Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench

Theoretical and Applied Genetics

Volumn 105, Issue 6-7, 2002, Pages 912-920

  Schloss, S J ^a   Mitchell, S E ^a   White, G M ^a   Kukatla, R ^a   Bowers, J E ^b   Paterson, A H ^b   Kresovich, S ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

BLAST; Database search; EST; Genetic diversity; Germplasm; Microsatellite

Indexed keywords

ALGORITHMS; GENES; GENETIC ENGINEERING; PROTEINS;

NUCLEOTIDES;

DNA SEQUENCES;

EMBRYOPHYTA; SORGHUM BICOLOR;

EID: 0346195650     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-002-0991-4     Document Type: Article

References (29)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Anderson I, Brass A (1998) Searching DNA databases for similarities to DNA sequences: When is a match significant? Bioinformatics 14:349-356
3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Pl Mol Biol Rep 9:208-218
4. Bhattramakki D, Dong JM, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988-1002
5. Bowers JE, Schertz KF, Abbey C, Anderson S, Chang C, Chittenden LM, Draye X, Hoppe AH, Jessup R, Lennington J, Paterson AH (2000) A high-density 2,399-locus genetic map of Sorghum. Plant and Animal Genome VIII Conference, San Diego, (http://www.intl-pag.org/pag/8/abstracts/pag8712.html)
6. Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (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. Chen MS, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435-443
8. Chittenden LM, Schertz KF, Lin YR, Wing RA, Paterson AH (1994) A detailed RFLP map of Sorghum bicolor xS. propinquum, suitable for high-density mapping, suggests ancestral duplication of sorghum chromosomes or chromosomal segments. Theor Appl Genet 87:925-933
9. Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66-71
10. Daly MJ, Lincoln SE, Lander ES (1991) "PRIMER", unpublished software, Whitehead Institute/MIT Center for Genome Research
11. Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D, Staebell M, Xu G, Polacco M, Koster L, Melia-Hancock S, Houchins K, Chao S, Coe EH (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1,736-locus map. Genetics 152:1137-1172
12. Doggett H (1988) Sorghum, 2nd Edn. John Wiley and Sons Inc, New York
13. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small amounts of leaf tissue. Phytochem Bull 19:11-15
14. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809-6814
15. Harlan JR, de Wet JMJ (1972) A simplified classification of cultivated sorghum. Crop Sci 12:172-176
16. Harushima Y, Yano M, Shomura P, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2,275 markers using a single F-2 population. Genetics 148:479-494
17. Innan H, Terauchi R, Miyashita T (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics 146:1441-1452
18. Kimura M, Crow JF (1964) The numbers of alleles that can be maintained in a finite population. Genetics 49:725-738
19. Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs). Theor Appl Genet 101:438-448
20. Levinson G, Gutman GA (1987) Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 4:203-221
21. Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J (2002) Microsatellites in Zea-variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104:436-450
22. Michalek W, Kunzel G, Graner A (1999) Sequence analysis and gene identification in a set of mapped RFLP markers in barley (Hordeum vulgate). Genome 42:849-853
23. Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of Saccharum and Sorghum chromosomes: Comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663-1682
24. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321-3323
25. Peng Y, Schertz DF, Cartinhour S, Hart GE (1999) Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines. Plant Breed 118:225-235
26. Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF (1998) The mutation rates of di-, tri-, and tetra-nucleotide repeats in Drosophila melanogaster. Mol Biol Evol 5:1751-1760
27. Senior ML, Murphy JP, Goodman MM, Stuber CW (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose-gel system. Crop Sci 38:1088-1098
28. Ventelon M, Deu M, Garsmeur O, Doligez A, Ghesquiere A, Lorieux M, Rami JF, Glaszmann JC, Grivet L (2001) A direct comparison between the genetic maps of sorghum and rice. Theor Appl Genet 102:379-386
29. Weber JL (1990) Informativeness of human (dC-dA)n (dG-dT)n polymorphisms. Genomics 7:524-530