Development and characterization of microsatellite markers for Cryptomeria japonica D.Don

Theoretical and Applied Genetics

Volumn 106, Issue 4, 2003, Pages 751-758

  Moriguchi, Y ^a   Iwata, H ^b   Ujino Ihara, T ^b   Yoshimura, K ^b   Taira, H ^a   Tsumura, Y ^b  

^a NIIGATA UNIVERSITY   (Japan)

^b FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

Author keywords

Conifers; Cryptomeria japonica; Microsatellite; Microsatellite enriched library; Simple sequence repeat (SSR)

Indexed keywords

CORRELATION METHODS; DATABASE SYSTEMS; DNA; FORESTRY; GENETIC ENGINEERING;

MICROSATELLITE MARKERS;

CROPS;

CORRELATION; FARM CROPS; GENETIC ENGINEERING; NUCLEIC ACIDS;

CONIFEROPHYTA; CRYPTOMERIA; CRYPTOMERIA JAPONICA; EMBRYOPHYTA; JAPONICA;

EID: 0037517043     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-002-1149-0     Document Type: Article

References (43)

1. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
2. n microsatellite markers. Am J Hum Genet 52:922-927
3. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847-854
4. Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215-220
5. Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866-873
6. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativaL.). Theor Appl Genet 100:713-722
7. Davis BJ (1964) Disc electophoresis. II. Method and application to human serum protein. Ann NY Acad Sci 121:404-427
8. Echt CS, May-Marquardt P (1997) Survey of microsatellite DNA in pine. Genome 40:9-17
9. Elsik CG, Williams CG (2001) Low-copy microsatellite recovery from a conifer genome. Theor Appl Genet 103:1189-1195
10. Elsik CG, Virginia T, Minihan T, Hall SE, Scarpa AM, Williams CG (2000) Low-copy microsatellite markers for Pinus taeda L. Genome 43:550-555
11. Fischer D, Bachmann K (1998) Microsatellite enrichment in organisms with large genomes (Allium cepa L.). Biotechniques 24:796-802
12. Fisher PJ, Richardson TE, Gardner RC (1998) Characteristics of single- and multi-copy microsatellites from Pinus radiata. Theor Appl Genet 96:969-979
13. Goldstein DB, Clark AG (1995) Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Res 23:3882-3886
14. Hamilton MB, Pincus EL, DiFiore A, Fleischer R (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques 27:500-507
15. Hodgetts RB, Aleksiuk MA, Brown A, Clarke C, Macdonald E, Nadeem S, Khasa D (2001) Development of microsatellite markers for white spruce (Picea glauca) and related species. Theor Appl Genet 102:1252-1258
16. Iwata H, Ujino-Ihara T, Yoshimura K, Nagasaka K, Mukai Y, Tsumura Y (2001) Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Theor Appl Genet 163:881-895
17. Jones AG, Stockwell CA, Walker D, Avise JC (1998) The molecular basis of a microsatellite null allele from the white sands pupfish. J Hered 89:339-342
18. Kendall MG (1970) Rank Correlation Methods, 3rd edn. Charles Griffin London
19. Khasa PD, Newton CH, Rahman MH, Jaquish B, Dancik BP (2000) Isolation, characterizaton, and inheritance of microsatellite loci in alpine larch and western larch. Genome 43:439-448
20. Kijas JMH, Fowler JCS, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Bio Techniques 16:657-662
21. Kostia S, Varvio SL, Vakkari P, Pulkkinen P (1995) Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244-1248
22. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111-1115
23. Lench NJ, Norris A, Bailey A, Booth A, Markham AF (1996) Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers. Nucleic Acids Res 24:2190-2191
24. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397-401
25. Lunt DH, Hutchinson WF, Carvalho GR (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Mol Ecol 8:891-894
26. Mukai Y, Suyama Y, Tsumura Y, Kawahara T, Yoshimaru H, Kondo T, Tomaru N, Kuramoto N, Murai M (1995) A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci. Theor Appl Genet 90:835-840
27. Nikaido AM, Ujino T, Iwata H, Yoshimura K, Yoshimaru H, Suyama Y, Murai M, Nagasaka K, Tsumura Y (2000) AFLP and CAPS linkage maps of Cryptomeria japonica. Theor Appl Genet 100:825-831
28. Ornstein L (1964) Disc electophoresis. I. Background and theory. Ann NY Acad Sci 121:321-349
29. Pfeiffer A, Olivieri M, Morgante M (1997) Identification and characterization of microsatellites in Norway spruce (Picea abies K.). Genome 40:411-419
30. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225-238
31. Russel JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714-722
32. Schug MD, Hutter CH, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF (1998) The mutation rates of di-, tri- and tetra-nucleotide repeats in D. melanogaster. Mol Biol Evol 15:1751-1760
33. Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE (2000) Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 43:41-46
34. Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977-983
35. Stachel M, Lelley T, Grausgruber H, Vollmann J (2000) Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theor Appl Genet 100:242-248
36. n repetitive sequences in mammalian genomes. Genomics 10:807-815
37. Takahashi H, Nirasawa K, Furukawa T (1996) An efficient method to clone chicken microsatellite repeat sequences. Jap Poultry Sci 33:292-299
38. Tsumura Y, Yoshimura K, Tomaru N, Ohba K (1995) Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91:1222-1236
39. Tsumura Y, Suyama Y, Yoshimura K, Shirato N, Mukai Y (1997) Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theor Appl Genet 94:764-772
40. Ujino-Ihara T, Yoshimura K, Ugawa Y, Yoshimaru H, Nagasaka K, Tsumura Y (2000) Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Mol Biol 43:451-457
41. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1-6
42. n polymorphisms. Genomics 7:524-530
43. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388-396