Main Article Content


O.N. Khapilina

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

A.Z. Daniyarov

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

А.А. Аmenov

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

А.P. Novakovskaya

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

А.S. Тurzhanova

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

D.S. Тagimanova

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan

N.I. Filippova

Scientific-Production Center of Grain Farming named after A.I. Barayev, Akmola reg., Kazakhstan

R.N. Каlendar

National Center for Biotechnology, 13/5, Korgalzhyn hwy, Astana,  Kazakhstan


Retrotransposon-based molecular markers were used to assess variation in the perennial legumes alfalfa, sweet clover, and lupin from local (Kazakhstan) and world gene pools. Specific retrotransposons were found for species in the Fabaceae family. Conserved regions of LTR retrotransposon sequences were used to design PCR primers to detect polymorphisms by the IRAP method. Universal primers for retrotransposon primer binding site (PBS) sequences were also used. A preliminary screen was used to select the most informative primers that identified up to 80% of polymorphisms. Cluster analysis was carried out to quantify polymorphism and divergence. LTR primers can be used for the simultaneous detection of polymorphic loci that are distributed evenly across the genome. In addition, the study of genetic polymorphism using retrotransposons is distinguished with availability and informative of the method. LTR retrotransposons were employed to study genetic variability and were able to separate the perennial legume varieties according to their relationships and genetic diversity. The results obtained using this method provides a basis for better control of germplasm, future systematic studies, and genetic improvement. This method can also be applied to thestudy of the role of retrotransposons in the genetic variability of species and the dynamics of their genomes.


perennial legumes, molecular markers, iPBS, retrotransposons, genotyping

Article Details


Dost M., Ates S. Intercropping of legumes with cereal crops in particular with the perennials to enhance forage yields and quality. Proc. of the FAO expert workshop «Perennial crops for food security», FAO, Rome, 2014, рр. 221-229.

Zhakeev M.K. (2013) K 2020 godu posevnaja ploshhad' kormovyh kul'tur v Kazahstane uvelichitsja do 10,2 millionov gektar (By 2020, the sown area of fodder crops in Kazakhstan will increase to 10.2 million hectares). Available at: URL.

Vasin V.G., Tolpekin A.A. idr. Jenergeticheskaja effektivnost' polevyh agrofitocenozov v Srednem Povolzh'e [Energy efficiency of field agrophytocenosis in the Middle Volga region]. Samara, 2005, 124 p.

Serebrovskij A.S. Geneticheskij analiz [Genetic Analysis]. Moscow: Mir, 1970, 342 p.

Carelli M., Gnocchi S., et al. Genetic diversity and dynamics of Sinorhizobium meliloti population’s nodulating different alfalfa cultivars in Italian soils. Applied and Environmental Microbiology, 2000, vol. 66, no. 11, pp. 4785-4789. Crossref

Khlestkina E.K. Molecular markers in genetic studies and in breeding. Russian Journal of Genetics: Applied Research, 2014, vol. 4, no. 3, pp. 236-244. Crossref.

Kalendar R., Schulman A.H. Transposon-based tagging IRAP, REMAP, and iPBS. Methods in Molecular Biology, 2014, vol. 1115, pp. 233-255. Crossref.

Hora A., Malik C.P. Evaluation of genetic relationship between Trigonella‐Melilotus complex using CCMP markers. Plant Tissue Culture and Biotechnology, 2013, vol 23, no 1, pp. 59-66. Crossref.

Schmutz J., McClean Ph.E., Mamidi S., Wu G.A. et al A reference genome for common bean and genome wide analysis of dual domestications. Nature Genetics, 2014, vol. 46, pp. 707-713. Crossref.

Kalendar R., Antonius K., et al. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 2010, vol.121, no. 8, pp.1419-1430. Crossref.

Tagimanova D.S., Novakovskaya A.P., Uvashov A.O., Khapilina O.N., Kalendar R.N. Use of retrotransposon markers for analyzing the genetic diversity of wild emmer wheat (Triticum dicoccoides). Biotechnology. Theory and Practice, 2015, vol. 4, pp. 28-37. Crossref.

Kalendar R.N., Aizharkyn K.S., Khapilina O.N., Amenov A.A., Tagimanova D.S. Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers. Vavilov Journal of Genetics and Breeding, 2017, vol. 21(1), pp.128-134. Crossref.

Smykal P., Bačová-Kerteszová N. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theoretical and Applied Genetics, 2011, vol. 122, pp. 1385-1397. Crossref.

Guo D.L., Guo M.X., Hou X.G., Zhang G.H. Molecular diversity analysis of grape varieties based on iPBS markers. Biochemical Systematic and Ecology, 2014, vol. 52, pp. 27-32. Crossref.

Baranek M., Meszaros M., Sochorova J., Cechova J., et al. Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovicka. Scientia Horticulturae, 2012, vol. 143, pp.1-6. Crossref.

Borna F., Luo S., Ahmad N.M., Nazeri V., Shokrpour M., Trethowan R. Genetic diversity in populations of the medicinal plant Leonurus cardiaca L. revealed by inter-primer binding site (iPBS) markers.Genet Resourses and Crop Evolution, 2016. Crossref.

Andeden E.E. et al. iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. Journal of Plant Bio chemistry and Biotechnology, 2013, vol. 22 (4), pp. 453-466. Crossref. 0.1007/s13562-012-0175-5.

Nemli S. et al. Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turkish Journal of Agriculture and Forestry, 2015, vol 39, pp. 940-948. Crossref.

Balish F.S. et al. DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochemical Systematics and Ecology, 2015, no. 61, pp. 244-252. Crossref.

Kalendar R., Muterko A., Shamekova M., Zhambakin K. 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology (Clifton, N.J.), vol. 1620, pp. 1-31. Crossref.