Main Article Content


D.S. Tagimanova

National Center for Biotechnology, 13/5 Korghalzhyn Road, Astana, 010000, Kazakhstan

A.P. Novakovskaya

National Center for Biotechnology, 13/5 Korghalzhyn Road, Astana, 010000, Kazakhstan

A.O. Uvashov

National Center for Biotechnology, 13/5 Korghalzhyn Road, Astana, 010000, Kazakhstan

O.N. Khapilina

National Center for Biotechnology, 13/5 Korghalzhyn Road, Astana, 010000, Kazakhstan

R.N. Kalendar

National Center for Biotechnology, 13/5 Korghalzhyn Road, Astana, 010000, Kazakhstan


The wild ancestor of all cultivated tetra- and hexaploid wheat, wild emmer wheat (Triticum dicoccoides), harbours considerable genetic diversity. This diversity might be expected to display eco-geographical patterns of variation, conflating gene flow, and local adaptation. Similarly, retrotransposons, as self-replicating entities comprising the bulk of genomic DNA in wheat, are expected to generate generally neutral variation due to their transpositional activity. Here, we examined the genetic diversity of 14 Israeli and one Turkish population of wild emmer wheat, based on the retrotransposon marker methods IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). The level of genetic diversity we detected was in agreement with previous studies that have used a variety of marker systems to assay genes and other genomic components. The genetic distances failed to correlate with the geographical distances, suggesting local selection on geographically widespread haplotypes (“weak selection”). However, the proportion of polymorphic loci correlated with the latitude of the population and the genetic diversity correlated with the longitude. Principal component analysis of the marker data resulted in separation of some of the populations.


Triticum dicoccoides, wild emmer wheat, IRAP, REMAP, genetic diversity

Article Details


Nevo E., Baum B., Beiles A., Johnson D.A. Ecological correlates of RAPD DNA diversity of wild barley, Hordeum spontaneum, in the Fertile Crescent. Genetic Resources and Crop Evolution, 1998, vol. 45, no. 2, рp. 151-159. doi:10.1023/A:1008616923427.

Fahima T., Sun G.L., Beharav A., Krugman T., Beiles A., Nevo E. RAPD polymorphism of wild emmer wheat populations, Triticum dicoccoides, in Israel. Theoretical and Applied Genetics, 1999, vol. 98, no. 3-4, рp. 434-447. doi:10.1007/s001220051089.

Nevo E. Evolution in action across phylogeny caused by microclimatic stresses at "evolution canyon". Theoretical Population Biology, 1997, vol. 52, no. 3, рp. 231-243. doi:10.1006/tpbi.1997.1330.

Nevo E., Beiles A. Genetic diversity of wild emmer wheat in Israel and Turkey: Structure, evolution, and application in breeding. Theoretical and Applied Genetics, 1989, vol. 77, no. 3, рp. 421-455. doi:10.1007/BF00305839.

Fahima T., Roder M.S., Wendehake K., Kirzhner V.M., Nevo E. Microsatellite polymorphism in natural populations of wild emmer wheat, Triticum dicoccoides, in Israel. Theoretical and Applied Genetics, 2002, vol. 104, no. 1, рp. 17-29. doi:10.1007/s001220200002.

Flavell A.J., Smith D.B., Kumar A. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Molecular and General Genetics, 1992, vol. 231, no. 2, рp. 233-242. URL.

Kumar A., Bennetzen J.L. Plant retrotransposons. Annu Rev Genet, 1999, vol. 33, рp. 479-532. doi:10.1146/annurev.genet.33.1.479.

Kalendar R., Grob T., Regina M., Suoniemi A., Schulman A.H. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 1999, vol. 98, no. 5, рp. 704-711. doi:10.1007/s001220051124.

Kalendar R., Schulman A.H. Transposon-based tagging: IRAP, REMAP, and iPBS. Methods in Molecular Biology, 2014, vol. 1115, рp. 233-255. doi:10.1007/978-1-62703-767-9_12.

Kalendar R., Schulman A.H. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 2006, vol. 1, no. 5, рp. 2478-2484. doi:10.1038/nprot.2006.377.

Manninen O., Kalendar R., Robinson J., Schulman A. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Molecular and General Genetics, 2000, vol. 264, no. 3, рp. 325-334. doi:10.1007/s004380000326.

Kalendar R., Tanskanen J., Immonen S., Nevo E., Schulman A.H. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proceedings of the National Academy of Sciences of the United States of America, 2000, vol. 97, no. 12, рp. 6603-6607. doi:10.1073/pnas.110587497.

Manninen I., Schulman A.H. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Molecular Biology, 1993, vol. 22, no. 5, рp. 829-846. doi:10.1007/Bf00027369.

Baumel A., Ainouche M., Kalendar R., Schulman A.H. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica CE Hubbard (Poaceae). Molecular Biology and Evolution, 2002, vol. 19, no. 8, рp. 1218-1227. URL.

Ellis T.H.N., Poyser S.J., Knox M.R., Vershinin A.V., Ambrose M.J. Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Molecular and General Genetics, 1998, vol. 260, рp. 9-19. URL.

Waugh R., McLean K., Flavell A.J., Pearce S.R., Kumar A., Thomas B.B., Powell W. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Molecular and General Genetics, 1997, vol. 253, no. 6, pр. 687-694. URL.

Gribbon B.M., Pearce S.R., Kalendar R., Schulman A.H., Paulin L., Jack P., Kumar A., Flavell A.J. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Molecular and General Genetics, 1999, vol. 261, no. 6, рp. 883-891. doi:10.1007/PL00008635.

Boyko E., Kalendar R., Korzun V., Fellers J., Korol A., Schulman A.H., Gill B.S. A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. Plant Molecular Biology, 2002, vol. 48, no. 5, рp. 767-790. doi:10.1023/A:1014831511810.

Hosid E., Brodsky L., Kalendar R., Raskina O., Belyayev A. Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics, 2012, vol. 190, no. 1, рp. 263-274. doi:10.1534/genetics.111.134643.

Belyayev A., Kalendar R., Brodsky L., Nevo E., Schulman A.H., Raskina O. Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mobile DNA, 2010, vol. 1, no. 1, рp. 6. doi:10.1186/1759-8753-1-6.

Nevo E., Golenberg E., Beiles A., Brown A.H., Zohary D. Genetic diversity and environmental associations of wild wheat, Triticum dicoccoides, in Israel. Theoretical and Applied Genetics, 1982, vol. 62, no. 3, рp. 241-254. doi:10.1007/BF00276247.

Nevo E., Beiles A. Genetic Parallelism of Protein Polymorphism in Nature - Ecological Test of the Neutral Theory of Molecular Evolution. Biological Journal of the Linnean Society, 1988, vol. 35, no. 3, pр. 229-245. doi:10.1111/j.1095-8312.1988.tb00468.x.

Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res, 1988, vol. 16, no. 22, pр. 10881-10890. URL.

Kalendar R., Lee D., Schulman A. FastPCR Software for PCR, In Silico PCR, and Oligonucleotide Assembly and Analysis // DNA Cloning and Assembly Methods. Valla S., Lale R.: Humana Press, 2014, vol. 1116, рр. 271-302. doi:10.1007/978-1-62703-764-8_18.

Kalendar R., Lee D., Schulman A.H. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, 2011, vol. 98, no. 2, рp. 137-144. doi:10.1016/j.ygeno.2011.04.009.

Excoffier L., Laval G., Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online, 2005, vol. 1, рp. 47-50. URL.

Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland MA, USA.: Sinauer Associates, 1998.

Peakall R., Smouse P.E. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics, 2012, vol. 28, no. 19, рp. 2537-2539. doi:10.1093/bioinformatics/bts460.

Vicient C.M., Jääskeläinen M.J., Kalendar R., Schulman A.H. Active retrotransposons are a common feature of grass genomes. Plant Physiology, 2001, vol. 125, no. 3, рp. 1283-1292. doi:10.1104/pp.125.3.1283.