Skip to main content
SpringerLink
Log in

Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (~30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (P<0.01) deviation from the expected segregation ratio. In total, 136 polymorphic markers were developed using C. japonica-based STS primers without any sequence modification. In addition, the applicability of STS-based markers developed in one species to other species was found to closely reflect the evolutionary distance between the species, which is roughly concordant with the difference between their rbcL sequences. We plan to use these markers for genetic studies in C. obtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • 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

    CAS  PubMed  Google Scholar 

  • Brown GR, Kandel EE III, Bassoni DL, Kiehne KL, Temesgen B, van Buijtnen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809

    CAS  PubMed  Google Scholar 

  • Brunsfeld SJ, Soltis PS, Soltis DE, Gadek PA, Quinn CJ, Strenge DD, Ranker TA (1994) Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae: evidence from rbcL sequences. Syst Bot 19:253–262

    Google Scholar 

  • Chagne D, Brown G, Lalanne C, Madur D, Pot D, Neale D, Plomion C (2003) Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 12:185–195

    Article  CAS  Google Scholar 

  • Dirlewanger E, Cosson P, Tavaud M, Jaranzana M, Poizat C, Zanetto A, Arus P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105:127–138

    Article  CAS  PubMed  Google Scholar 

  • Eckenwalder JE (1976) Re-evaluation of Cupressaceae and Taxodiaceae: a proposed merger. Madrono 23:237–300

    Google Scholar 

  • Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282:656–659

    Article  CAS  PubMed  Google Scholar 

  • Hart JA (1987) A cladistic analysis of conifers: preliminary results. J Arnold Arboretum 68:269–307

    Google Scholar 

  • Hizume M, Kondo T, Shibata F, Ishizuka R (2001) Flow cytometric detamination of genome size in the Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. Cytologia 66:307–311

    Google Scholar 

  • Isagi Y, Suhandono S (1997) PCR primers amplifying microsatellite loci of Quercus myrsinifolia Blume and their conservation between oak species. Mol Ecol 6:897–899

    Article  CAS  PubMed  Google Scholar 

  • 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 location on a linkage map. Theor Appl Genet 103:881–895

    Article  CAS  Google Scholar 

  • Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359

    Article  Google Scholar 

  • Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O‘Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678

    Article  CAS  PubMed  Google Scholar 

  • Kusumi J, Tsumura Y, Yoshimaru H, Tachida H (2000) Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. Am J Bot 87(10):1480–1488

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Price RA, Lowenstein JM (1989) An immunological comparison of the Sciadopityaceae, Taxodiaceae, and Cupressaceae. Syst Bot 14:141–149

    Google Scholar 

  • Stefanovic S, Jager M, Broutin DJ, Masselot M (1998) Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences. Am J Bot 85:688–697

    CAS  Google Scholar 

  • Steinkellner H, Lexer C, Turetschek E, Glossl J (1997) Conservation of (GA)n microsatellite loci between Quercus species. Mol Ecol 6:1189–1194

    Article  CAS  Google Scholar 

  • Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K, Tsumura Y (2003a) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165:1551–1568

    CAS  PubMed  Google Scholar 

  • Tani N, Tsumura Y, Sato H (2003b) Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period. Mol Ecol 12(4):859–868

    CAS  PubMed  Google Scholar 

  • Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB (2001) Genetic mapping of expressed sequence tag polymorphism (EST) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664–675

    Article  CAS  Google Scholar 

  • Tsumura Y, Tomaru N (1999) Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites. Theor Appl Genet 98:396–404

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Tsumura Y, Tomaru N, Suyama Y, Bacchus S (1999) Genetic diversity and differentiation of Taxodium in the southeastern United States using cleaved amplified polymorphic sequences. Heredity 83:229–238

    Article  CAS  PubMed  Google Scholar 

  • Ujino T, Kawahara T, Tsumura Y, Nagamitsu T, Yoshimaru H, Ratnam W (1998) Development and polymorphism of simple sequence repeat DNA markers for Shorea cuetisii and Dipterocarpaceae species. Heredity 81:422–428

    Article  CAS  PubMed  Google Scholar 

  • Ujino-Ihara T, Yoshimura K, 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

    Article  CAS  PubMed  Google Scholar 

  • Ujino-Ihara T, Matsumoto A, Iwata H, Yoshimura K, Tsumura Y (2002) Single-strand conformation polymorphism of sequence-tagged site markers based on partial sequences of cDNA clones in Cryptomeria japonica. Genes Genet Syst 77:251–257

    Article  CAS  PubMed  Google Scholar 

  • Wakamiya I, Newton RJ, Johnston JS, Price HJ (1993) Genome size and environmental factors in the genus Pinus. Am J Bot 80:1235–1241

    Google Scholar 

Download references

Acknowledgements

The authors would like to thank T. Kondo and M. Okamura, who provided plant materials. We also thank K. Aoyagi, M. Koshiba, Y. Kawamata, and Y. Taguchi for their technical support and N. Tani, H. Iwata, T. Ujino-Ihara, K. Yoshimura, H. Yoshimaru, and K. Nagasaka for their helpful suggestions during this study, which was supported by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) and the Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), No. 16380112.

Author information

Authors and Affiliations

  1. Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan

    A. Matsumoto & Y. Tsumura

Authors
  1. A. Matsumoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Y. Tsumura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Y. Tsumura.

Additional information

Communicated by D.B. Neale

Appendix

Appendix

Table 4 shows size and polymorphic information content (PIC) of sequence-tagged site (STS) markers detected in hinoki (Chamaecyparis obtusa), using primers developed in sugi (Cryptomeria japonica)

Table 4  
Full size table

Rights and permissions

Reprints and permissions

About this article

Cite this article

Matsumoto, A., Tsumura, Y. Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica. Theor Appl Genet 110, 80–91 (2004). https://doi.org/10.1007/s00122-004-1754-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1754-1

Keywords

Search

Navigation