Data mining of ESTs to develop dbEST-SSRs for use in a polymorphism study of cauliflower (Brassica oleracea var. botrytis)

Journal of Horticultural Science and Biotechnology

Volumn 87, Issue 1, 2012, Pages 57-63

  Vaidya, E ^a   Kaur, R ^a   Bhardwaj, S V ^a  

^a DR Y S PARMAR UNIVERSITY OF HORTICULTURE AND FORESTRY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; BOTRYTIS; BRASSICA OLERACEA; BRASSICA OLERACEA VAR. BOTRYTIS; BRASSICA OLERACEA VAR. CAPITATA; BRASSICA OLERACEA VAR. GEMMIFERA; BRASSICA OLERACEA VAR. ITALICA; CAPITATA; TETRA;

EID: 84856318500     PISSN: 14620316     EISSN: None     Source Type: Journal    
DOI: 10.1080/14620316.2012.11512831     Document Type: Article

References (26)

1. AGGARWAL, R. K., HENDRE, P. S., VARSHNEY, R. K., BHAT, P. R., KRISHNAKUMAR, V. and SINGH, L. (2007). Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics, 114, 359-372.
2. ANDERSON, J. A., CHURCHILL, G. A., AUTRIQUE, J. E., TANKSLEY, S. D. and SORRELLS, M. E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36, 181-186.
3. BERUBE, Y., ZHUANG, J., RUNGIS, D., RALPH, S.G., BOHLMANN, J. and RITLAND, K. (2001). Characterization of EST-SSRs in loblolly pine and spruce. Tree Genetics and Genomes, 3, 251-259.
4. BURGESS, B., MOUNTFORD, H., HOPKIN, C. J., LOVE, C., LING, A. E., SPANGERBERG, G. S., EDWARDS, D. and BATLEY, J. (2006). Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Molecular Ecology Notes, 6, 1191-1194.
5. CHO, Y. G., ISHII, T., TEMNYKH, S., CHEN, X., LIPOVICH, L., MCCOUCH, S. R., PARK, W. D., AYRES, N. and CARTINHOUR, S. (2000). Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100, 713-722.
6. CORDEIRO, G. M., CASU, R., MCINTYRE, C. L., MANNERS, J. M. and HENRY, R. J. (2001). Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross-transferable to Helianthus and sorghum. Plant Science, 160, 1115-1123.
7. DOYLE, J. J. and DOYLE, J. L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochemical Bulletin, 19, 11-15.
8. EUJAYL, I., SORRELS, M., BAUM, M., WALTERS, P. and POWELL, W. 2001). Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs. Euphytica, 119, 39-43.
9. EUJAYL, I., SLEDGE, M. K., WANG, L., MAY, G. D., CHEKHOVSKIY, K., WONITZER, J. C. Z. and MIAN, M. A. R. (2004). Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theoretical and Applied Genetics, 108, 414-422.
10. FRASER, L. G., HARVEY, C. F., CROWHURST, R. N. and DE SILVA, H. N. (2004). EST-derived microsatellites from Actinidia species and their potential for mapping. Theoretical and Applied Genetics, 108, 1010-1016.
11. GAO, L. F., TANG, J. F., LI, H. W. and JIA, J. Z. (2003). Analysis of microsatellites in major crops assessed by computational and experimental approaches. Journal of Molecular Breeding, 12, 245-261.
12. JIN, J. Q., CUI, H. R., CHEN, W.Y., LU, M. Z., YAO, Y. L., XIN, Y. and GONG, X. C. (2006). Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant (Camellia sinensis). Journal of Tea Science, 26, 17-23.
13. LI, X. B., ZHANG, M. L. and CUI, H. R. (2007). Data mining for SSRs in ESTs and development of EST-SSR marker in oilseed rape. Journal of Molecular Cell Biology, 40, 38-44.
14. LITT, M., LUTY, J., AM, A. and HUM, J. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within cardiac muscle actin gene. American Journal of Human Genetics, 44, 397-401.
15. LOUARN, S., TORP, A. M., HOLME, I. B., ANDERSEN, S. B. and JENSEN, B. D. (2007). Database derived microsatellite markers (SSRs) for cultivar differentiation in Brassica oleracea. Genetic Resources and Crop Evolution, 54, 1717-1725.
16. LOWE, A. J., MOULE, C., TRICK, M. and EDWARDS, K. J. (2003). Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theoretical and Applied Genetics, 108, 1103-1112.
17. PINTO, L. R., OLIVEIRA, K. M., ULIAN, E. C., GARCIA, A. A. F. and SOUZA, A. P. (2004). Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome, 47, 795-804.
18. ROHLF, F. J. (1998).NTSYS-pc Numerical Taxonomy and Multivariate Analysis. Version 2.0. Applied Biostatistics Inc., New York, USA.
19. ROZEN, S. and SKALETSKY, H. J. (2000). Primer 3 on the www for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology. (Krawetz, S. and Misener, S., Eds.). Humana Press, Totowa, NJ, USA. 365-386.
20. SZEWC-MCFADDEN, A. K., KRESOVICH, S., BLIEK, S. M., MITCHELL, S. E. and MCFERSON, J. R. (1996). Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species. Theoretical and Applied Genetics, 93, 534-538.
21. TEMNYKH, S., DECLERK, G., LUKASHOVA, A., LIPOVICH, L., CARTINHOUR, S. and MCCOUCH, S. R. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research, 11, 1441-1452.
22. THIEL, T., MICHALEK, W., VARSHNEY, R. K. and GRANER, A. (2003). Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 106, 411-422.
23. TONGUC, M. and GRIFFITHS, P. D. (2004). Genetic relationships of Brassica vegetables determined using database derived sequence repeats. Euphytica, 137, 193-201.
24. VARSHNEY, R. K., THIEL, T., STEIN, N., LANGRIDGE, P. and GRANER, A. (2002). In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cellular and Molecular Biology Letters, 7, 537-546.
25. VARSHNEY, R. K., GRANER, A. and SORRELS, M. E. (2005). Genic microsatellite markers in plants: features and applications. Trends in Biotechnology, 23, 48-55.
26. ZHANG, R., ZHU, A., WANG, X., YU, J., ZHANG, H., GAO, J., CHENG, Y. and DENG, X. (2010). Development of Juglans regia SSR markers by data mining of the EST database. Plant Molecular Biology Reporter, 28, 646-653.