Microsatellites in Zea - Variability, patterns of mutations, and use for evolutionary studies

Theoretical and Applied Genetics

Volumn 104, Issue 2-3, 2002, Pages 436-450

  Matsuoka, Y ^a   Mitchell, S E ^b   Kresovich, S ^b   Goodman, M ^c   Doebley, J ^a,d  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Department of Population Medicine and Diagnostic Sciences   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d FUKUI PREFECTURAL UNIVERSITY   (Japan)

Author keywords

Evolution; Genetic diversity; Indel; SSR; Teosinte

Indexed keywords

BIODIVERSITY; CROPS; MUTAGENESIS; PLANTS (BOTANY);

GERMPLASM;

GENETIC ENGINEERING;

EMBRYOPHYTA; ZEA; ZEA MAYS;

EID: 0347579843     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s001220100694     Document Type: Article

References (56)

1. Angers B, Bernatchez L (1997) Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size information. Mol Biol Evol 14:230-238
2. Ashley Jr CT, Warren ST (1995) Trinucleotide repeat expansion and human disease. Annu Rev Genet 29:703-728
3. Buckler IV ES, Holtsford TP (1996) Zea systematics: Ribosomal ITS evidence. Mol Biol Evol 13:612-622
4. Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939-943
5. Buteler MI, Jarret RL, LaBonte DR (1999) Sequence characterization of microsatellites in diploid and polyploid Ipomoea. Theor Appl Genet 99:123-132
6. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: Models and estimation procedures. Am J Hum Genet 19:233-257
7. Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: Abundance and allele variation. Genome 39:866-873
8. Colson I, Goldstein DB (1999) Evidence for complex mutations at microsatellite loci in Drosophila. Genetics 152:617-627
9. Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66-71
10. Doebley JF (1990) Molecular systematics of Zea (Gramineae). Maydica 35:143-150
11. Doebley JF, Iltis HH (1980) Taxonomy of Zea (Gramineae). I. A subgeneric classification with a key to taxa. Am J Bot 67:982-993
12. Doebley JF, Stec A (1991) Genetic analysis of the morphological differences between maize and teosinte. Genetics 129: 285-295
13. Doebley JF, Goodman MM, Stuber CW (1984) Isoenzymatic variation in Zea (Gramineae). Systematic Bot 9:203-218
14. Eichler EE, Holden JJ, Popovich BW, Reiss AL, Snow K, Thibodeau SN, Richards CS, Ward PA, Nelson DL (1994) Length of uninterrupted CGG repeats determines instability in the FMR1 gene. Nature Genet 8:88-94
15. Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite 'evolution': Directionality or bias? Nat Genet 11:360-362
16. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci USA 95:4441-4446
17. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) Version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle
18. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279-284
19. Forbes SH, Hogg JT, Buchanan FC, Crawford AM, Allendorf FW (1995) Microsatellite evolution in congeneric mammals: Domestic and bighorn sheep. Mol Biol Evol 12:1106-1113
20. Goldstein DB, Clark AG (1995) Microsatellite variation in north american populations of Drosophila melanogaster. Nucleic Acids Res 23:3882-3886
21. Goldstein DB, Pollock DD (1997) Launching microsatellites: A review of mutation processes and methods of phylogenetic inference. J Hered 88:335-342
22. Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92:6723-6727
23. Goldstein DB, Roemer GW, Smith DA, Reich DE, Bergman A, Wayne RK (1999) The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151:797-801
24. Grimaldi MC, Crouau-Roy B (1997) Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol 44:336-340
25. Helentjaris T, Weber D, Wright S (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118:353-363
26. Holton TA, Graham MW (1991) A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors. Nucleic Acids Res 19:1156
27. Hutter CM, Schug MD, Aquadro CF (1998) Microsatellite variation in Drosophila melanogaster and Drosophila simulans: A reciprocal test of the ascertainment bias hypothesis. Mol Biol Evol 15:1620-1636
28. Iltis HH, Doebley JF (1980) Taxonomy of Zea (Gramineae). II. Subspecific categories in the Zea mays complex and a generic synopsis. Am J Bot 67:994-1004
29. Innan H, Terauchi R, Miyashita NT (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics 1997:1441-1452
30. Kimura M, Crow JF (1964) The numbers of alleles that can be maintained in a finite population. Genetics 49:725-738
31. Kresovich S, Szewc-McFadden AK, Bliek SM, McFerson JR (1995) Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 91: 206-211
32. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95:10774-10778
33. Levinson G, Gutman GA (1987) Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 4:203-221
34. Liu ZW, Biyashev RM, Saghai-Maroof MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869-876
35. Lübberstedt T, Dussle C, Melchinger AE (1998) Application of microsatellites from maize to teosinte and other relatives of maize. Plant Breed 117:447-450
36. MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146:1071-1086
37. Mitchell SE, Kresovich S, Jester CA, Javier Hernandez C, Szewc-McFadden AK (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetics resources. Crop Sci 37:617-624
38. Nei M (1972) Genetic distance between populations. Am Nat 106:283-292
39. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321-3323
40. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19:153-170
41. Ohta T, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22:201-204
42. Rogers JS (1972) Measures of genetic similarity and genetic distance. Studies in Genetics VII. University of Texas Publication 7213, Austin, Texas, pp 145-153
43. Röder MS, Plaschke J, König SU, Börner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327-333
44. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007-2023
45. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014-8018
46. 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 15:1751-1760
47. Senior ML, Heun M (1993) Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36:884-889
48. 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
49. Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): Comparisons with data from RFLPS and pedigree. Theor Appl Genet 95:163-173
50. Taramino G, Tingey S (1996) Simple sequence repeats for germplasm analysis and mapping in maize. Genome 39:277-287
51. Tautz D, Renz M (1984) Simple sequences are ubiquitous components of eukaryotic genomes. Nucleic Acids Res 12: 4127-4138
52. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
53. Wang RL, Stec A, Hey J, Lukens L, Doebley J (1999) The limits of selection during maize domestication. Nature 398:236-239
54. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2:1123-1128
55. Zhang L, Leeflang EP, Yu J, Arnheim N (1994) Studying human mutations by sperm typing: Instability of CAG trinucleotide repeats in the human androgen receptor gene. Nature Genet 7:531-535
56. Zhivotovsky LA, Feldman MW, Grishechkin SA (1997) Biased mutations and microsatellite variation. Mol Biol Evol 14: 926-933