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Deans NC, Talbot JERB, Li M, Sáez-González C, Hövel I, Heavens D, Stam M, Hollick JB. Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats. PLoS Genet 2024; 20:e1011296. [PMID: 38814980 PMCID: PMC11166354 DOI: 10.1371/journal.pgen.1011296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/11/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Exceptions to Mendelian inheritance often highlight novel chromosomal behaviors. The maize Pl1-Rhoades allele conferring plant pigmentation can display inheritance patterns deviating from Mendelian expectations in a behavior known as paramutation. However, the chromosome features mediating such exceptions remain unknown. Here we show that small RNA production reflecting RNA polymerase IV function within a distal downstream set of five tandem repeats is coincident with meiotically-heritable repression of the Pl1-Rhoades transcription unit. A related pl1 haplotype with three, but not one with two, repeat units also displays the trans-homolog silencing typifying paramutations. 4C interactions, CHD3a-dependent small RNA profiles, nuclease sensitivity, and polyadenylated RNA levels highlight a repeat subregion having regulatory potential. Our comparative and mutant analyses show that transcriptional repression of Pl1-Rhoades correlates with 24-nucleotide RNA production and cytosine methylation at this subregion indicating the action of a specific DNA-dependent RNA polymerase complex. These findings support a working model in which pl1 paramutation depends on trans-chromosomal RNA-directed DNA methylation operating at a discrete cis-linked and copy-number-dependent transcriptional regulatory element.
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Affiliation(s)
- Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Joy-El R. B. Talbot
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Mowei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Cristian Sáez-González
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | | | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Jay B. Hollick
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
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2
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Liébana C, Torres L, Ordóñez A. Cytogenetic Characterization of Three Populations of Hedeoma multiflorum Benth. (Lamiaceae) Native from Córdoba, Argentina. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Cintia Liébana
- Cátedra de Genética, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing
| | - Lorena Torres
- Cátedra de Genética, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing
| | - Adriana Ordóñez
- Cátedra de Genética, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing
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3
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Lo KL, Wang LC, Chen IJ, Liu YC, Chung MC, Lo WS. Transcriptional consequence and impaired gametogenesis with high-grade aneuploidy in Arabidopsis thaliana. PLoS One 2014; 9:e114617. [PMID: 25514186 PMCID: PMC4267805 DOI: 10.1371/journal.pone.0114617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/12/2014] [Indexed: 12/11/2022] Open
Abstract
Aneuploidy features a numerical chromosome variant that the number of chromosomes in the nucleus of a cell is not an exact multiple of the haploid number, which may have an impact on morphology and gene expression. Here we report a tertiary trisomy uncovered by characterizing a T-DNA insertion mutant (aur2-1/+) in the Arabidopsis (Arabidopsis thaliana) AURORA2 locus. Whole-genome analysis with DNA tiling arrays revealed a chromosomal translocation linked to the aur2-1 allele, which collectively accounted for a tertiary trisomy 2. Morphologic, cytogenetic and genetic analyses of aur2-1 progeny showed impaired male and female gametogenesis to various degrees and a tight association of the aur2-1 allele with the tertiary trisomy that was preferentially inherited. Transcriptome analysis showed overlapping and distinct gene expression profiles between primary and tertiary trisomy 2 plants, particularly genes involved in response to stress and various types of external and internal stimuli. Additionally, transcriptome and gene ontology analyses revealed an overrepresentation of nuclear-encoded organelle-related genes functionally involved in plastids, mitochondria and peroxisomes that were differentially expressed in at least three if not all Arabidopsis trisomics. These observations support a previous hypothesis that aneuploid cells have higher energy requirement to overcome the detrimental effects of an unbalanced genome. Moreover, our findings extend the knowledge of the complex nature of the T-DNA insertion event influencing plant genomic integrity by creating high-grade trisomy. Finally, gene expression profiling results provide useful information for future research to compare primary and tertiary trisomics for the effects of aneuploidy on plant cell physiology.
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Affiliation(s)
- Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Long-Chi Wang
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Liu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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4
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Kamenarova K, Gecheff K, Stoyanova M, Muhovski Y, Anzai H, Atanassov A. Production of Recombinant Human Lactoferin in Transgenic Barley. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2007.10817407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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5
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Mehrotra S, Goyal V. Evaluation of designer crops for biosafety--a scientist's perspective. Gene 2012; 515:241-8. [PMID: 23266812 DOI: 10.1016/j.gene.2012.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/26/2012] [Accepted: 12/04/2012] [Indexed: 01/16/2023]
Abstract
With the advent of transgenic technology, it has become possible to mobilize and express foreign genes into plants and to design crop varieties with better agronomic attributes and adaptability to challenging environmental conditions. Recent advances in transgenic technology have led to concerns about safety of transgenic crops to human and animal health and environment. Biosafety focuses on preventing, minimizing and eliminating risks associated with the research, production, and use of transgenic crops. Food biosafety involves studies of substantial equivalence related to compositional analysis, toxicity and allergenicity. Environmental biosafety involves glasshouse and field trials and study of unintended effects on non-target organisms. Transgenics are characterized at phenotypic and molecular levels for understanding the location of transgene insertion site, ploidy level, copy number, integrated vector sequences, protein expression and stability of the transgene. Various techniques employed for transgene characterization include flow cytometry, southern, northern and western analyses, real-time (qRT) PCR, competitive PCR, FISH, fiber-FISH, DNA micro-arrays, mRNA profiling, 2DE-MS, iTRAQ, FT-MS, NMR, GC-MS, CE-MS and biosensor-based approaches. Evaluation of transgene expression involves the application of integrated phenomics, transcriptomics, proteomics and metabolomics approaches. However, the relevance and application of these approaches may vary in different cases. The elaborate analysis of transgenic crops will facilitate the safety assessment and commercialization of transgenics and lead to global food security for the future.
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Affiliation(s)
- Shweta Mehrotra
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi-110012, India.
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6
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Sidorchuk YV, Deineko EV, Shumny VK. Peculiarities of cytomixis in pollen mother cells of transgenic tobacco plants (Nicotiana tabacum L.) with mutant phenotype. ACTA ACUST UNITED AC 2007. [DOI: 10.1134/s1990519x07060144] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Henry IM, Dilkes BP, Comai L. Genetic basis for dosage sensitivity in Arabidopsis thaliana. PLoS Genet 2007; 3:e70. [PMID: 17465685 PMCID: PMC1857734 DOI: 10.1371/journal.pgen.0030070] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 03/16/2007] [Indexed: 11/19/2022] Open
Abstract
Aneuploidy, the relative excess or deficiency of specific chromosome types, results in gene dosage imbalance. Plants can produce viable and fertile aneuploid individuals, while most animal aneuploids are inviable or developmentally abnormal. The swarms of aneuploid progeny produced by Arabidopsis triploids constitute an excellent model to investigate the mechanisms governing dosage sensitivity and aneuploid syndromes. Indeed, genotype alters the frequency of aneuploid types within these swarms. Recombinant inbred lines that were derived from a triploid hybrid segregated into diploid and tetraploid individuals. In these recombinant inbred lines, a single locus, which we call SENSITIVE TO DOSAGE IMBALANCE (SDI), exhibited segregation distortion in the tetraploid subpopulation only. Recent progress in quantitative genotyping now allows molecular karyotyping and genetic analysis of aneuploid populations. In this study, we investigated the causes of the ploidy-specific distortion at SDI. Allele frequency was distorted in the aneuploid swarms produced by the triploid hybrid. We developed a simple quantitative measure for aneuploidy lethality and using this measure demonstrated that distortion was greatest in the aneuploids facing the strongest viability selection. When triploids were crossed to euploids, the progeny, which lack severe aneuploids, exhibited no distortion at SDI. Genetic characterization of SDI in the aneuploid swarm identified a mechanism governing aneuploid survival, perhaps by buffering the effects of dosage imbalance. As such, SDI could increase the likelihood of retaining genomic rearrangements such as segmental duplications. Additionally, in species where triploids are fertile, aneuploid survival would facilitate gene flow between diploid and tetraploid populations via a triploid bridge and prevent polyploid speciation. Our results demonstrate that positional cloning of loci affecting traits in populations containing ploidy and chromosome number variants is now feasible using quantitative genotyping approaches.
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Affiliation(s)
- Isabelle M Henry
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Brian P Dilkes
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Luca Comai
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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Yang G, Lee YH, Jiang Y, Kumpatla SP, Hall TC. Organization, not duplication, triggers silencing in a complex transgene locus in rice. PLANT MOLECULAR BIOLOGY 2005; 58:351-66. [PMID: 16021400 DOI: 10.1007/s11103-005-5101-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 04/04/2005] [Indexed: 05/03/2023]
Abstract
Despite the presence in nature of many functional gene families that contain several to many highly similar sequences, the presence of identical DNA sequence repeats is widely thought to predispose transgene inserts to homology dependent gene silencing (HDGS). The induction of transcriptional gene silencing (TGS) by RNAs homologous to promoter sequences has been reported recently in Arabidopsis and humans. However, mechanisms for TGS have not been studied in detail for rice, the most widely cultivated crop plant. Taking advantage of a well-characterized homozygous silenced transgenic rice line (siJKA), supertransformation was performed with a binary vector bearing mUbi1 and 35S promoter sequences identical to those in the resident transgenes. Analysis of the incoming and resident transgenes in the supertransformants revealed that the incoming mUbi1 transgene promoter was not silenced whereas the incoming 35S transgene promoter was silenced. That the resident silenced mUbi1-bar was not reactivated in these experiments as a result of passage through tissue culture and regeneration was established by the finding that regenerants from siJKA immature embryos were all silenced for mUbi1-bar. In a parallel experiment, when wild type rice calli were transformed with the same binary vector, neither of the incoming transgene promoters was silenced. Following 5-azacytidine (5-azaC) treatment of siJKA, aberrant RNA species corresponding to the 35S promoter, but not to the mUbi1 promoter, were detected. Nevertheless, no 21-25 nt RNAs corresponding to the 35S promoter sequence were detected. These results, together with detailed analyses of the progenies from the primary transformants and supertransformants, revealed that HDGS of the resident silenced locus was caused not by simple transgene duplication, but by aberrant transcripts derived from rearranged promoters present in siJKA. Practical consequences of this study include a justification for the use of multiple copies of a given promoter for transformation without inducing silencing, provided that their genomic integration does not result in aberrant transcription of the promoters.
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Affiliation(s)
- Guojun Yang
- Institute of Developmental and Molecular Biology and Department of Biology, Texas A and M University, College Station, TX 77843-3155, USA
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9
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Abstract
There are some mammalian alleles that display the unusual characteristic of variable expressivity in the absence of genetic heterogeneity. It has recently become evident that this is because the activity of these alleles is dependent on their epigenetic state. Interestingly, the epigenetic state is somewhat labile, resulting in phenotypic mosaicism between cells (variegation) and also between individuals (variable expressivity). The establishment of the epigenetic state occurs during early embryogenesis and is a probabilistic event that is influenced by whether the allele is carried on the paternal or maternal alleles. In addition, the epigenetic state determines whether these alleles are dominant. We propose that mammalian alleles with such characteristics should be termed metastable epialleles to distinguish them from traditional alleles. At this stage, it is unclear how common these alleles are, but an appreciation of their existence will aid in their identification.
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Affiliation(s)
- Vardhman K Rakyan
- School of Molecular and Microbial Biosciences, University of Sydney, NSW-2006, Sydney, Australia
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10
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Variation induced by DNA rearrangement in a transgenicBt+CpTI cotton strain. ACTA ACUST UNITED AC 2001. [DOI: 10.1007/bf02900408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Choi HW, G Lemaux P, Cho MJ. High frequency of cytogenetic aberration in transgenic oat (Avena sativa L.) plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:763-772. [PMID: 11448750 DOI: 10.1016/s0168-9452(01)00369-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Cytological abnormalities were observed in transgenic oat (Avena sativa L. cv. GAF/Park-1) produced by microprojectile bombardment of mature seed-derived highly regenerative tissues. Of the plants from 48 independent transgenic lines examined, plants from only 20 lines (42%) were karyotypically normal (2n=6x=42) without detectable chromosomal aberrations; plants from 28 lines (58%) had chromosomal variation, i.e. aneuploids and structural changes. No significant difference in cytological aberration was observed between the two different culturing systems used for transformation: 57% chromosomal abnormalities in plants derived from D'BC2 medium (2.0 mg/l 2,4-D, 0.1 mg/l BAP and 5.0 &mgr;M cupric sulfate) used for tissue initiation and maintenance and 60% in plants from tissue initiated on D'BC2 and maintained on DBC3 (1.0 mg/l 2,4-D, 0.5 mg/l BAP and 5.0 &mgr;M cupric sulfate). Comparative differences in chromosomal status frequently occurred among plants regenerated from the same T(0) line. The most common cytological aberration in transgenic plants was aneuploidy, followed by deletion of chromosomal segments; no change in ploidy level was observed. In contrast, nontransgenic plants, regenerated from tissues comparable in age and culture media to that used for transgenic tissues, had a much lower percentage of karyotypic abnormality (0-14%). Our data indicate that some stress(es) imposed by the transformation process, e.g. osmotic treatment, bombardment and selection, leads to cytological variation in transgenic oat plants, an observation similar to that observed in our recent studies with transgenic barley plants.
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Affiliation(s)
- H -W. Choi
- Department of Plant and Microbial Biology, University of California, 94720, Berkeley, CA, USA
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12
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Choi H, Cho M. High frequency of cytogenetic aberration in transgenic oat (Avena sativa L.) plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 156:85-94. [PMID: 10908808 DOI: 10.1016/s0168-9452(00)00241-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Cytological abnormalities were observed in transgenic oat (Avena sativa L. cv. GAF/Park-1) produced by microprojectile bombardment of mature seed-derived highly regenerative tissues. Of the plants from 48 independent transgenic lines examined, plants from only 20 lines (42%) were karyotypically normal (2n=6x=42) without detectable chromosomal aberrations; plants from 28 lines (58%) had chromosomal variation, i.e. aneuploids and structural changes. No significant difference in cytological aberration was observed between the two different culturing systems used for transformation: 57% chromosomal abnormalities in plants derived from D'BC2 medium (2.0 mg/l 2,4-D, 0. 1 mg/l BAP and 5.0 µM cupric sulfate) used for tissue initiation and maintenance and 60% in plants from tissue initiated on D'BC2 and maintained on DBC3 (1.0 mg/l 2,4-D, 0.5 mg/l BAP and 5.0 µM cupric sulfate). Comparative differences in chromosomal status frequently occurred among plants regenerated from the same T(0) line. The most common cytological aberration in transgenic plants was aneuploidy, followed by deletion of chromosomal segments; no change in ploidy level was observed. In contrast, nontransgenic plants, regenerated from tissues comparable in age and culture media to that used for transgenic tissues, had a much lower percentage of karyotypic abnormality (0-14%). Our data indicate that some stress(es) imposed by the transformation process, e.g. osmotic treatment, bombardment and selection, leads to cytological variation in transgenic oat plants, an observation similar to that observed in our recent studies with transgenic barley plants.
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Affiliation(s)
- H Choi
- Department of Plant and Microbial Biology, University of California, 94720, Berkeley, CA, USA
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Mittelsten Scheid O, Jakovleva L, Afsar K, Maluszynska J, Paszkowski J. A change of ploidy can modify epigenetic silencing. Proc Natl Acad Sci U S A 1996; 93:7114-9. [PMID: 8692954 PMCID: PMC38945 DOI: 10.1073/pnas.93.14.7114] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A silent transgene in Arabidopsis thaliana was reactivated in an outcross but not upon selfing of hemizygous plants. This result could only be explained by assuming a genetic difference between the transgene-free gametes of the wild-type and hemizygous transgenic plants, respectively, and led to the discovery of ploidy differences between the parental plants. To investigate whether a change of ploidy by itself can indeed influence gene expression, we performed crosses of diploid or tetraploid plants with a strain containing a single copy of a transgenic resistance gene in an active state. We observed reduced gene expression of the transgene in triploid compared with diploid hybrids. This led to loss of the resistant phenotype at various stages of seedling development in part of the population. The gene inactivation was reversible. Thus, an increased number of chromosomes can result in a new type of epigenetic gene inactivation, creating differences in gene expression patterns. We discuss the possible impact of this finding for genetic diploidization in the light of widespread, naturally occurring polyploidy and polysomaty in plants.
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