Abstract
Microsatellites (SSRs) are the most informative and popular class of molecular markers used for diverse purposes, particularly in plants: genetic diversity study, marker assisted selection, breeding, mapping, phylogenetics and phylogeography, systematics, etc. They have become a routine technique practically in each laboratory for studying molecular plant genetics. Despite their wide utilization, however, setup and optimization of various conditions involved in PCR amplification is a prerequisite for reliable inference of results. In this chapter, we describe optimization of SSR-PCR conditions and give ranges of concentrations for different parameters. The protocol provided here is inspired from bench work on the use of microsatellite to study diversity of Vitis vinifera germplasm.
The two authors contributed equally to this work.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dreisigacker S, Zhang P, Warburton ML et al (2004) SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci 44:381–388
McCouch SR, Chen X, Panaud O et al (2004) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:89–99
Ruiz C, Breto MP, Asíns MJ (2004) A quick methodology to identify sexual seedlings in citrus breeding programs using SSR markers. Euphytica 112:89–94
Song QJ, Marek LF, Shoemaker RC et al (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128
N’Diaye A, Van de Weg WE, Kodde LP et al (2008) Construction of an integrated consensus map of the apple genome based on four mapping populations. Tree Genet Genomes 4:727–743
Hasnaoui N, Buonamici A, Sebastiani F, Mars M, Zhang D, Vendramin GG (2012) Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR). Gene 493:105–112
Rafalsky JA, Tingey SV (1993) Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 9:275–279
Powell W, Gordon MC, Provan J (1996) Polymorphism revealed by simple sequence repeats. (Reviews). Trends Plant Sci 1:215–222
Ogliari JB, Boscariol RL, Camargo LEA (2000) Optimization of PCR amplification of maize microsatellite loci. Genet Mol Biol 23:395–398
Doğrar N, Aakkaya MS (2001) Optimization of PCR amplification of wheat simple sequence repeat DNA markers. Turk J Biol 25:153–158
Mogali SC, Basavaraj M, Krishna Naik L, Nadaf HL (2011) Optimization of PCR amplification of wheat simple sequence repeat DNA markers. Karnataka J Agric Sci 24:239–240
Li M, Lü XL, Luo CD, Zhang F, Wu ZX, Zhong JY (2009) Optimizing system of SSR-PCR in Pinus radiate and Pinus tabulaeformis. J Mol Genet 1:44–49
Kramer MF, Coen DM (2004) Enzymatic amplification of DNA by PCR: standard procedures and optimization. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (ed) Current protocols in molecular biology, vol 2. Wiley, New York, pp 1–15
Saiki RK (1992) The design and optimization of the PCR. In: Erlich HA (ed) PCR technology: principles and applications for DNA amplification. Oxford University Press, New York, pp 7–8
Rahman MH, Jaquish B, Khasa PD (2000) Optimization of PCR protocol in microsatellite analysis with silver and SYBR stains. Plant Mol Biol Reporter 18:339–348
Ramsay L, Macaulay M, degli Ivanissevich S et al (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005
Niens M, Spijker GT, Diepstra A, te Meerman GJ (2005) A factorial experiment for optimizing the PCR conditions in routine genotyping. Biotechnol Appl Biochem 42:157–162
Masi O, Spagnoletti-Zeuli PL, Donini P (2003) Development and analysis of multiplex microsatellite marker sets in common bean (Phaseolus vulgaris L.). Mol Breed 11:303–313
Zhang LS, Becquet V, Li SH, Zhang D (2003) Optimization of multiplex PCR and multiplex gel electrophoresis in sunflower SSR analysis using infrared fluorescence and tailed primers. Acta Bot Sin 45:1312–1318
Bencina M (2002) Optimization of multiple PCR using a combination of full factorial design and three dimensional simplex optimization methods. Biotechnol Lett 24:489–495
Ahmed I, Islam M, Mannan A, Naeem R, Mirza B (2009) Optimization of conditions for assessment of genetic diversity in barley (Hordeum vulgare L.) using microsatellite markers. Barley Genet Newslett 39:5–12
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Ghaffari, S., Hasnaoui, N. (2013). Microsatellite Amplification in Plants: Optimization Procedure of Major PCR Components. In: Kantartzi, S. (eds) Microsatellites. Methods in Molecular Biology, vol 1006. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-389-3_10
Download citation
DOI: https://doi.org/10.1007/978-1-62703-389-3_10
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-388-6
Online ISBN: 978-1-62703-389-3
eBook Packages: Springer Protocols