Plant Systematics and Evolution

, Volume 300, Issue 5, pp 1137–1145 | Cite as

Plasmon analysis in wheat alloplasmic lines using morphological and chloroplast microsatellite markers

Original Article


Inheritance of plant traits mainly depends upon nuclear genes, cytoplasmic factors and their interactions. In the present study, 32 alloplasmic lines accompanied by a euplasmic parental line (control) were evaluated using molecular (chloroplast microsatellite) and morpho-physiological traits during 2010–2011 and 2011–2012. The results of combined analysis of variance showed the significant effect of growing seasons on most of the studied traits as well as the significant effect of cytoplasm on plant height, leaf net CO2 assimilation rate and grain yield per plant. Results of cluster analysis divided the six plasmons based on their phenotypic effects into three groups: (1) R and Sv type, D (Aegilops typica and Ae. ventricosa) and D2 type, as well as B-type plasmon (euplasmic line); (2) a single plasmon of M type and three plasmons of B type; (3) all other B-type and a single D-type plasmon (Aegilops cylindrica). Molecular analysis showed that 20 primer pairs out of 26 chloroplastic microsatellite markers (cpSSR) produced polymorphic bands in the alloplasmic lines. A total of 50 alleles were identified with an average of 2.5 alleles per locus. In this study, polymorphism information content (PIC) ranged from 0.05 (WCt17 primer) to 0.49 (WCt9 primer). Cluster analysis of molecular data revealed that the alloplasmic lines belong to two major clusters, in which differentiation of cytoplasmic types belonging to the genus Triticum and Aegilops has been evident. Likewise, analysis of molecular variance showed significant differences between two studied groups (F ST = 0.67, P < 0.001). Overall, our findings indicated that the cpSSR markers can be valuable resources of polymorphic markers for the analysis of cytoplasm of Triticeae species, with the potential for clear differentiation in close species and genera of this tribe.


Cytoplasmic diversity cpSSR Triticum Aegilops Photosynthesis Yield 



We thank Professor S.F. Koval at Institute of Cytology and Genetics, Novosibirsk, Russia, for providing the genetic material used in this study.


  1. Bryan GJ, Nicool J, Ramsay G, Meyer RC, De Jong WS (1999) Polymorphic simple sequences repeat markers in chloroplast genomes of Solanaceous plants. Theor Appl Genet 99:859–867CrossRefGoogle Scholar
  2. Chaïr H, Perrier X, Agbangla C, Marchand JL, Dainou O, Noyer JL (2004) Use of cpSSRs for the characterisation of yam phylogeny in Benin. Genome 48:674–684CrossRefGoogle Scholar
  3. Evans JR, Austin RB (1986) The specific activity of ribulose-1,5-bisphosphate carboxylase in relation to genotype in wheat. Planta 167:344–350PubMedCrossRefGoogle Scholar
  4. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinf Online 1:47–50Google Scholar
  5. Goryunova SV, Chikida NN, Badaeva ED, Pukhalski VA (2010) Polymorphism and phylogeny of D genome species of Aegilops L. based on the results of analysis of the microsatellite loci of the chloroplast genome. Biology 4:21–24Google Scholar
  6. Ishii T, McCouch SR (2000) Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theor Appl Genet 100:1257–1266CrossRefGoogle Scholar
  7. Ishii T, Mori N, Ogihara Y (2001) Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species. Theor Appl Genet 103:896–904CrossRefGoogle Scholar
  8. Jones P, Keane EM, Osborne BA (1998) Effects of alien cytoplasmic variation on carbon assimilation and productivity in wheat. Exp Bot 49:1519–1528CrossRefGoogle Scholar
  9. Jun-ying Ch, Nai-yu X (2000) Studies on the utilization potentiality of the nucleo-cytoplasmic hybrid in wheat. Wuhan Univ J Nat Sci 5:114–118Google Scholar
  10. Kofoid RD, Maan SS (1982) Agronomic and bread-making performance of fertile alloplasmic wheats. Crop Sci 22:725–729CrossRefGoogle Scholar
  11. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245PubMedCrossRefGoogle Scholar
  12. Lichtenthaler HK, Buschmann C (2001) In: Wrolstad RE, Acree TE, An H, Decker EA, Penner MH, Reid DS, Schwartz SJ, Shoemaker CF, Sporns P (eds) Current protocols in food analytical chemistry. Wiley, New York, pp F4.3.1–F4.3.8Google Scholar
  13. Liu CG, Wu YW, Hou H, Zhang C, Zhang Y (2002) Value and utilization of alloplasmic common wheats with Aegilops crassa cytoplasm. Plant Breed 121:407–410CrossRefGoogle Scholar
  14. Liu L, Zhu X, Gong Y, Song X, Wang Y, Zhao L, Wang L (2007) Genetic diversity analysis of radish germplasm with RAPD, AFLP and SRAP markers. Acta Hort 760:125–130Google Scholar
  15. Liu B, Xu Ch, Zhao N, Qi B, Kimatu JN, Pang J, Han F (2009) Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genomic improvement. J Genet Genomics 36:519–528PubMedCrossRefGoogle Scholar
  16. Mizumoto K, Hatano H, Hirabayashi C, Murai K, Takumi S (2011) Characterization of wheat Bell1-type homeobox genes in floral organs of alloplasmic lines with Aegilops crassa cytoplasm. Plant Biol 11:1–15Google Scholar
  17. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325PubMedCentralPubMedCrossRefGoogle Scholar
  18. Nakamura C, Kasai K, Kubota Y, Yamagami C, Suzuki T, Mori N (1991) Cytoplasmic diversity in alloplasmic common wheats with cytoplasms of Triticum and Aegilops revealed by photosynthetic and respiratory characteristics. Jpn J Genet 66:471–483CrossRefGoogle Scholar
  19. Provan J, Biss P, Meel D, Mathews S (2004a) Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Mol Ecol Note 4:262–264CrossRefGoogle Scholar
  20. Provan J, Wolters P, Caldwell KH, Powell W (2004b) High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat. Theor Appl Genet 108:1182–1190PubMedCrossRefGoogle Scholar
  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  22. SAS Institute (2002) SAS version 9.1. SAS Institute, Cary, North Carolina, USAGoogle Scholar
  23. 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 RFLP sand pedigree. Theor Appl Genet 95:163–173CrossRefGoogle Scholar
  24. Tsunewaki K, Maekawa M, Tsujimoto H (1984) Genetic diversity of the cytoplasm in Triticum and Aegilops.X the haxaploid triticale as an effective tester for plasma type distinction. Jpn J Genet 59:215–224CrossRefGoogle Scholar
  25. Tsunewaki K, Wang GZ, Matsuoka Y (1996) Plasmon analysis of Triticum (wheat) and Aegilops. 1: Production of alloplasmic common wheats and their fertilities. Genes Genet Syst 71:293–311PubMedCrossRefGoogle Scholar
  26. Tsunewaki K, Wang GZ, Matsuoka Y (2002) Plasmon analysis of Triticum (wheat) and Aegilops. 2. Characterization and classification of 47 plasmons based on their effects on common wheat phenotype. Genes Genet Syst 77:409–427PubMedCrossRefGoogle Scholar
  27. Wang GZ, Miyhita NT, Tsunewaki K (1997) Plasmon analyses of Triticum (wheat) and Aegilops: PCR–single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs. Genetics 94:14570–14577Google Scholar
  28. Yamane K, Kawahara T (2005) Intra- and interspecific phylogenetic relationships among diploid TriticumAegilops species (Poaceae) based on base-pair substitutions, indels, and microsatellites in chloroplast noncoding sequences. Am J Bot 92:1887–1898PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Mahboobeh Hodaei
    • 1
  • Ahmad Arzani
    • 1
  • Mehdi Rahimmalek
    • 1
  1. 1.Department of Agronomy and Plant Breeding, College of AgricultureIsfahan University of TechnologyIsfahanIran

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