ASSESSMENT OF GENETIC DIVERSITY IN YEAST AND BARLEY BY RETROTRANSPOSON-BASED MOLECULAR MARKERS
Abstract
Five Molecular genetics techniques (RAPD, ISSRs, IRAP, REMAP and RRAP) were used to study the genetic diversity in five yeast strains and six barley cultivars. New two retrotransposon-based primers (ScM1 and ScM2) were designed. RAPD technique represented the highest polymorphism percentages per primer compared with the other four techniques. ISSR primers represented polymorphism percentages more than IRAP primers in yeast, but lower in barley. Both REMAP and RRAP combinations showed similar results either in yeast or barley. Retrotransposon-based techniques (IRAP, RAP and REMAP) showed more number of bands more than those non-retrotransposon (RAPD and ISSRs) based techniques which make them a useful approach as molecular markers.References
Aalami, A., Samira Safiyar and B. A. Mandoulakani (2012). R-RAP: a retrotransposon-based DNA fingerprinting technique in plants. Plant Omics J., 5: 359-364.
Agrawal, A., A. Chhatre and R. Hardin (2008). Changing governance of the world’s forests. Science, 320: 1460.
Biswas, M. K., Q. Xu and X. Deng (2010). Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Scientia Horticulturae, 124: 254-261.
Boeke, J. D. and S. B. Sandmeyer (1991). In The molecular and cellular biology of the yeast Saccharomyces, pp. Yeast transposable elements. Broach, J., E. Jones and J. Pringle. 193-261. Cold Spring Harbor, NY.
Branco, C. J. S., E. A. Vieira, G. Malone, M. M. Kopp, E. Malone, A. Bernardes, C. C. Mistura, F. I. F. Carvalho and C. A. Oliveira (2007). IRAP and REMAP assessments of genetic similarity in rice. J. Appl. Genet., 48: 107-113.
Bublyk, O. M., I. O. Andreev, R. N. Kalendar, Kateryna V. Spiridonova and V. A. Kunakh (2013). Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity. Biologia, 68: 613-620.
Curran, B. P. G. and Virginia Bugeja (2006). In Yeast protocols basic investigations in Saccharomyces cerevisiae., Xiao, W. 2nd ed., Methods in Mol. Biol., (313). Humana Press Inc. Totowa, New Jersey, USA. p. 1-13.
Du, X. Y., Q. N. Hu, Q. L. Zhang, Y. B. Wang and Z. R. Luo (2013). Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species. Genet. Mol. Res., 12: 1781-1795.
Esselman, E. J., J. Q. Li, D. J. Crawford, J. L. Winduss and A. D. Wolfe (1999). Clonal diversity in the rare Calamagrostis porteri ssp. Insperata (Poaceae): comparative results for allozymes and random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. Mol. Ecol., 8: 443-451.
Fedoroff, N. (2000). Transposons and genome evolution in plants. Proc. Natl. Acad. Sci. USA, 97: 7002-7007.
Havecker, E. R., X. Gao and D. F. Voytas (2004). The diversity of LTR retrotransposons. Genome Biol., 5: 225.
Holderegger, R., U. Kamm and F. Gugerli (2006). Adaptive vs. neutral genetic diversity: Implications for landscape genetics. Landscape Ecol., 21: 797-807.
Kalendar, R. and A. H. Schulman (2006). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1: 2478-2484.
Kalendar, R., A. J. Flavell, T. H. N. Ellis, T. Sjakste, C. Moisy and A. H. Schulman (2011). Analysis of plant diversity with retrotran-sposon-based molecular markers. Heredity, 106: 520-530.
Kalendar, R., T. Grob, M. Regina, A. Suoniemi and A. Schulman (1999). IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet., 98: 704-711.
Kang, H. W., Y. G. Cho, U. H. Yoon and M. Y. Eun (1998). A rapid DNA extraction method for RFLP and PCR analysis from a single dry seed. Plant Mol. Rep., 16: 1-9.
Kim, J. M., S. Vanguri, J. D. Boeke, A. Gabriel and D. F. Voytas (1998). Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res., 8: 464-478.
Kumar, A. and J. L. Bennetzen (1999). Plant retrotransposon. Annu. Rev. Genet., 33: 479-532.
Le, Q. V., H. K. Won, T. S. Lee, C. Y. Lee, H. S. Lee and H. S. Ro (2008). Retrotransposon microsatellite amplified polymorphism strain fingerprinting markers applicable to various mushroom species. Mycobiology, 36: 161-166.
Leigh, F., R. Kalendar, V. Lea, D. Lee, P. Donini and A. H. Schulman (2003). Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol. Genet. Genomics, 269: 464-474.
Mansour, A., J. A. T. da Silva, S. Edris and Rania A. A. Younis (2010). Comparative assessment of genetic diversity in tomoto cultivars using IRAP, ISSR and RAPD molecular markers. Genes, Genomes and Genomics, 4: 41-47.
Mondini, L., A. Noorani and M. A. Pagnotta (2009). Assessing plant genetic diversity by molecular tools. Diversity, 1: 19-35.
Poczai, P., I. Varga, N. E. Bell and J. Hyvonen (2012). In Genomics meets biodiversity: Advances in molecular marker development and their applications in plant genetic diversity assessment. Caliskan, M., Agric. Biol. Sci., Publisher: Tech. (DOI: 10.5772/2639).
Rao, V. R. and T. Hodgkin (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tiss. Org. Cult., 68: 1-19.
Russel, J. R., J. D. Fuller, M. Macaulay, B. G. Hatz, A. Jahoor, W. Powell and R. Waugh (1997). Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet., 95: 714-722.
Saleh, B. (2013). Genetic diversity in Ficus sycomorus L. species (Moraceae) using RAPD and IRAP markers. Agriculture, 59: 120-130.
Santana, M. F., Elza F. de Araújo, J. T. de Souza, E. S. G. Mizubuti and M. V. de Queiroz (2012). Development of molecular markers based on retrotransposons for the analysis of genetic variability in Moniliophthora perniciosa. Eur. J. Plant Pathol., 134: 497-507.
Schulman, A. H. (2007). Molecular markers to assess genetic diversity. Euphytica, 158: 313-321.
Templeton, A. R. (1991). In Genetics and conservation biology. Species conservation a population‐biological approach. Seitz, A. and V., Loeschche Basel, Birkhauser Verlag., 15‐29.
Templeton, A. R. (1993). In Translocation as conservation tool. Biodiversity in mangrove landscapes, theory and practice. Szaro R., Oxford Univ. Press.
Williams, J. G., A. R. Kubelik, K. J. Livak, J. A. Rafalski and S. V. Tingey (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nuc. Acids Res., 18: 6531-6535.
Xiong Y. and T. H. Eickbush (1990). Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J., 9: 3353-3362.
Zietkiewicz, E., A. Rafalski and D. Labuda (1994). Genome fingerprinting by simple sequence repeat (SSR) anchored polymerase chain reaction amplification. Genomics, 20: 176-183.
Zou, J., H. Gong, T. J. Yang and J. Meng (2009). Retrotransposons - a major driving force in plant genome evolution and a useful tool for genome analysis. J. Crop Sci. Biotech., 12: 1-8.
