Theoretical and Applied Genetics

, Volume 113, Issue 2, pp 261–269 | Cite as

Phylogenetic analysis of the rDNA intergenic spacer subrepeats and its implication for the domestication history of foxtail millet, Setaria italica

  • Kenji Fukunaga
  • Katsuyuki Ichitani
  • Makoto Kawase
Original Paper

Abstract

We sequenced ribosomal DNA intergenic spacer subrepeats and their flanking regions of foxtail millet landraces from various regions in Europe and Asia and its wild ancestor to elucidate phylogenetic differentiation within each of types I–III found in our previous work and to elucidate relationships among these three types. Type I was classified into seven subtypes designated as Ia–Ig based on subrepeat sequences; C repeats downstream of those subrepeats are also polymorphic. Of these, subtypes Ia–Id and Ig were found in foxtail millet landraces. Subtypes Ia and Ib were distributed broadly throughout Asia and Europe. Subtype Ic was distributed in China, Korea and Japan. Subtype Id has a 20-bp deletion in subrepeat 3 and has a unique C repeat sequence. This subtype was found in a morphologically primitive landrace group from Afghanistan and northwestern Pakistan and differed greatly from other type I subtypes, implying that these landraces were domesticated independently. Subtypes Ig was found in a landrace from Pakistan and Ia and Ie–Ig were in six wild ancestor accessions. Type II was also highly polymorphic and four subtypes were found and designated as subtypes IIa–IId, but sequence analyses indicated type III as monomorphic. The present work indicates that type III should be classified as a subtype of type II (subtype IIe). Sequence polymorphism of subrepeats of types I–III indicated that subrepeats of subtype IIa are greatly divergent from others. Relationships among types I–III are much more complicated than anticipated based on previous RFLP work.

Notes

Acknowledgements

This work has been partially funded by a Research Institute For Humanity and Nature (RIHN) project 2-5PR(Project Leader Prof. Y.I.Sato). KF also thank Prof. Y. Yasuda, IRCJS, for his encouragement and supports.

References

  1. Benabdelmouna A, Abirached-Darmency M, Darmency H (2001) Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S and 18S-5.8S-25S rDNA genes. Theor Appl Genet 103:668–677CrossRefGoogle Scholar
  2. Buckler IV ES, Holtsford TP (1996) Zea systematics: ribosomal ITS evidence. Mol Biol Evol 13:612–622PubMedGoogle Scholar
  3. Chou CH, Chiang Y-H,Chiang T-Y (1999) Within- and between- individual length heterogeneity of rDNA-IGS in Miscanthus sinensis var. glaber (Poaceae): Phylogenetic analyses. Genome 42:1088–1093PubMedCrossRefGoogle Scholar
  4. De Wet JMJ, Oestry-Stidd LL, Cubero JI (1979) Origins and evolution of foxtail millet (Setaria italica), Journ d’Agric et de Bot 26:53–64Google Scholar
  5. Fukunaga K, Domon E, Kawase M (1997) Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P.Beauv. and a survey of variation from Europe and Asia. Theor Appl Genet 97:751–756CrossRefGoogle Scholar
  6. Fukunaga K, Wang ZM, Kato K, Kawase M (2002) Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet Res Crop Evol 49:95–101CrossRefGoogle Scholar
  7. Fukunaga K, Ichitani K, Taura S, Sato M, Kawase M (2005) Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces. Hereditas 142:38–44PubMedCrossRefGoogle Scholar
  8. Harlan JR (1975) Crops and Man. Soc Amer Agron Crop Sci Soc America, Madison, WIGoogle Scholar
  9. Jusuf M, Pernes J (1985) Genetic variability of foxtail millet (Setaria italica (L.) P. Beauv): Electrophoretic study of five isoenzyme systems. Theor Appl Genet 71:385–391CrossRefGoogle Scholar
  10. Kawase M, Sakamoto S (1982) Geographical distribution and genetic analysis of phenol color reaction in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 63:117–119CrossRefGoogle Scholar
  11. Kawase M, Sakamoto S (1984) Variation, geographical distribution and genetic analysis of esterase isozymes in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 67:529–533CrossRefGoogle Scholar
  12. Kawase M, Sakamoto S (1987) Geographical distribution of landrace groups classified intraspecific pollen sterility in foxtail millet, Setaria italica (L.) P.Beauv. Jpn J Breed 37:1–9Google Scholar
  13. Kawase M, Fukunaga K, Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions. Mol Genet Genomics 274:131–140PubMedCrossRefGoogle Scholar
  14. Kihara H, Kishimoto E (1942) Bastarde zwischen Setaria italica und S. viridis (in Japanese with German summary). Bot Mag 20:63–67Google Scholar
  15. Küster H (1984) Neolithic plant remains from Eberdingenhochdorf, southern Germany. In: Van Zeist WV, Casparoe WA (eds) Plants and ancient man (studies in palaeoethnobotany). AA Bakame, Rotterdam, Boston, pp 307–311Google Scholar
  16. Le Thierry d’Ennequin M, Panaud O, Toupance B, Sarr A (2000) Assessment of genetic relationships between Setaria italica and its wild relatives S. viridis using AFLP marker. Theor Appl Genet 100:1061–1066CrossRefGoogle Scholar
  17. Li Y, Wu SZ (1996) Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv) landraces in China. Euphytica 87:33–38CrossRefGoogle Scholar
  18. Li HW, Li CH, Pao WK (1945) Cytological and genetic studies of interspecific cross of the cultivated foxtail millet, Setaria italica P. Beauv. and the green foxtail millet, S. viridis L. J Amer Soc Agron 37:32–54Google Scholar
  19. Li Y, Cao YS, Wu SZ, Zhang XZ (1995a) A diversity analysis of foxtail millet (Setaria italica (L.) P.Beauv.) landraces of Chinese origin. Genet Res Crop Evol 45:279–285CrossRefGoogle Scholar
  20. Li Y, Wu SZ, Cao YS (1995b) Cluster analysis of an international collection of foxtail millet (Setaria italica (L.) P. Beauv). Genet Res Crop Evol 45:279–285CrossRefGoogle Scholar
  21. Li Y, Jia J, Wang W, Wu S (1998) Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet Res Crop Evol 45:279–285CrossRefGoogle Scholar
  22. Lisitsina A (1976) Main types of ancient farming on the Caucasus on the basis of palaeo-ethnobotanical research. Ber Deut Bot Ges 91:47–57Google Scholar
  23. Nakayama H, Namai H, Okuno K (1999) Geographical variation of the alleles at the two prolamin loci, Pro1 and Pro2, in foxtail millet, Setaria italica (L.) P. Beauv. Genes Genet Syst 74:293–297PubMedCrossRefGoogle Scholar
  24. Ochiai Y (1996) Variation in tillering and geographical distribution of foxtail millet (Setaria italica P. Beauv.) Breed Sci 46:143–146Google Scholar
  25. Ochiai Y, Kawase M, Sakamoto S (1994) Variation and distribution of foxtail millet (Setaria italica P. Beauv.) in the mountainous areas of northern Pakistan. Breed Sci 44:413–418Google Scholar
  26. Rogers BO, Bendich AJ (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520CrossRefGoogle Scholar
  27. 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 81:8014–8018PubMedCrossRefGoogle Scholar
  28. Sallares R, Brown TA (2004) Phylogenetic analysis of complete 5 external transcribed spacers of the 18S ribosomal RNA genes of diploid Aegilops and related species (Triticeae, Poaceae). Genet Res Crop Evol 51:701–712CrossRefGoogle Scholar
  29. Sakamoto S (1987) Origin and dispersal of common millet and foxtail millet. Japan Agric Res Quart 21:84–89Google Scholar
  30. Sano Y, Sano R (1990) Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33:209–218Google Scholar
  31. 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 22:4673–4680PubMedCrossRefGoogle Scholar
  32. Vavilov NI (1926) Studies on the origin of cultivated plants. Inst Appl Bot Plant Breed, LeningradGoogle Scholar
  33. Wang RL, Wendell J,Dekker J (1995) Weedy adaptation in Setaria spp.: I. Isozyme analysis of the genetic diversity and population genetic structure in S. viridis. Am J Bot 82:308–317CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Kenji Fukunaga
    • 1
  • Katsuyuki Ichitani
    • 2
  • Makoto Kawase
    • 3
  1. 1.International Research Center for Japanese StudiesKyotoJapan
  2. 2.Faculty of AgricultureKagoshima UniversityKagoshimaJapan
  3. 3.National Institute of Agrobiological SciencesIbarakiJapan

Personalised recommendations