Hostname: page-component-7dd5485656-wxk4p Total loading time: 0 Render date: 2025-10-30T00:21:59.522Z Has data issue: false hasContentIssue false
  • English
  • Français

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
Get access Rights & Permissions [Opens in a new window]

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

Information

Type
Research Article
Information
Plant Genetic Resources , Volume 9 , Issue 2 , July 2011 , pp. 177 - 180
Copyright
Copyright © NIAB 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Article purchase

Temporarily unavailable

References

Arnholdt-Schmitt, (2009) Alternative oxidase (AOX) and stress tolerance – approaching a scientific hypothesis. Physiologia Plantarum 137: 314–315.CrossRefGoogle ScholarPubMed
Arnholdt-Schmitt, B, Costa, JH and Fernandes de Melo, D (2006) AOX – a functional marker for efficient cell reprogramming under stress? Trends in Plant Science 11: 281–287.CrossRefGoogle ScholarPubMed
Bi, McMullenMD IV, Sanchez-Villeda, H, Schroedor, S, Gardiner, J, Polacco, M, Soderlund, C, Wing, R, Fang, Z and Coe, EH (2006) Single-nucleotide polymorphisms and insertion–deletions for genetic markers and anchoring the maize fingerprint contig physical map. Genomics, Molecular Genetics and Biotechnology 46: 12–21.Google Scholar
Braglia, L, Manca, A, Mastromauro, F and Breviario, D (2010) cTBP: a successful intron length polymorphisms (ILP)-based genotyping method targeted to well defined experimental needs. Diversity 2: 572–582.CrossRefGoogle Scholar
Breviario, D, Baird, W, Sangoi, S, Hilu, K, Blumetti, P and Gianì, S (2007) High polymorphism and resolution in targeted fingerprinting with combined β-tubulin introns. Molecular Breeding 20: 249–259.CrossRefGoogle Scholar
Campos, MD, Cardoso, HG, Linke, B, Costa, JH, Fernandes de Melo, D, Justo, L, Frederico, AM and Arnholdt-Schmitt, B (2009) Differential expression and co-regulation of carrot AOX genes (Daucus carota). Physiologia Plantarum 137: 578–591.CrossRefGoogle ScholarPubMed
Cardoso, HG, Campos, MD, Costa, AR, Campos, MC, Nothnagel, T and Arnholdt-Schmitt, B (2009) Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3. Physiologia Plantarum 137: 592–608.CrossRefGoogle Scholar
Chiou, TJ, Aung, K, Lin, SI, Wu, CC, Chiang, SF and Su, CL (2006) Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell 18: 412–421.CrossRefGoogle ScholarPubMed
Costa, JH, Jolivet, Y, Hasenfratz-Sauder, M-P, Orellano, EG, Lima, MGS, Dizengremel, P and Fernandes de Melo, D (2007) Alternative oxidase regulation in roots of Vigna unguiculata cultivars differing in drought/salt tolerance. Journal of Plant Physiology 164: 718–727.CrossRefGoogle ScholarPubMed
Costa, JH, Cardoso, HC, Campos, MD, Zavattieri, A, Frederico, AM, Fernandes de Melo, D and Arnholdt-Schmitt, B (2009 a) D. carota L. – an old model for cell reprogramming gains new importance through a novel expansion pattern of AOX genes. Plant Physiology and Biochemistry 47: 753–759.CrossRefGoogle Scholar
Costa, JH, Fernandes de Melo, D, Gouveia, Z, Cardoso, HG, Peixe, A and Arnholdt-Schmitt, B (2009 b) The alternative oxidase family of Vitis vinifera reveals an attractive model for genomic design. Physiologia Plantarum 137: 553–565.CrossRefGoogle ScholarPubMed
Ferreira, A, Cardoso, HG, Macedo, ES, Breviario, D and Arnholdt-Schmitt, B (2009) Intron polymorphism pattern in AOX1b of wild St John's wort (Hypericum perforatum) allows discrimination between individual plants. Physiologia Plantarum 137: 520–531.CrossRefGoogle Scholar
Fiume, E, Christou, P, Gianì, S and Breviario, D (2004) Introns are key elements of rice tubulin expression. Planta 218: 693–703.CrossRefGoogle ScholarPubMed
Gianì, S, Morello, L, Bardini, M and Breviario, D (2003) Tubulin intron sequences: multi-functional tools. Cell Biology International 27: 203–205.CrossRefGoogle ScholarPubMed
Gregory, TR (2004) Insertion–deletion bases and the evolution of genome size. Gene 423: 15–34.CrossRefGoogle Scholar
McCabe, TC, Finnegan, PM, Millar, H, Day, DA and Whelan, J (1998) Differential expression of alternative oxidase genes in soybean cotyledons during postgerminative development. Plant Physiology 118: 675–682.CrossRefGoogle ScholarPubMed
McDonald, AE and Vanlerberghe, GC (2006) The organization and control of plant mitochondrial metabolism. In: Plaxton WC and McManus MT (eds) Control of Primary Metabolism in Plants. Annual Plant Reviews 22: 290–324.Google Scholar
Nasu, S, Suzuki, J, Ohta, R, Hasegawa, K, Yui, R, Kitazawa, N, Monna, L and Minobe, Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Research 9: 163–171.CrossRefGoogle ScholarPubMed
Naydenov, N, Takumi, S, Sugie, A, Ogihara, Y, Atanassov, A and Nakamura, C (2005) Structural diversity of the wheat nuclear gene WAOX1a encoding mitochondrial alternative oxidase, a single unique enzyme in the cyanide-resistant alternative pathway. Biotechnology and Biotechnological Equipment 19: 48–56.CrossRefGoogle Scholar
Orgel, LE and Crick, FH (1980) Selfish DNA: the ultimate parasite. Nature 284: 604–607.CrossRefGoogle ScholarPubMed
Plaxton, WC and Podestá, FE (2006) The functional organisation and control of plant respiration. Critical Reviews in Plant Sciences 25: 159–198.CrossRefGoogle Scholar
Polidoros, AN, Mylona, PV and Arnholdt-Schmitt, B (2009) Aox gene structure, transcript variation and expression in plants. Physiologia Plantarum 137: 342–353.CrossRefGoogle ScholarPubMed
Rose, AB, Elfersi, T, Parra, G and Korf, I (2008) Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell 20: 543–551.CrossRefGoogle ScholarPubMed
Wang, XJ, Reyes, JL, Chua, NH and Gaasterland, T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology 5: R65–R6515.CrossRefGoogle ScholarPubMed
Wang, X, Zhao, X, Zhu, J and Wu, W (2005) Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Research 12: 417–427.CrossRefGoogle ScholarPubMed