Abstract
Microsatellite alleles are detected by PCR (polymerase chain reaction) that provides a manifold increase in the number of copies (amplification) of a given DNA fragment. The fragment visualization can be reached by two different methods. These are fragment analysis by capillary electrophoresis in denaturing gel and fragment separation in non-denaturing gel with subsequent gel staining. The first method is more accurate and automated, but expensive. The second method is much cheaper but less convenient. It requires manual processing and is presumably less accurate. In this study, we present the results of comparison of the allele typing at nine microsatellite loci using these two methods for one of the species of Pacific salmon, sockeye salmon Oncorhynchus nerka Walbaum. In most cases, both methods give identical fragment sizes or with a constant difference if the alleles are relatively small (not larger than 200–220 bp).
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Weber, J.L. and Broman, K.W., Genotyping for human whole-genome scans: past, present, and future, Adv. Genet., 2001, vol. 42, pp. 77–96.
Dib, C., Faure, S., Fizames, C., et al., A comprehensive genetic map of the human genome based on 5264 microsatellites, Nature, 1996, vol. 380, pp. 152–154.
Zhivotovsky, L.A., Microsatellite variation in human populations and the methods of their analysis, Inf. Vestn. Vses. O-va Genet. Sel., 2006, vol. 10, no. 1, pp. 74–96.
Butler, J.M., Advansed Topics in Forensic DNA Typing: Methodology, Amsterdam: Elsevier, 2011.
Afanasiev, K.I., Rubtsova, G.A., Malinina, T.V., et al., Microsatellite variability and differentiation of hatchery stocks of chum salmon Oncorhynchus keta Walbaum in Sakhalin, Russ. J. Genet., 2006, vol. 42, no. 12, pp. 1431–1438.
Ellis, J.S., Gilbey, J., Armstrong, A., et al., Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.), Genetics, 2011, vol. 139, no. 3, pp. 353–367.
Afanasiev, K.I., Rubtsova, G.A., Shitova, M.V., et al., Interregional differentiation of chum salmon from Sakhalin and South Kurils inferred from microsatellite markers, Russ. J. Genet., 2008, vol. 44, no. 7, pp. 833–840.
Rubtsova, G.I., Afanasiev, K.I., Malinina, T.V., et al., Differentiation of chum salmon Oncorhynchus keta Wallbaum populations as revealed with microsatellite and allozyme markers: a comparative study, Russ. J. Genet., 2008, vol. 44, no. 7, pp. 841–848.
Shitova, M.V., Afanasiev, K.I., Rubtsova, G.A., et al., Microsatellite variability of factory-produced chum salmon populations (Oncorhynchus keta Walbaum) in Sakhalin Island, Vopr. Rybolov., 2009, vol. 10, no. 1, pp. 102–115.
Zhivotovsky, L.A., Rubtsova, G.I., Shitova, M.V., et al., Data base of microsatellite DNA for chum salmon in the Russian Far East, in Realizatsiya “Kontseptsii dal’nevostochnoi basseinovoi programmy izucheniya tikhookeanskikh lososei,” (Implementation of the “Concept of the Far Eastern Basin Study Program of Pacific Salmon”), Shuntov, V.P., Ed., Vladivostok: Tikhookean. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr. Tsentr, (Byull., no. 5) pp. 53–63.
Olsen, J.B., Wilson, S.L., and Kretschmer, E.J., et al., Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon, Mol. Ecol., 2000, vol. 9, no. 12, pp. 2185–2187.
Rexroad, C.E, Coleman, R.L., Martin, A.M., et al., Thirty five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss), Anim. Genet., 2001, vol. 32, no. 5, pp. 317–319.
Nelson, R.J. and Beachem, T.D., Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon, Anim. Genet., 1999, vol. 30, no. 3, pp. 228–229.
Khrustaleva, A.M., Kompleksnyi metod differentsiatsii nerki (Oncorhynchus nerka) (Complex Method for Differentiation of Sockeye Salmon), Moscow: Vsross. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2007.
Smith, C.T., Koop, B.F., and Nelson, R.J., Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids, Mol. Ecol., 1998, vol. 7, no. 11, pp. 1614–1616.
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Original Russian Text © G.A. Rubtsova, E.V. Ponomareva, K.I. Afanasiev, E.G. Shaikhaev, M.V. Kholodova, S.D. Pavlov, L.A. Zhivotovsky, 2016, published in Genetika, 2016, Vol. 52, No. 4, pp. 482–487.
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Rubtsova, G.A., Ponomareva, E.V., Afanasiev, K.I. et al. A detection of allelic variants at microsatellite markers by using capillary and traditional electrophoresis. Russ J Genet 52, 423–427 (2016). https://doi.org/10.1134/S1022795416040086
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DOI: https://doi.org/10.1134/S1022795416040086