with utility potentials in cyprinid fishes. Journal of Applied Ichthyology 2005; 21(3):232-235.
16. Marshall TC, Slate J, Kruuk LEB, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 1998; 7(5):639-655.
17. Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S. Development and transferability of apricot and grape EST microsatellite markers across taxa. Theoretical and Applied Genetics 2003; 106(5):912-922.
18. Ruyter-Spira CP, de Koning DJ, van der Poel JJ, Crooijmans RPMA, Dijkhof RJM, Groenen MAM. Developing microsatellite markers from cDNA: A tool for adding expressed sequence tags to the genetic linkage map of the chicken. Animal Genetics 1998; 29(2):85-90.
19. Liu Z, Karsi A, Dunham RA. Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Marine Biotechnology 1999; 1(5):437-447.
20. Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Research 2004; 32(3):e37.
21. O'Brien SJ. Mammalian genome mapping: Lessons and prospects. Current Opinion in Genetics & Development 1991; 1(1):105-111.
22. Rexroad C, Rodriguez M, Coulibaly I, Gharbi K, Danzmann R, DeKoning J, Phillips R, Palti Y. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 2005; 6(1):54.
23. Pérez F, Ortiz J, Zhinaula M, Gonzabay C, Calderón J, Volckaert F. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Marine Biotechnology 2005; 7(5): 554-569.
24. Saha M, Mian M, Eujayl I, Zwonitzer J, Wang L, May G. Tall fescue EST-SSR markers with transferability across several grass species. Theoretical and Applied Genetics 2004; 109(4):783-791.
25. Liao XL, Wang D, Yu XM, Li WT, Cheng L, Wang JW, Tong J. Characterization of novel microsatellite loci in rare minnow (Gobiocypris rarus) and amplification in closely related species in Gobioninae. Conservation Genetics 2007; DOI 10.1007/s10592-006-9222-x.