Potential of (GATA)n microsatellites from rice for inter- and intraspecific variability studies

BMC Evolutionary Biology

Volumn 1, Issue , 2001, Pages

  Davierwala, Armaity P ^a   Ramakrishna, Wusirika ^b   Chowdari, Venkat ^c   Ranjekar, Prabhakar K ^a   Gupta, Vidya S ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

^b PURDUE UNIVERSITY   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); HORDEUM VULGARE SUBSP. VULGARE; ORYZA LONGISTAMINATA; ORYZA SATIVA; TRITICUM AESTIVUM; ZEA MAYS;

EID: 3042684572     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-1-7     Document Type: Article

References (76)

1. Litt M, Luty JA: A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle action gene. Am J Hum Genet 1989, 44:397
2. Weber JL, May PE: Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 1989, 44:388-396
3. Tautz D: Hypervariability of simple sequence as a general source for polymorphic DNA markers. Nucleic Acids Res 1989, 17:6463-6471
4. Epplen JT: On simple repeat GAT/CA sequences in animal genomes: a critical reappraisal. J Hered 1988, 79:409-417
5. Goodfellow PN: Variation is now the theme. Nature 1992, 359:777-778
6. Wu KS, Tanksley SD: Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 1993, 24:225-235
7. Bell CJ, Ecker JR: Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 1994, 19:137-144
8. Tautz D, Renz M: Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 1984, 12:4127-4138
9. Field D, Willis C: Long, polymorphic microsatellites in simple organisms. Proc R Soc Lond 1996, 263:209-215
10. Schlotterer C, Vogel C, Tautz D: Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. Genetics 1997, 146:309-320
11. Beckmann JS, Soller M: Towards a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellites. Bio / technology 1990, 8:930-932
12. Love JM, Knight AM, McAleer MA, Todd JA: Towards construction of a high resolution map of the mouse genome using PCR-analyzed microsatellites. Nucleic Acids Res 1990, 18:4123-4130
13. Weber JL: Human DNA polymorphisms and methods of analysis. Curr Opin Biotechnol 1990, 1:166-171
14. Morgante M, Olivieri AM: PCR-amplified microsatellite markers in plant genetics. Plant J 1993, 3:175-182
15. Thomas MR, Scott NS: Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequencetagged sites (STSs). Theor Appl Genet 1993, 86:985-990
16. Weber JL: Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 1990, 7:524-530
17. Rafalski JA, Tingey SV: Genetic diagnostics in plant breeding: RAPDs, microsatellites, and machines. Trends Genet 1993, 9:275-280
18. Gupta PK, Balyan IS, Sharma PC, Ramesh B: Microsatellite in plants - a new class of molecular markers. Curr Sci 1996, 70:45-54
19. Jarne P, Lagoda PJL: Microsatellites, from molecules to populations and back. Trends Ecol Evol 1996, 11:424-429
20. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR: Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 1997, 40:370-378
21. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM: Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 1994, 245:187-194
22. Xiao J, Li J, Grandillo S, Ahn SN, McCouch SR, Tanksley SD, Yuan L: A wild species contains genes that may significantly increase the yield of rice. Nature 1996, 384:223-224
23. Xiao J, Li J, Yuan L, McCouch SR: Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theor Appl Genet 1996, 92:637-643
24. Koh HJ, Heu MH, McCouch SR: Molecular mapping of the gene controlling the super-giant embryo character in rice (Oryza sativa L.). Theor Appl Genet 93:257-261
25. Blair MW, McCouch SR: Microsatellite sequence tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa5. Theor Appl Genet 1997, 95:174-184
26. Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD: Microsatellites and a single nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 1997, 94:773-781
27. McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M: Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 1997, 35:89-99
28. Deshpande VG, Ranjekar PK: Repetitive DNA in three Gramineae species with low DNA content. Hoppe-Seyler Z Physiol Chem 1980, 361:1223-1233
29. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S: Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 2000, 100:713-722
30. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR: Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 2000, 100:697-712
31. Ramakrishna W, Lagu MD, Gupta VS, Ranjekar PK: DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 1994, 88:402-406
32. Ramakrishna W, Chowdari KV, Lagu MD, Gupta VS, Ranjekar PK: DNA fingerprinting to detect genetic variation in rice using hypervariable DNA sequences. Theor Appl Genet 1995, 90:1000-1006
33. Gupta VS, Ramakrishna W, Rawat SR, Ranjekar PK: (CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice. Biochem Genet 1994, 32:1-8
34. Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS: Genetic diversity and phylogenetic relationship as revealed by intersimple sequence repeat (ISSR) polymorphisms in the genus Oryza. Theor Appl Genet 2000, 100:1311-1320
35. Ramakrishna W, Davierwala AP, Gupta VS, Ranjekar PK: Expansion of (GA)n dinucleotide at a microsatellite locus associated with domestication in rice. Biochem Genet 1998, 36:323-327
36. Davierwala AP, Ramakrishna W, Ranjekar PK, Gupta VS: Sequence variations at a complex microsatellite locus in rice and its conservation in cereals. Theor Appl Genet 2000, 101:1291-1298
37. Chowdari KV, Davierwala AP, Gupta VS, Ranjekar PK, Govila OP: Genotype identification and assessment of genetic relationships in pearl millet [Penissetum glaucum (L.) R. Br.] using microsatellites and RAPDs. Theor Appl Genet 1998, 97:154-162
38. Chowdari KV, Venkatachalam SR, Davierwala AP, Gupta VS, Ranjekar PK, OP Govila: Hybrid performance and genetic distance as revealed by the (GATA)4 microsatellite and RAPD markers in pearl millet. Theor Appl Genet 1998, 97:163-169
39. Sastry JG, Ramakrishna W, Sivaramakrishnan S, Thakur RP, Gupta VS, PK Ranjekar: DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora gramicola). Theor Appl Genet 1995, 91:856-861
40. Parasnis AS, Ramakrishna W, Chowdari KV, Gupta VS, Ranjekar PK: Microsatellite (GATA)n reveals sex-specific differences in Papaya. Theor Appl Genet 1999, 99:1047-1052
41. Rychlik W, Rhoads RE: A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 1989, 17:8543-8551
42. Panaud O, Chen X, McCouch SR: Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome 1995, 38:1170-1176
43. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410
44. Davierwala AP, Chowdari KV, Kumar Shiv, Reddy APK, Ranjekar PK, Gupta VS: Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties. Genetica 2000, 108:269-284
45. Zhao X, Kochert G: Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet 1992, 231:353-359
46. Zhao X, Kochert G: Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.). Plant Mol Biol 1993, 21:607-614
47. Akagi H, Yokozeki Y, Inagaki A, Fujimura T: Microsatellite DNA markers for rice chromosomes. Theor Appl Genet 1996, 93:1071-1077
48. Panaud O, Chen X, McCouch SR: Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 1996, 252:597-607
49. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR: Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 1997, 95:553-567
50. Wang Z, Weber JL, Zhong G, Tanksley SD: Survey of plant short tandem DNA repeats. Theor Appl Genet 1994, 88:1-6
51. Epplen JT: The methodology of multilocus DNA fingerprinting using radioactive or non-radioactive oligonucleotide probes specific for simple repeat motifs. In advances in electrophoresis. Vol. 5 Edited by A. Chrambach, M.J. Dunn and B.J. Radola. VCH Publishers Inc., New York 199262-112
52. Garza JC, Slatkin M, Freimer NB: Microsatellite allele frequencies in humans and chimpanzees with implications for constraints on allele size. Mol Biol Evol 1995, 12:594-603
53. Morchen M, Cuguen J, Michaelis G, Hanni C, Saumitou-Laprade P: Abundance and length polymorphism of microsatellite repeats in Beta vulgaris l. Theor Appl Genet 1996, 92:326-333
54. van Treuren R, Kuittinen H, Karkkainen K, Baena-Gonzalez K, Savolainen O: Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana. Mol Biol Evol 1997, 14:220-229
55. Smulders MJM, Bredemeijer G, Ruskortekaas W, Arens P, Vosman B: Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 1997, 84:264-272
56. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A: Cross species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants. Mol Biol Evol 1998, 15:1275-1287
57. Provan J, Corbett G, McNicol JW, Powell W: Chloroplast DNA variability in wild and cultivated rice (Oryza ssp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 1997, 40:104-110
58. SM Udupa, Robertson LD, Weigand F, Baum M, Kahl G: Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 1999, 261:354-363
59. Weising K, Gardner RC: A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genome of dicotyledonous angiosperms. Genome 1999, 42:9-19
60. Roder M, Plaschke J, Koenig SU, Boerner A, Sorrells ME, Tanksley SD, MW Ganal: Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 1995, 246:327-333
61. Ishii T, McCouch SR: Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species members. Theor Appl Genet 2000, 100:1257-1266
62. Levinson G, Gutman GA: Slipped strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 1987, 4:203-221
63. Wolff RK, Plaeke KR, Jeffreys AJ, White R: Unequal crossing over between homologous chromosomes is not the major mechanism involved in generation of new alleles at VNTR loci. Genomics 1991, 5:382-384
64. Innan H, Terauchi R, Miyashita T: Microsatellite polymorphism in natural populations of the wild plant Arabidoposis thaliana. Genetics 1997, 146:1441-1452
65. Song WY, Wang GP, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P: A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 1995, 270:1804-1806
66. Ronald PC: The molecular basis of disease resistance in rice Plant Mol Biol 1997, 35:179-186
67. Davierwala AP, Reddy APK, Lagu MD, Ranjekar PK, Gupta VS: Marker Assisted Selection Of Bacterial Blight Resistance Genes In Rice. Biochemical Genetics 2001, 39:261-278
68. Tautz D, Trick M, Dover GA: Cryptic simplicity in DNA is a major source of genetic variation. Nature 1986, 322:652-656
69. Xie Y, Wu R: Rice alcohol dehydrogenase genes: anaerobic induction, organ specific expression and characterization of cDNA clones. Plant Mol Biol 1989, 13:53-68
70. Kay SA, Keith B, Shinozaki K, Chye ML, Chua NH: The sequence of the rice phytochrome gene. Nucleic Acids Res 1989, 17:2865-2866
71. Bligh HFJ, Till RI, Jones CA: A microsatellite sequence closely linked to the Waxy gene of Oryza sativa. Euphytica 1995, 86:83-85
72. Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2nd ed, 1989
73. Yanisch-Perron C, Vieira J, Messing J: Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18, and pUC19 vectors. Gene 1985, 33:103-119
74. Rogers SO, Bendich AJ: Extraction of DNA from plant tissues. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual A6.1. Kluwer Academic Publishers, Dordrecht, 1988
75. Schaffer HE, Sederoff RR: Improved estimation of DNA fragment lengths from agarose gels. Anal Biochem 1981, 115:113-122
76. Yap IV, Nelson RJ: Winboot: A program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI discussion paper series no 14, Manila, Philippines, 1996