Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench)

DNA Research

Volumn 16, Issue 3, 2009, Pages 187-193

  Yonemaru, Jun Ichi ^a   Ando, Tsuyu ^b   Mizubayashi, Tatsumi ^b   Kasuga, Shigemitsu ^c   Matsumoto, Takashi ^a   Yano, Masahiro ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b Institute of the Society for Techno innovation of Agriculture   (Japan)

^c SHINSHU UNIVERSITY   (Japan)

Author keywords

Fragment analysis; Genome wide; Simple sequence repeat (SSR); Sorghum (Sorghum bicolor (L.) Moench)

Indexed keywords

ARTICLE; GENE AMPLIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC POLYMORPHISM; MARKER GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; POLYMERASE CHAIN REACTION; SIMPLE SEQUENCE REPEAT; SORGHUM; UNINDEXED SEQUENCE; VALIDATION PROCESS; DNA SEQUENCE; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; PLANT CHROMOSOME; PLANT GENE;

SORGHUM BICOLOR; SORGHUM X DRUMMONDII;

MICROSATELLITE DNA; PLANT DNA;

CHROMOSOMES, PLANT; DNA, PLANT; GENES, PLANT; GENETIC MARKERS; GENETIC VARIATION; GENOME, PLANT; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SORGHUM;

EID: 70149117838     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsp005     Document Type: Article

References (29)

1. Doggett, H. 1988, Sorghum, 2nd Ed., John Wiley and Sons, Inc.: New York.
2. Pereira, M. G., Lee, M., Bramel-Cox, P., Woodman, W., Doebley, J. and Whitkus, R. 1994, Construction of an RFLP map in sorghum and comparative mapping in maize, Genome, 37, 236-243.
3. Nagamura, Y., Tanaka, T., Nozawa, H., Kaidai, H., Kasuga, S. and Sasaki, T. 1998, Syntenic regions between rice and sorghum genomes, In: Nakagawa, H., and Kobayashi, M. (eds.), Proceedings of the International Workshop; Utilization of Transgenic Plant and Genome Analysis in Forage Crops, National Grassland Research Institute: Tochigi, pp. 97-103.
4. Bowers, J. E., Abbey, C., Anderson, S., et al. 2003, A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses, Genetics, 165, 367-386.
5. Menz, M. A., Klein, R. R., Mullet, J. E., Obert, J. A., Unruh, N. C. and Klein, P. E. 2002, A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP and SSR markers, Plant Mol. Biol., 48, 483-499.
6. Brown, S. M., Hopkins, M. S., Mitchell, S. E., et al. 1996, Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench], Theor. Appl. Genet., 93, 190-198.
7. Bhattramakki, D., Dong, J., Chhabra, A. K. and Hart, G. E. 2000, An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench, Genome, 43, 988-1002.
8. Kong, L., Dong, J. and Hart, G. E. 2000, Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs), Theor. Appl. Genet., 101, 438-448.
9. Schloss, J., Mitchell, E., White, M., et al. 2002, Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench, Theor. Appl. Genet., 105, 912-920.
10. Tao, Y. Z., Jordan, D. R., McIntyre, C. L. and Henzell, R. G. 1998, Construction of a genetic map in a sorghum recombinant inbred line using probes from different sources and its comparison with other sorghum maps, Aust. J. Agric. Res., 49, 729-736.
11. Taramino, G., Tarchini, R., Ferrario, S., Lee, M. and Pé, M. E. 1997, Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor, Theor. Appl. Genet., 95, 66-72.
12. Arumuganathan, K. and Earle, E. D. 1991, Nuclear DNA content of some important plant species, Plant Mol. Biol. Rep., 9, 208-218.
13. Doebley, J., Durbin, M., Golenberg, E. M., Clegg, M. T. and Ma, D. P. 1990, Evolutionary analysis of the large subunit of carboxylase (rbcL) nucleotide sequence among the grasses (Gramineae), Evolution, 44, 1097-1108.
14. Sobral, B. W. S., Braga, D. P. V., LaHood, E. S. and Keim, P. 1994, Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. sub-tribe of the Andropogoneae Dumort. tribe, Theor. Appl. Genet., 87, 843-853.
15. Bedell, J. A., Budiman, M. A., Nunberg, A., et al. 2005, Sorghum genome sequencing by methylation filtration, PLoS Biol., 3, e13.
16. Paterson, A. H., Bowers, J. E., Bruggmann, R., et al. 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551-556.
17. Schuler, G. D. 1997, Sequence mapping by electronic PCR, Genome Res., 7, 541-550.
18. Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. and McCouch, S. 2001, Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transpo-son associations, and genetic marker potential, Genome Res., 11, 1441-1452.
19. Fukuoka, H., Nunome, T., Minamiyama, Y., Kono, I., Namiki, N. and Kojima, A. 2005, Read 2 Marker: a data processing tool for microsatellite marker development from a large data set, Biotechniques, 39, 472, 474, 476.
20. Rozen, S. and Skaletsky, H. 2000, Primer3 on the WWW for general users and for biologist programmers, In: Misener, S., and Krawetz, S. A. (eds.), Methods in Molecular Biology, Humana Press Inc: Totowa, pp. 365-386.
21. McCouch, S. R., Teytelman, L., Xu, Y., et al. 2002, Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.), DNA Res., 9, 199-207.
22. Yu, J. K., Dake, T. M., Singh, S., et al. 2004, Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat, Genome, 47, 805-818.
23. Thiel, T., Michalek, W., Varshney, R. and Graner, A. 2003, Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.), Theor. Appl. Genet., 106, 411-422.
24. 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 erianthus and sorghum, Plant Sci., 160, 1115-1123.
25. Asp, T., Frei, U. K., Didion, T., Nielsen, K. K. and Lubberstedt, T. 2007, Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa, BMC Plant Biol., 7, 36.
26. Kantety, R. V., La Rota, M., Matthews, D. E. and Sorrells, M. E. 2002, Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat, Plant Mol. Biol., 48, 501-510.
27. Inazuka, M., Tahira, T. and Hayashi, K. 1996, One-tube post-PCR fluorescent labeling of DNA fragments, Genome Res., 6, 551-557.
28. Nei, M. 1973, Analysis of gene diversity in subdivided populations, Proc. Natl. Acad. Sci. USA, 70, 3321-3323.
29. Gregorius, H. R. 1987, The relationship between the concepts of genetic diversity and differentiation, Theor. Appl. Genet., 74, 397-401.