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Comparing two microarray platforms for identifying mutated genes in barley (Hordeum vulgare L.)

Zakhrabekova, Shakhira LU ; Gough, Simon LU ; Lundqvist, Udda LU and Hansson, Mats LU (2007) In Plant Physiology and Biochemistry 45(8). p.617-622
Abstract
We have previously described the evaluation of a cDNA microarray platform to identify and clone mutated barley (Hordeum vulgare L.) genes, using their transcriptionally defective mutant alleles (S. Zakhrabekova, C.G. Karmangara, D. von Wettstein, M. Hansson, A microarray approach for identification of mutated genes, Plant Physiol. Biochem. 40 (2002) 189-197). It was concluded that competitive hybridization between phenotypically similar mutants could specifically highlight an arrayed clone, corresponding to the mutated gene. In this study we evaluate whether the Affymetrix microarray platform can be used for the same purpose. The Affymetrix barley microarray contains a large number of clones (22,792 probe sets). In this and the previous... (More)
We have previously described the evaluation of a cDNA microarray platform to identify and clone mutated barley (Hordeum vulgare L.) genes, using their transcriptionally defective mutant alleles (S. Zakhrabekova, C.G. Karmangara, D. von Wettstein, M. Hansson, A microarray approach for identification of mutated genes, Plant Physiol. Biochem. 40 (2002) 189-197). It was concluded that competitive hybridization between phenotypically similar mutants could specifically highlight an arrayed clone, corresponding to the mutated gene. In this study we evaluate whether the Affymetrix microarray platform can be used for the same purpose. The Affymetrix barley microarray contains a large number of clones (22,792 probe sets). In this and the previous study we used two barley mutant strains, xantha-h.57 and xantha-f.27, with known mutations in different subunit genes of the chlorophyll biosynthetic enzyme magnesium chelatase (EC 6.6. 1. 1). Mutant xantha-h.57 produces no Xantha-h mRNA whereas in xantha-f27 the nonsense mutation in the last exon of the gene, results in nonsense-mediated decay of Xantha-f mRNA. We conclude that the Affyinetrix platform meets our requirements and that our approach successfully highlighted the arrayed Xantha-h clone and that Xantha-f was among the top fourteen candidates. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
keywords
mutant, Xantha, microarray, magnesium chelatase, Hordeum vulgare, barley, cloning
in
Plant Physiology and Biochemistry
volume
45
issue
8
pages
617 - 622
publisher
Elsevier
external identifiers
  • wos:000249084800011
  • scopus:34547129336
ISSN
1873-2690
DOI
10.1016/j.plaphy.2007.05.004
language
English
LU publication?
yes
id
0d155fe5-64f7-4d89-8942-af5bb4a8c170 (old id 688693)
date added to LUP
2007-12-19 09:52:17
date last changed
2017-01-01 07:15:59
@article{0d155fe5-64f7-4d89-8942-af5bb4a8c170,
  abstract     = {We have previously described the evaluation of a cDNA microarray platform to identify and clone mutated barley (Hordeum vulgare L.) genes, using their transcriptionally defective mutant alleles (S. Zakhrabekova, C.G. Karmangara, D. von Wettstein, M. Hansson, A microarray approach for identification of mutated genes, Plant Physiol. Biochem. 40 (2002) 189-197). It was concluded that competitive hybridization between phenotypically similar mutants could specifically highlight an arrayed clone, corresponding to the mutated gene. In this study we evaluate whether the Affymetrix microarray platform can be used for the same purpose. The Affymetrix barley microarray contains a large number of clones (22,792 probe sets). In this and the previous study we used two barley mutant strains, xantha-h.57 and xantha-f.27, with known mutations in different subunit genes of the chlorophyll biosynthetic enzyme magnesium chelatase (EC 6.6. 1. 1). Mutant xantha-h.57 produces no Xantha-h mRNA whereas in xantha-f27 the nonsense mutation in the last exon of the gene, results in nonsense-mediated decay of Xantha-f mRNA. We conclude that the Affyinetrix platform meets our requirements and that our approach successfully highlighted the arrayed Xantha-h clone and that Xantha-f was among the top fourteen candidates.},
  author       = {Zakhrabekova, Shakhira and Gough, Simon and Lundqvist, Udda and Hansson, Mats},
  issn         = {1873-2690},
  keyword      = {mutant,Xantha,microarray,magnesium chelatase,Hordeum vulgare,barley,cloning},
  language     = {eng},
  number       = {8},
  pages        = {617--622},
  publisher    = {Elsevier},
  series       = {Plant Physiology and Biochemistry},
  title        = {Comparing two microarray platforms for identifying mutated genes in barley (Hordeum vulgare L.)},
  url          = {http://dx.doi.org/10.1016/j.plaphy.2007.05.004},
  volume       = {45},
  year         = {2007},
}