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Polymorphisms in intron 1 of carrot AOX2b – a useful tool to develop a functional marker?

Published online by Cambridge University Press:  20 April 2011

Hélia Cardoso ,
Maria Doroteia Campos ,
Thomas Nothnagel  and
Birgit Arnholdt-Schmitt
Hélia Cardoso
Affiliation:
EU Marie Curie Chair – Laboratory of Molecular Biology, ICAAM, University of Évora, Apartado 94, 7002-554 Évora, Portugal
Maria Doroteia Campos
Affiliation:
EU Marie Curie Chair – Laboratory of Molecular Biology, ICAAM, University of Évora, Apartado 94, 7002-554 Évora, Portugal
Thomas Nothnagel
Affiliation:
Federal Center of Breeding Research on Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, Neuer Weg 22/23, D-06484 Quedlinburg, Germany
Birgit Arnholdt-Schmitt*
Affiliation:
EU Marie Curie Chair – Laboratory of Molecular Biology, ICAAM, University of Évora, Apartado 94, 7002-554 Évora, Portugal
*
*Corresponding author. E-mail: eu_chair@uevora.pt
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Abstract

Alternative oxidase (AOX) has been proposed as a promising functional marker candidate for multiple plant stress behaviour. The present paper describes natural polymorphism in AOX2b of Daucus carota L. (DcAOX2b). Exon-primed intron crossing-PCR (EPIC-PCR) revealed length variation (intron length polymorphisms, ILPs) in intron 1. Six fragment patterns were identified in 40 genotypes. However, no more than two fragments were found per genotype, suggesting the presence of two alleles. The ILPs were able to discriminate between single plant genotypes in cv. Rotin and to distinguish individual wild carrot plants. The repetitive pattern of intron 1 length variation allows the grouping of genotypes for functional analysis in future studies. Sequence analysis in intron 1 of polymorphic but also of obviously identical PCR-fragments revealed underlying high levels of sequence polymorphisms between alleles and genotypes. Variation was due to repetitive insertion/deletion (InDel) events and single-nucleotide polymorphisms (SNPs). The results suggest that high AOX2b gene diversity in D. carota may be a source of functional markers for agronomic traits related to environmental stress responses.

Keywords

Daucus carotaexon-primed intron crossing-PCRinsertion/deletionintron length polymorphismmiRNAsingle-nucleotide polymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 9 , Issue 2 , July 2011 , pp. 177 - 180
Copyright
Copyright © NIAB 2011

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