Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass

Theoretical and Applied Genetics

Volumn 111, Issue 5, 2005, Pages 956-964

  Tobias, Christian M ^a   Twigg, Paul ^b   Hayden, Daniel M ^a   Vogel, Kenneth P ^c   Mitchell, Rob M ^c   Lazo, Gerard R ^a   Chow, Elaine K ^a   Sarath, Gautam ^c  

^a WESTERN REGIONAL RESEARCH CENTER   (United States)

^b UNIVERSITY OF NEBRASKA AT KEARNEY   (United States)

^c UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; DATABASE SYSTEMS; DNA; GENES; GENETIC ENGINEERING;

CDNA LIBRARIES; EXPRESSED SEQUENCE TAGS (EST); GENE ONTOLOGY; SWITCHGRASS;

CROPS;

PLANT DNA; VEGETABLE PROTEIN;

ARTICLE; EXPRESSED SEQUENCE TAG; GENE; GENE LIBRARY; GENETICS; MILLET; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PLANT LEAF; PLANT STEM;

BASE SEQUENCE; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, PLANT; PANICUM; PLANT LEAVES; PLANT PROTEINS; PLANT STEMS; REPETITIVE SEQUENCES, NUCLEIC ACID;

DATA BASES; GENES; GENETIC ENGINEERING; GRASSES; NUCLEIC ACIDS;

PANICUM VIRGATUM;

EID: 26944466326     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-005-0030-3     Document Type: Article

References (34)

1. Adams M, Kelley J, Gocayne J, Dubnick M, Polymeropoulos M, Xiao H, Merril C, Wu A, Olde B, Moreno R et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651-1656
2. Altschul SF, Gish W, W M, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
3. Anterola AM, Lewis NG (2002) Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochem 61:221-294
4. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2004) Uni-Prot: the universal protein knowledge base. Nucleic Acids Res 32:D115-D119
5. Barnett FL, Carver RF (1967) Meiosis and pollen stainability in switchgrass, Panicum virgatum L. Crop Sci 7:301-304
6. Barrett B, Griffiths A, Schreiber M, Ellison N, Mercer C, Bouton J, Ong B, Forster J, Sawbridge T, Spangenberg G, Bryan G, Woodfield D (2004) A microsatellite map of white clover. Theor Appl Genet 109:596-608
7. Bennetzen J, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128-133
8. Carpita NC (1996) Structure and biogenesis of the cell walls of grasses. Ann Rev of Plant Physiol Plant Mol Biol 47:445-476
9. Chakraborty R, Kimmel M, Strivers D, Davison L, Deka R (1997) Relative mutation rates at di- tri- and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 94:1041-1046
10. Chin E, Senior M, Shu H, JSC S (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866-873
11. Cho Y, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch S, Park W, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713-722
12. Devos K, Gale M (2000) Genome relationships: the grass model in current research. Plant Cell 12:637-646
13. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194
14. Ewing B, Hillier L, Wendl M, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185
15. Gunter LE, Tuskan GA, Wullschleger SD (1996) Diversity among populations of switchgrass based on RAPD markers. Crop Sci 36:1017-1022
16. Hultquist S, Vogel KP, Lee D, Arumuganathan K, Kaeppler S (1996) Chloroplast DNA and nuclear DNA content variations among cultivars of switchgrass, Panicum virgatum L. Crop Sci 36:1049-1052
17. Jurka J, Pethiyagoda C (1995) Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol 40:120-126
18. Kantety R, La Rota M, Matthews D, Sorrells M (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501-510
19. Kellogg E (2001) Evolutionary history of the grasses. Plant Physiol 125:1198-1205
20. Lazo GR et al (2004) Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168:585-593
21. Lerner DR, Raikhel NV (1989) Cloning and characterization of root-specific barley lectin. Plant Physiol 91:124-129
22. McLaughlin SB, Walsh ME (1998) Evaluating environmental consequences of producing herbaceous crops for bioenergy. Biomass Bioenergy 14:317-324
23. Moore KJ, Moser LE, Vogel KP, Waller SS, Johnson BE, Pedersen JF (1991) Describing and quantifying growth stages of perennial forage grasses. Agron J 83:1073-1077
24. Moser LE, Vogel KP (1995) Switchgrass, big bluestem, and indiangrass. In: Barnes RF, Miller DA, Nelson CJ (eds) An introduction to grassland agriculture, chapter 32. Iowa State University Press, Ames, pp 409-420
25. Picoult-Newberg L, Ideker T, Pohl M, Taylor S, Donaldson M, Nickerson D, Boyce-Jacino M (1999) Mining SNPs from EST databases. Genome Res 9:167-174
26. Richards HA, Rudas VA, Sun H, McDaniel JK, Tomaszewski Z, Conger BV (2001) Construction of a GFP-BAR plasmid and its use for switchgrass transformation. Plant Cell Rep 20:48-54
27. Saha M, Mian M, Eujayl I, Zwonitzer J, Wang L, May G (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783-791
28. Somleva MN, Tomaszewski Z, Conger BV (2002) Agrobacterium-mediated genetic transformation of switchgrass. Crop Sci 42:2080-2087
29. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (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
30. Vogel KP, Haskins FA, Gorz HJ, Anderson BA, Ward JK (1991) Registration of "Trailblazer" switchgrass. Crop Sci 31:1388
31. Vogel KP, Hopkins AA, Moore KJ, Johnson KD, Carlson IT (1996) Registration of "Shawnee" switchgrass. Crop Sci 36:1713
32. Weber J (1990) Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 7:524-530
33. Wu X-L, Griffin K, Garcia M, Michal J, Xiao Q, Wright R, Jiang Z (2004) Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus). Gene 340:213-225
34. Yu J, La Rota M, Kantety R, Sorrells M (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742-751