SSR genotyping

Mason, Annaliese S. (2015). SSR genotyping. In Jacqueline Batley (Ed.), Plant genotyping: methods and protocols (pp. 77-89) New York, NY, United States: Springer Science and Business Publishing. doi:10.1007/978-1-4939-1966-6_6


Author Mason, Annaliese S.
Title of chapter SSR genotyping
Title of book Plant genotyping: methods and protocols
Place of Publication New York, NY, United States
Publisher Springer Science and Business Publishing
Publication Year 2015
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-4939-1966-6_6
Series Methods in Molecular Biology
ISBN 9781493919659
9781493919666
ISSN 1064-3745
Editor Jacqueline Batley
Volume number 1245
Chapter number 6
Start page 77
End page 89
Total pages 13
Total chapters 22
Collection year 2016
Language eng
Abstract/Summary 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.
Keyword Simple sequence repeats
PCR-based markers
Molecular markers
Plant genotyping
Polymorphism
Primer design
Agarose gel electrophoresis
Q-Index Code BX
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Book Chapter
Collections: Non HERDC
School of Agriculture and Food Sciences
 
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Created: Mon, 17 Nov 2014, 17:10:22 EST by Annaliese Mason on behalf of School of Agriculture and Food Sciences