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Plant Genotyping pp 77–89Cite as

SSR Genotyping

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1245))

Abstract

SSR genotyping involves the use of simple sequence repeats (SSRs) as DNA markers. SSRs, also called microsatellites, are a type of repetitive DNA sequence ubiquitous in most plant genomes. SSRs contain repeats of a motif sequence 1–6 bp in length. Due to this structure SSRs frequently undergo mutations, mainly due to DNA polymerase errors, which involve the addition or subtraction of a repeat unit. Hence, SSR sequences are highly polymorphic and may be readily used for detection of allelic variation within populations. SSRs are present within both genic and nongenic regions and are occasionally transcribed, and hence may be identified in expressed sequence tags (ESTs) as well as more commonly in nongenic DNA sequences. SSR genotyping involves the design of DNA-based primers to amplify SSR sequences from extracted genomic DNA, followed by amplification of the SSR repeat region using polymerase chain reaction, and subsequent visualization of the resulting DNA products, usually using gel electrophoresis. These procedures are described in this chapter. SSRs have been one of the most favored molecular markers for plant genotyping in the last 20 years due to their high levels of polymorphism, wide distribution across most plant genomes, and ease of use and will continue to be a useful tool in many species for years to come.

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Author information

Authors and Affiliations

  1. School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia

    Annaliese S. Mason

  2. Centre for Integrative Legume Research, University of Queensland, Brisbane, QLD, 4072, Australia

    Annaliese S. Mason

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  1. Annaliese S. Mason
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Correspondence to Annaliese S. Mason .

Editor information

Editors and Affiliations

  1. School of Plant Biology, The University of Western Australia, Crawley, West Australia, Australia

    Jacqueline Batley

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© 2015 Springer Science+Business Media New York

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Mason, A.S. (2015). SSR Genotyping. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_6

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  • DOI: https://doi.org/10.1007/978-1-4939-1966-6_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1965-9

  • Online ISBN: 978-1-4939-1966-6

  • eBook Packages: Springer Protocols

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