OJGen  Vol.3 No.4 , December 2013
Genetic structure and diversity of Ukrainian red clover cultivars revealed by microsatellite markers
ABSTRACT

Polymorphism of microsatellite loci of Ukrainian red clover cultivars has been studied. 87 microsatellite alleles, which occurred in different combinations, were identified. The number of alleles ranged from 7 to 10. Microsatellite allele distribution showed that 15 alleles were common for all the red clover cultivars (17.2%). The red clover cultivars were represented by homozygous and heterozygous genotypes. The observed and expected heterozygosity ranged from 0.067 to 0.269 and from 0.225 to 0.807, respectively. An analysis of molecular variance revealed that the largest proportion of variation (68.5%) resided at the intrapopulation level. Differentiation of the Ukrainian cultivars was moderately expressed (FST = 0.07). 


Cite this paper
Dugar, Y. and Popov, V. (2013) Genetic structure and diversity of Ukrainian red clover cultivars revealed by microsatellite markers. Open Journal of Genetics, 3, 235-242. doi: 10.4236/ojgen.2013.34026.
References
[1]   Roussel, V., Leisova, L., Exbrayat, F., Stehno, Z. and Balfourier, F. (2005) SSR allelic diversity changes in 480 European bread wheat cultivars released from 1840 to 2000. Theoretical and Applied Genetics, 111, 162-170.
http://dx.doi.org/10.1007/s00122-005-2014-8

[2]   Kolodinska Brantestam, A., von Bothmer, R., Dayteg, C., Rashal, I., Tuvesson, S. and Weibull, J. (2007) Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of Nordic and Baltic areas as shown by SSR markers. Genetic Resources and Crop Evolution, 54, 749-758.
http://dx.doi.org/10.1007/s10722-006-9159-4

[3]   Mimura, M., Coyne, C.J., Bambuck, M.W. and Lumpkin, T.A. (2007) SSR diversity of vegetable soybean [Glycine max (L.) Merr.]. Genetic Resources and Crop Evolution, 54, 497-508.
http://dx.doi.org/10.1007/s10722-006-0006-4

[4]   van Inghelandt, D., Melchinger, A.E., Lebreton, C. and Stich B. (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theoretical and Applied Genetics, 120, 1289-1299.
http://dx.doi.org/10.1007/s00122-009-1256-2

[5]   Heesacker, A., Kishore, V., Gao, W., Tang, S., Kolkman, J., Gingle, A., Matvienko, M., Kozik, A., Michelmore, R., Lai, Z., Rieseberg, L. and Knapp, S. (2008) SSRs and INDELs mined from the sunflower EST database: Abundance, polymorphisms, and cross-taxa utility. Theoretical and Applied Genetics, 117, 1021-1029.
http://dx.doi.org/10.1007/s00122-008-0841-0

[6]   Gupta, S. and Prasad, M. (2009) Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome, 52, 761-771.
http://dx.doi.org/10.1139/G09-051

[7]   Saha, M.C., Cooper, J.D., Mian, M.A.R., Chekhovskiy, K. and May, G.D. (2006) Tall fescue genomic SSR markers: Development and transferability across multiple grass species. Theoretical and Applied Genetics, 113, 1449-1458. http://dx.doi.org/10.1007/s00122-006-0391-2

[8]   Kongkiatngam, P., Waterway, M.J., Fortin, M.G. and Coulman, B.E. (1995) Genetic variation within and between two cultivars of red clover (Trifolium pratense L.): Comparisons of morphological, isozyme, and RAPD markers. Euphytica, 84, 237-246.
http://dx.doi.org/10.1007/BF01681816

[9]   Kongkiatngam, P., Waterway, M.J., Coulman, B.E. and Fortin, M.G. (1996) Genetic variation among cultivars of red clover (Trifolium pratense L.) detected by RAPD markers amplified from bulk genomic DNA. Euphytica, 89, 355-361.

[10]   Campos-de-Quiroz, H. and Ortega-Klose, F. (2001) Genetic variability among elite red clover (Trifolium pratense L.) parents used in Chile as revealed by RAPD markers. Euphytica, 122, 61-67.
http://dx.doi.org/10.1023/A:1012617504493

[11]   Grljusic, S., Bolaric, S., Popovic, S., Cupic, T., Tucak, M. and Kozumplik, V. (2005) Assessment of morphological and RAPD variation among and within red clover cultivars after natural selection. Die Bodenkultur, 56, 183-188.

[12]   Dugar, Yu.N. and Popov, V.N. (2011) RAPD analysis of Ukrainian red clover (Trifolium pratense L.) cultivars of different ecology-geographical origin. Vestnik KNU nd. a V.N. Karazin. Series Biology, 13, 81-86.

[13]   Rizza, M.D., Real, D., Reyno, R., Porro, V., Burgueсo, J., Errico, E. and Quesenberry, K.H. (2007) Genetic diversity and DNA content of three South American and three Eurasiatic Trifolium species. Genetics and Molecular Biology, 30, 1118-1124.

[14]   Dugar, Yu.N. (2012) ISSR-analyses of the Ukrainian red clover cultivars (Trifolium pretense L.). Vestnik KNAU. Series Biology, 2, 98-103.

[15]   Weising, K., Nybom, H., Wolff, K. and Kahl, G. (2005) DNA fingerprinting in plants: Principles, methods, and applications. 2nd Edition, CRC Press Taylor & Francis Group, Boca Raton.
http://dx.doi.org/10.1201/9781420040043

[16]   Kalia, R.K., Rai, M.K., Kalia, S., Singh, R. and Dhawan, A.K. (2011) Microsatellite markers: An overview of the recent progress in plants. Euphytica, 177, 309-334.
http://dx.doi.org/10.1007/s10681-010-0286-9

[17]   Sato, S. Isobe, S., Asamizu, E., Ohmido, N., Kataoka, R., Nakamura, Y., Kaneko, T., Sakurai, N., Okumura, K., Klimenko, I., Sasamoto, S., Wada, T., Watanabe, A., Kohara, M., Fujishiro, T. and Tabata, S. (2005) Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.). DNA Research, 12, 301-364.
http://dx.doi.org/10.1093/dnares/dsi018

[18]   Isobe, S., Kolliker, R., Hisano, H., Sasamoto, S., Wada, T., Klimenko, I., Okumura, K. and Tabata, S. (2009) Construction of a consensus linkage map for red clover (Trifolium pratense L.). BMC Plant Biology, 9.

[19]   Klimenko, I, Razgulayeva, N., Gau, M., Okumura, K., Nakaya, A., Tabata, S., Kozlov, N. and Isobe, S. (2010) Mapping candidate QTLs related to plant persistency in red clover. Theoretical and Applied Genetics, 120, 1253-1263. http://dx.doi.org/10.1007/s00122-009-1253-5

[20]   Mukhina, N.A. and Stankevich, A.K. (1993) Cultured flora: V. ХIII. Perennial legume grasses. Kolos, Moscow.

[21]   Ausubel, F.M., Brent, R., Kingston, R.E., Moor, D.D. and Seidman, J.G. (1987) Current protocols in molecular biology. John Wiley & Sons, New York.

[22]   Kolliker, R., Enkerli, J. and Widmer, F. (2006) Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries. Molecular Ecology Notes, 6, 50-53.
http://dx.doi.org/10.1111/j.1471-8286.2005.01133.x

[23]   Brody, J.R. and Kern, S.E. (2004) Sodium boric acid: A Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques, 36, 214-216.

[24]   http://www.totallab.com

[25]   http://animalgenomics.ucd.ie/sdepark/ms-toolkit

[26]   Berg, E.E. and Hamrick, J.L. (1997) Quantification of genetic diversity at allozyme loci. Canadian Journal of Forest Research, 27, 415-424.
http://dx.doi.org/10.1139/x96-195

[27]   http://cmpg.unibe.ch/software/arlequin3/

[28]   Balloux, F. and Lugon-Moulin, N. (2002) The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11, 155-165.
http://dx.doi.org/10.1046/j.0962-1083.2001.01436.x

[29]   http://evolution.genetics.washington.edu/phylip.html

[30]   http://pritchardlab.stanford.edu/structure.html

[31]   Zhivotovsky, L.A. (1991) Population biometry. Nauka, Moscow.

[32]   Evanno, G., Regnaut, S. and Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611-2620.
http://dx.doi.org/10.1111/j.1365-294X.2005.02553.x

[33]   Taylor, N.L. (2008) A Century of Clover Breeding Developments in the United States, Crop Science, 48, 1-13.
http://dx.doi.org/10.2135/cropsci2007.08.0446

[34]   Berzina, I., Zhuk, A., Veinberga, I., Rashal, I. and Rungis, D. (2008) Genetic fingerprinting of Latvian red clover (Trifolium pratense L.) cultivars using simple sequence repeat (SSR) markers: Comparisons over time and space. Latvian Journal of Agronomy, 11, 28-32.

[35]   Dias, P.M.B., Julier, B., Sampoux, J.-P., Barre, P. and Dall’Agnol, M. (2008) Genetic diversity in red clover (Trifolium pratense L.) revealed by morphological and microsatellite (SSR) markers. Euphytica, 160, 189-205.
http://dx.doi.org/10.1007/s10681-007-9534-z

[36]   Martina, S. (2007) New microsatellite loci for red clover (Trifolium pratense L.) and study its polymorphism. Proceeding of the XXVIIth Eucarpia Symposium on Improvement of Fodder Crops and Amenity Grasses, Copenhagen, 19-23 August 2007, Denmark, 217-219.

[37]   Vymyslicky, T., Smarda, P., Pelikan, J., Cholastova, T., Nedelnik, J., Moravcova, H., Pokorny, R., Soldanova, M. and Polakova, M. (2012) Evaluation of the Czech core collection of Trifolium pratense, including morphological, molecular and phytopathological data. African Journal of Biotechnology, 11, 3583-3595.

[38]   Yu, J., Mosjidis, J.A., Klingler, K.A. and Woods, F.M. (2001) Isozyme diversity in North American cultivated red clover. Crop Science, 41, 1625-1628
http://dx.doi.org/10.2135/cropsci2001.4151625x

[39]   Semerikov, V.L. and Belyaev, A.Y. (1995) Allozyme polymorphism in natural populations and cultivars of red clover Trifolium pratense L. Genetika, 31, 815-819.

[40]   Semerikov, V.L., Belyaev, A.Y. and Lascoux, M. (2002) The origin of Russian cultivars of red clover (Trifolium pratense L.) and their genetic relationships to wild populations in the Urals. Theoretical and Applied Genetics, 106, 127-132

[41]   Mosjidis, J.A., Greene, S.L., Klingler, K.A. and Afonin, A. (2004) Isozyme diversity in wild red clover populations from the Caucasus. Crop Science, 44, 665-670.
http://dx.doi.org/10.2135/cropsci2004.1039

[42]   Ulloa, O., Ortega, F. and Campos, H. (2003) Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers. Genome, 46, 529-535.
http://dx.doi.org/10.1139/g03-030

[43]   Herrmann, D., Boller, B., Widmer, F. and Kolliker, R. (2005) Optimization of bulked AFLP analysis and its application for exploring diversity of natural and cultivated populations of red clover. Genome, 48, 474-486.
http://dx.doi.org/10.1139/g05-011

 
 
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