Genome-wide distribution and organization of Microsatellites in plants: An insight into marker development in Brachypodium

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Sonah, Humira ^a   Deshmukh, Rupesh K ^a,c   Sharma, Anshul ^a   Singh, Vinay P ^a   Gupta, Deepak K ^a   Gacche, Raju N ^c   Rana, Jai C ^b   Singh, Nagendra K ^a   Sharma, Tilak R ^a  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

^c SWAMI RAMANAND TEERTH MARATHWADA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; ASPEN; BRACHYPODIUM; CHLOROPLAST GENOME; CONTROLLED STUDY; GC RICH SEQUENCE; GENOME ANALYSIS; MEDICAGO; MICROSATELLITE MARKER; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; RICE; SIMPLE SEQUENCE REPEAT; SORGHUM; SPECIES DIFFERENCE; CHLOROPLAST; GENETIC MARKER; GENETICS;

ARABIDOPSIS; BRACHYPODIUM; DICOTYLEDONEAE; LILIOPSIDA; MEDICAGO; POPULUS;

MICROSATELLITE DNA; PLANT DNA;

BRACHYPODIUM; CHLOROPLASTS; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; MICROSATELLITE REPEATS;

EID: 79959358444     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021298     Document Type: Article

References (41)

1. Powell W, Machray G, Provan J, (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215-222.
2. Gupta PK, Rustogi S, Sharma S, Singh R, Kumar N, et al. (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270: 315-23.
3. Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, et al. (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109: 783-91.
4. Asp T, Frei UK, Didion T, Nielsen KK, Lübberstedt 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 127: 36.
5. The International Brachypodium Initiative, (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
6. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 (5793): 1596-604.
7. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
8. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
9. Arabidopsis Genome Initiative, (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
10. McCouch SR, 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.
11. Parida SK, Rajkumar KA, Dalal V, Singh NK, Mohapatra T, (2006) Unigene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112: 808-817.
12. Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K, et al. (2010) Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breeding 25 (2): 359-364.
13. Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, et al. (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology 127 (4): 1539-1555.
14. Garvin DF, Gu YQ, Hasterok R, Hazen SP, Jenkins G, et al. (2008) Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research. Crop Science 48: S-69-S-84.
15. Garvin DF, Mckenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, et al. (2010): An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 53 (1): 1-13.
16. Levinson G, Gutman, GA, (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221.
17. Schlötterer C, Tautz D, (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20: 211-215.
18. Hancock JM, (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. 1-9 New York Oxford University Press In Microsatellites: Evolution and applications Ed Goldstein D, Schlötterer C,.
19. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R, (1997) Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci U S A 94: 1041-1046.
20. Anderson TJ, Su XZ, Roddam A, Day KP, (2000) Complex mutations in a high proportion of microsatellite loci from the protozoan parasite Plasmodium falciparum. Mol Ecol 9: 1599-1608.
21. Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, et al. (2003) Likelihood-based estimation of microsatellite mutation rates. Genetics 164: 781-787.
22. Modrich P, Lahue R, (1996) Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Ann Rev Biochem 65: 101-133.
23. Harr B, Todorova J, Schlötterer C, (2002) Mismatch repair-driven mutational bias in D melanogaster. Mol Cell 10: 199-205.
24. Riley DE, Jeon JS, Krieger JN, (2007) Simple repeat evolution includes dramatic primary sequence changes that conserve folding potential. Biochem Biophys Res Commun 355: 619-625.
25. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH, (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86 (16) U S A: 6201-6205.
26. Yu J, Hu S, Wang J, Wong GKS, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
27. Vision TJ, Brown DG, Tanksley SD, (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
28. Blanc G, Hokamp K, Wolfe KH, (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144.
29. Goff SA, Ricke D, Lan TH, Presting G, Wang RL, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92-100.
30. Li S, Yin T, Wang M, Tuskan GA, (2011) Characterization of microsatellites in the coding regions of the Populus genome Mol Breeding 27: 59-66.
31. Sonah H, Deshmukh RK, Singh VP, Gupta DK, Singh NK, et al. (2010) Genomic resources in horticultural crops: Status, Utility and Challenges. Biotechnological Advances 29: 199-209.
32. Weber JL, Wong C, (1993) Mutation of human short tandem repeats. Hum Mol Genet 2: 1123-1128.
33. Xu X, Peng M, Fang Z, Xu X, (2000) The direction of microsatellite mutations is dependent upon allele length. Nat Genet 24: 396-399.
34. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, et al. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11 (8): 1441-52.
35. Vogel J, Hill T, (2008) High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep 27: 471-478.
36. Alves SC, Worland B, Thole V, Snape JW, Bevan MW, et al. (2009) A protocol for Agrobacterium-mediated transformation of Brachypodium distachyon community standard line Bd21. Nature Protocols 4: 638-649.
37. Vogel J, Tuna M, Budak H, Huo N, Gu Y, et al. (2009) Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol 9: 88.
38. Parida SK, Yadava DK, Mohapatra T, (2010) Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis. Genome 53: 55-67.
39. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, et al. (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L). Theor Appl Genet 100: 713-722.
40. Chabane K, Ablett GA, Cordeiro GM, Valkoun J, Henry RJ, (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Resour Crop Evol 52: 903-909.
41. Schuler GD, (1997) Sequence Mapping by Electronic PCR. Genome Res 7: 541-550.