A hidden T-DNA-linked inversion-duplication is associated with a light-dependent Arabidopsis mutant phenotype
7 affiliations
- 1Molecular Plant Physiology, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
- 2Plant Biotechnology and Bioinformatics, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
- 3Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
- 4Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, 48143 Münster, Germany
- 5Plant Metabolism and Metabolomics Facility, Institute for Plant Sciences, University of Cologne, and Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Strasse 47B, 50674 Cologne, Germany
- 6Plant Metabolism and Metabolomic Facility, Düsseldorf and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
- 7Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149 Münster, Germany
Abstract
Key message: A hidden T-DNA-linked genomic rearrangement alters gene dosage and exacerbates light-dependent phenotypes in Arabidopsis, highlighting the importance of structural genome validation for reliable interpretation of mutantphenotypes.
Abstract: T-DNA insertion mutants are widely used to study gene function, yet associated genomic alterations can confound phenotypic interpretation. We investigated mutants affecting mitochondrial malate dehydrogenase (MDH1) and heterodimeric NAD-dependent malic enzyme (ME1/ME2) under different photoperiods and irradiance regimes. Under long-day conditions, mutant combinations showed no major phenotypic differences from wild type. Under short-day, low-light conditions, mdh1.1 me2 mutants were markedly smaller than wild type and, unexpectedly, more severely affected than mdh1.1 me1 me2 triple mutants. ME1 was undetectable in mdh1.1 me2, indicating that both genotypes effectively lack heterodimeric NAD-ME. Whole-genome analysis identified a 137-kbp inverted duplication downstream of the MDH1 insertion in mdh1.1 me2, absent from the triple mutant. The original mdh1.1 population segregated for the severe phenotype, whereas an independent mdh1.2 allele did not reproduce it, linking the defect to the mdh1.1-associated rearrangement. The duplication increased gene dosage and transcript abundance, particularly under low light. Proteomics detected only five of 38 proteins encoded within the duplicated region, including phosphoenolpyruvate carboxylase 1 (PEPC1). mdh1.1 me2 accumulated oxaloacetate-derived amino acids and exhibited altered carbon/nitrogen balance. These findings suggest that the duplication contributes to the phenotype, potentially through increased PEPC1 activity and consequent perturbation of carbon–nitrogen metabolism. However, interactions with MDH1 deficiency cannot be excluded, making PEPC1 a candidate contributor rather than the sole causal determinant. Our results highlight how T-DNA-linked structural variation can confound condition-dependent phenotypes and emphasize the need for structural validation of insertion loci, particularly given the widespread use of Agrobacterium-mediated DNA transfer in plant genome editing.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1007/s00299-026-04030-1.
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BibTeX
@article{martinez2026hidden,
title = {{A hidden T-DNA-linked inversion-duplication is associated with a light-dependent Arabidopsis mutant phenotype}},
author = {María del Pilar Martinez and Julie Anne V. S. de Oliveira and Ioana Nica and Noah Ditz and Ke Zheng and Vera Wewer and Sabine Metzger and Philipp Westhoff and Holger Eubel and Iris Finkemeier and Markus Schwarzländer and Boas Pucker and Veronica G. Maurino},
journal = {Plant Cell Reports},
year = {2026},
month = nov,
doi = {10.1007/s00299-026-04030-1},
url = {https://doi.org/10.1007/s00299-026-04030-1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A hidden T-DNA-linked inversion-duplication is associated with a light-dependent Arabidopsis mutant phenotype
AU - María del Pilar Martinez
AU - Julie Anne V. S. de Oliveira
AU - Ioana Nica
AU - Noah Ditz
AU - Ke Zheng
AU - Vera Wewer
AU - Sabine Metzger
AU - Philipp Westhoff
AU - Holger Eubel
AU - Iris Finkemeier
AU - Markus Schwarzländer
AU - Boas Pucker
AU - Veronica G. Maurino
PY - 2026
DA - 2026/11/03
JO - Plant Cell Reports
DO - 10.1007/s00299-026-04030-1
UR - https://doi.org/10.1007/s00299-026-04030-1
AB - Key message: A hidden T-DNA-linked genomic rearrangement alters gene dosage and exacerbates light-dependent phenotypes in Arabidopsis, highlighting the importance of structural genome validation for reliable interpretation of mutantphenotypes. Abstract: T-DNA insertion mutants are widely used to study gene function, yet associated genomic alterations can confound phenotypic interpretation. We investigated mutants affecting mitochondrial malate dehydrogenase (MDH1) and heterodimeric NAD-dependent malic enzyme (ME1/ME2) under different photoperiods and irradiance regimes. Under long-day conditions, mutant combinations showed no major phenotypic differences from wild type. Under short-day, low-light conditions, mdh1.1 me2 mutants were markedly smaller than wild type and, unexpectedly, more severely affected than mdh1.1 me1 me2 triple mutants. ME1 was undetectable in mdh1.1 me2, indicating that both genotypes effectively lack heterodimeric NAD-ME. Whole-genome analysis identified a 137-kbp inverted duplication downstream of the MDH1 insertion in mdh1.1 me2, absent from the triple mutant. The original mdh1.1 population segregated for the severe phenotype, whereas an independent mdh1.2 allele did not reproduce it, linking the defect to the mdh1.1-associated rearrangement. The duplication increased gene dosage and transcript abundance, particularly under low light. Proteomics detected only five of 38 proteins encoded within the duplicated region, including phosphoenolpyruvate carboxylase 1 (PEPC1). mdh1.1 me2 accumulated oxaloacetate-derived amino acids and exhibited altered carbon/nitrogen balance. These findings suggest that the duplication contributes to the phenotype, potentially through increased PEPC1 activity and consequent perturbation of carbon–nitrogen metabolism. However, interactions with MDH1 deficiency cannot be excluded, making PEPC1 a candidate contributor rather than the sole causal determinant. Our results highlight how T-DNA-linked structural variation can confound condition-dependent phenotypes and emphasize the need for structural validation of insertion loci, particularly given the widespread use of Agrobacterium-mediated DNA transfer in plant genome editing. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1007/s00299-026-04030-1.
SN - 0721-7714
SN - 1432-203X
ER -