Conservation Genetics Resources

, Volume 1, Issue 1, pp 373–376

Characterization of EST–SSRs from Cryptomeria japonica

  • Yoshinari Moriguchi
  • Saneyoshi Ueno
  • Tokuko Ujino-Ihara
  • Norihiro Futamura
  • Asako Matsumoto
  • Kenji Shinohara
  • Yoshihiko Tsumura
Technical Note

Abstract

Simple sequence repeat (SSR) markers were developed for Cryptomeria japonica from 55,530 expressed sequence tags (ESTs). Of the 219 designed primer pairs, 176 showed clear PCR amplification products and 27 of these revealed polymorphisms in six individuals sampled at sites across Japan. When these 27 loci were examined in 48 individuals from a single population, the number of alleles and the Polymorphism Information Content (PIC) ranged from 2 to 17 and 0.09 to 0.86, respectively. The average PIC value obtained from EST–SSR markers (0.40) was lower than that from genomic SSR markers (0.67 and 0.62). We observed a significant departure from Hardy–Weinberg equilibrium in five of the 27 loci. These EST–SSR markers will be useful for the evaluation of genetic variation in C. japonica and for genetic mapping.

Keywords

Cryptomeria japonica EST–SSR 

References

  1. Eillis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132Google Scholar
  2. Fukuoka H, Nunome T, Minamiyama Y, Kono I, Namiki N, Kojima A (2005) Read2Marker: a data processing tool for microsatellite marker development from a large data set. Biotechniques 39:472–476CrossRefPubMedGoogle Scholar
  3. Futamura N, Ujino-Ihara T, Nishiguchi M, Kanamori H, Yoshimura K, Sakaguchi M, Shinohara K (2006) Analysis of expressed sequence tags from Cryptomeria japonica pollen reveals novel pollen-specific transcripts. Tree Physiol 26:1517–1528CrossRefPubMedGoogle Scholar
  4. Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M, Sakaki Y, Mari A, Shinozaki K, Shinohara K (2008) Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. BMC Genomics 9:383CrossRefPubMedGoogle Scholar
  5. Goudet J (1995) Fstat version 1.2: a computer program to calculate F-statistics. J Hered 86:485–486. http://www2.unil.ch/popgen/softwares/fstat.htm
  6. Kondo H, Tahira T, Hayashi H, Oshima K, Hayashi K (2000) Microsatellite genotyping of post-PCR fluorescently labeled markers. Biotechniques 29:868–872PubMedGoogle Scholar
  7. Moriguchi Y, Iwata H, Ihara T, Yoshimura K, Taira H, Tsumura Y (2003) Development and characterization of microsatellite markers for Cryptomeria japonica D. Don. Theor Appl Genet 106:751–758PubMedGoogle Scholar
  8. Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K, Tsumura Y (2003) A consensus linkage map for Sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165:1551–1568PubMedGoogle Scholar
  9. Tani N, Takahashi T, Ujino-Ihara T, Iwata H, Yoshimura K, Tsumura Y (2004) Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) from microsatellite enriched libraries. Ann For Sci 61:569–575CrossRefGoogle Scholar
  10. 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 94:764–772CrossRefGoogle Scholar
  11. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H (2007) Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 176:2393–2403CrossRefPubMedGoogle Scholar
  12. 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 43:451–457CrossRefPubMedGoogle Scholar
  13. Ujino-Ihara T, Taguchi Y, Yoshimura K, Tsumura Y (2003) Analysis of expressed sequence tags derived from developing seed and pollen cones of Cryptomeria japonica. Plant Biol 5:600–607CrossRefGoogle Scholar
  14. Ujino-Ihara T, Kanamori H, Yamane H, Taguchi Y, Namiki N, Mukai Y, Yoshimura K, Tsumura Y (2005) Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers. Plant Mol Biol 59:895–907CrossRefPubMedGoogle Scholar
  15. Yoshida K, Nishiguchi M, Futamura N, Nanjo T (2007) Expressed sequence tags from Cryptomeria japonica sapwood during the drying process. Tree Physiol 27:1–9PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Yoshinari Moriguchi
    • 1
  • Saneyoshi Ueno
    • 1
  • Tokuko Ujino-Ihara
    • 1
  • Norihiro Futamura
    • 2
  • Asako Matsumoto
    • 1
  • Kenji Shinohara
    • 2
  • Yoshihiko Tsumura
    • 1
  1. 1.Department of Forest GeneticsForestry and Forest Products Research InstituteTsukuba, IbarakiJapan
  2. 2.Department of Molecular and Cell BiologyForestry and Forest Products Research InstituteTsukuba, IbarakiJapan

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