IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley

Campbell, Bradley C., LeMare, Sophie, Piperidis, George and Godwin, Ian D. (2011) IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Molecular Breeding, 27 2: 193-206. doi:10.1007/s11032-010-9422-4


Author Campbell, Bradley C.
LeMare, Sophie
Piperidis, George
Godwin, Ian D.
Title IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley
Journal name Molecular Breeding   Check publisher's open access policy
ISSN 1380-3743
1572-9788
Publication date 2011-02
Year available 2010
Sub-type Article (original research)
DOI 10.1007/s11032-010-9422-4
Volume 27
Issue 2
Start page 193
End page 206
Total pages 14
Place of publication Dordrecht, The Netherlands
Publisher Springer Netherlands
Collection year 2012
Language eng
Abstract The retrotransposon-based marker system, inter-retrotransposon amplified polymorphism (IRAP), and inter-simple sequence repeats (ISSRs) were used to detect somaclonal variation induced by tissue culture. IRAPs use a single primer designed to amplify out from the 5′ LTR sequence of the BARE-1 retrotransposon combined with a degenerate 3′ anchor, similar to that of ISSR primers. We analysed DNA polymorphisms in 147 primary regenerants and parental controls from three cultivars of barley (Hordeum vulgare). The ISSR marker system generated an average of 218 bands per primer, with 29 polymorphisms of which 12 were novel non-parental bands. In comparison, the IRAP system generated an average of 121 bands per primer, with 15 polymorphisms of which nine were novel non-parental bands. Polymorphism detected for IRAP and ISSR markers was more than twofold higher in Golden Promise than Mackay and Tallon cultivars. However, there was no significant difference in the frequency of novel non-parental bands. Cluster analysis revealed that the level of polymorphism and genetic variability detected was comparable between IRAP and ISSR markers. This suggests that retrotransposon-based marker systems, such as IRAP, based on retrotransposons such as BARE-1, are valuable tools for the detailed characterisation of mutation profiles that arise during tissue culture. Their use should improve our understanding of processes influencing mutation and somaclonal variation and allow for the design of methods that yield fewer genome changes in applications where maintaining clonal integrity is important.
Keyword Somaclonal variation
Retrotransposon
BARE-1
IRAP
ISSR
Hordeum vulgare
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 10 March 2010

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
School of Agriculture and Food Sciences
 
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Created: Sun, 06 Mar 2011, 00:05:51 EST