Design and application of microsatellite marker panels for semiautomated genotyping of rice (Oryza sativa L.)

Crop Science

Volumn 42, Issue 6, 2002, Pages 2092-2099

  Coburn, J R ^a   Temnykh, S V ^b   Paulb, E M ^a   McCouch, S R ^a,b  

^a Department of Obstetrics Gynecology   (United States)

^b GeneFlow Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA; ORYZA; ORYZA SATIVA;

EID: 0036889271     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2002.2092     Document Type: Article

References (29)

1. Blair, M.W., O. Panaud, and S.R. McCouch. 1999. Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice Oryza sativa L.). Theor. Appl. Genet. 98:780-792.
2. Blair, M.W., V. Hedetale, and S.R. McCouch. 2002. Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theor. Appl. Genet. (DOI 10.1007/s00122-002-0921-5).
3. Brownstein, M.J., J.D. Carpten, and J.R. Smith. 1996. Modulation of non-templated nucleotide addition by Taq DNA polymerase: Primer modifications that facilitate genotyping. BioTechniques 20: 1004-1010.
4. Carrano, A.V., J. Lamerdin, L.K. Ashworth, B. Watkins, E. Branscomb, T. Slezak, M. Raff, P.J. De Jong, D. Keith, L. McBride, S. Meister, and M. Kronick. 1989. A high resolution, fluorescence-based, semi-automated method for DNA fingerprinting. Genomics 4:129-136.
5. Chen, X., S. Temnykh, Y. Xu, Y.G. Cho, S.R. McCouch. 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor. Appl. Genet. 95:553-567.
6. Cho, Y.G., T. Ishii, S. Temnykh, X. Chen, L. Lipovich, S.R. McCouch, W.D. Park, N. Ayres, and S. Cartinhour. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:713-722.
7. Diwan, N., and P.B. Cregan. 1997. Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor. Appl. Genet. 95:723-733.
8. Edwards, A., A. Civitello, H.A. Hammond, and C.T. Caskey. 1991. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 49:746-756.
9. Fulton, T.M., J. Chunwongse, and S.D. Tanskley. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol. Biol. Rep. 13:207-209.
10. Ginot, F., I. Bordelais, S. Nguyen, and G. Gyapay. 1996. Correction of some genotyping errors in automated fluorescent microsatellite analysis by enzymatic removal of one base overhangs. Nucleic Acids Res. 24:540-541.
11. Glaszmann, J.C. 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74:21-30.
12. Henegariu, O., N.A. Heerema, S.R. Dlouhy, G.H. Vance, and P.H. Vogt. 1997. Multiplex PCR: Critical Parameters and step-by-step protocol. Biotechniques 23:504-511.
13. Ji, H.S., H.J. Koh, S.U. Park, and S.R. McCouch. 1998. Varietal identification in japonica rice using microsatellite DNA markers. Korean J. Breed. 30:350-360.
14. Lexer, C., B. Heinze, H. Steinkellner, S. Kampfer, B. Ziegenhagen, and J. Glössl. 1999. Microsatellite analysis of maternal half-sib families of of Quercus robur, pedunculate oak: Detection of seed contaminations and inference of the seed parents from the offspring. Theor. Appl. Genet. 99:185-191.
15. Macaulay, M., L. Ramsay, W. Powell, and R. Waugh. 2001. A representative, highly informative genotyping set of barley SSRs. Theor. Appl. Genet. 102:801-809.
16. Mackill, J.D., Z. Zhang, E.D. Redona, and P.M. Colowit. 1996. Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969-977.
17. Mitchell, S.E., S. Kresovich, C.A. Jester, C.J. Hernandez, and A.K. Szewc-McFadden. 1997. Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci. 37:617-624.
18. Morishima, H., and H.I. Oka. 1981. Phylogenetic differentiation of cultivated rice. XXVII. Numerical evaluation of the Indica-Japonica differentiation. Japan. J. Breed. 31:402-413.
19. Ni, J., P.M. Colowit, and D.J. Mackill. 2002. Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci. 42:601-607.
20. Ponce, M.R., P. Robles, and J.L. Micol. 1999. High-throughput genetic mapping in Arabidopsis thaliana. Mol. Gen. Genet. 261:408-415.
21. Rhodes, M., R. Straw, S. Fernando, A. Evans, T. Lacey, A. Dearlove, J. Greystrong, J. Walker, P. Watson, P. Weston, M. Kelly, D. Taylor, K. Gibson, C. Mundy, F. Bourgade, C. Poirier, D. Simon, A.L.B. Brunialti, X. Montagutelli, J. Gunet, A. Haynes, and S.D.M. Brown. 1998. A high-resolution microsatellite map of the genome. Genome Res. 8:531-542.
22. Rohlf, F.J. 1998. NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.0. Exeter Software, Setauket, NY.
23. Second, G. 1986. Evolutionary relationships in the Oryza sativa group of Oryza based on isozyme data. Genet. Sel. Evol. (Versailles) 17: 89-114.
24. Smith, J.R., J.D. Carpten, M.J. Brownstein, S. Ghosh, V.L. Magnuson, D.A. Gilbert, J.M. Trent, and F.S. Collins. 1995. Approach to genotyping errors caused by non-templated nucleotide addition by Taq DNA polymerase. Genome Res. 5:312-317.
25. Tanaillon, M.I., M.C. Sawkins, A.D. Long, R.L. Gaut, J.F. Doebley, and B.S. Gaut. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea Mays ssp. mays L.). Proc. Natl. Acad. Sci. (USA) 98:9161-9166.
26. Temnykh, S., W.D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y.G. Cho, T. Ishii, and S.R. McCouch. 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet 100:697-712.
27. Temnykh, S., G. De Clerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S.R. McCouch. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1452.
28. Wang, Z.Y., and S.D. Tanksley. 1989. Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113-1118.
29. Ziegle, J.S., Y. Su, K.P. Corcoran, L. Nie, P.E. Mayrand, L.B. Hoff, L.J. McBide, M.N. Kronick, and S.R. Diehl. 1992. Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics 14:1026-1031.