CENH3-GFP: a visual marker for gametophytic and somatic ploidy determination in Arabidopsis thaliana

Background: The in vivo determination of the cell-specific chromosome number provides a valuable tool in several aspects of plant research. However, current techniques to determine the endosystemic ploidy level do not allow non-destructive, cell-specific chromosome quantification. Particularly in the gametophytic cell lineages, which are physically encapsulated in the reproductive organ structures, direct in vivo ploidy determination has been proven very challenging. Using Arabidopsis thaliana as a model, we here assess the applicability of recombinant CENH3-GFP reporters for the labeling of the cell’s chromocenters and for the monitoring of the gametophytic and somatic chromosome number in vivo. Results: By modulating expression of a CENH3-GFP reporter cassette using different promoters, we isolated two reporter lines that allow for a clear and highly specific labeling of centromeric chromosome regions in somatic and gametophytic cells respectively. Using polyploid plant series and reproductive mutants, we demonstrate that the pWOX2-CENH3-GFP recombinant fusion protein allows for the determination of the gametophytic chromosome number in both male and female gametophytic cells, and additionally labels centromeric regions in early embryo development. Somatic centromere labeling through p35S-CENH3-GFP shows a maximum of ten centromeric dots in young dividing tissues, reflecting the diploid chromosome number (2x = 10), and reveals a progressive decrease in GFP foci frequency throughout plant development. Moreover, using chemical and genetic induction of endomitosis, we demonstrate that CENH3-mediated chromosome labeling provides an easy and valuable tool for the detection and characterization of endomitotic polyploidization events. Conclusions: This study demonstrates that the introgression of the pWOX2-CENH3-GFP reporter construct in Arabidopsis thaliana provides an easy and reliable methodology for determining the chromosome number in developing male and female gametes, and during early embryo development. Somatically expressed CENH3-GFP reporters, on the other hand, constitute a valuable tool to quickly determine the basic somatic ploidy level in young seedlings at the individual cell level and to detect and to quantify endomitotic polyploidization events in a non-destructive, microscopy-based manner

Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants

GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP

The Status under EU Law of Organisms Developed through Novel Genomic Techniques

In a ruling on 25 July 2018, the Court of Justice of the European Union concluded that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs in the sense of Directive 2001/18, and that organisms obtained by means of techniques/methods of directed mutagenesis are not excluded from the scope of the Directive. Following the ruling, there has been much debate about the possible wider implications of the ruling. In October 2019, the Council of the European Union requested the European Commission to submit, in light of the CJEU ruling, a study regarding the status of novel genomic techniques under Union Law. For the purpose of the study, the Commission initiated stakeholder consultations early in 2020. Those consultations focused on the technical status of novel genomic techniques. This article aims to contribute to the discussion on the legal status of organisms developed through novel genomic techniques, by offering some historical background to the negotiations on the European Union (EU) GMO Directives as well as a technical context to some of the terms in the Directive, and by analysing the ruling. The article advances that (i) the conclusion that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs under the Directive means that the resulting organisms must comply with the GMO definition, ie the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination; (ii) the conclusion that organisms obtained by means of techniques/methods of directed mutagenesis were not intended to be excluded from the scope of the Directive is not inconsistent with the negotiation history of the Directive; (iii) whether an organism falls under the description of “obtained by means of techniques/methods of directed mutagenesis” depends on whether the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination. Finally, the article offers an analysis of the EU GMO definition, concluding that for an organism to be a GMO in the sense of the Directive, the technique used, as well as the genetic alterations of the resulting organism, must be considered.Peer Reviewe

The status under EU Law of Organisms developed through novel genomic techniques

In a ruling on 25 July 2018, the Court of Justice of the European Union concluded that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs in the sense of Directive 2001/18, and that organisms obtained by means of techniques/methods of directed mutagenesis are not excluded from the scope of the Directive. Following the ruling, there has been much debate about the possible wider implications of the ruling. In October 2019, the Council of the European Union requested the European Commission to submit, in light of the CJEU ruling, a study regarding the status of novel genomic techniques under Union Law. For the purpose of the study, the Commission initiated stakeholder consultations early in 2020. Those consultations focused on the technical status of novel genomic techniques. This article aims to contribute to the discussion on the legal status of organisms developed through novel genomic techniques, by offering some historical background to the negotiations on the European Union (EU) GMO Directives as well as a technical context to some of the terms in the Directive, and by analysing the ruling. The article advances that (i) the conclusion that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs under the Directive means that the resulting organisms must comply with the GMO definition, ie the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination; (ii) the conclusion that organisms obtained by means of techniques/methods of directed mutagenesis were not intended to be excluded from the scope of the Directive is not inconsistent with the negotiation history of the Directive; (iii) whether an organism falls under the description of “obtained by means of techniques/methods of directed mutagenesis” depends on whether the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination. Finally, the article offers an analysis of the EU GMO definition, concluding that for an organism to be a GMO in the sense of the Directive, the technique used, as well as the genetic alterations of the resulting organism, must be considered

New Phenotypes of Potato Co-induced by Mismatch Repair Deficiency and Somatic Hybridization

As plants are sessile they need a very efficient system for repairing damage done by external or internal mutagens to their DNA. Mismatch repair (MMR) is one of the systems that maintain genome integrity and prevent homeologous recombination. In all eukaryotes mismatches are recognized by evolutionary conserved MSH proteins often acting as heterodimers, the constant component of which is MSH2. Changes affecting the function of MSH2 gene may induce a ‘mutator’ phenotype and microsatellite instability (MSI), as is demonstrated in MSH2 knock-out and silenced lines of Arabidopsis thaliana. The goal of this study was to screen for ‘mutator’ phenotypes in somatic hybrids between potato cvs. ‘Delikat’ and ‘Désirée’ and MMR deficient Solanum chacoense transformed using antisense (AS) or dominant negative mutant (DN) AtMSH2 genes. The results demonstrate that first generation fusion hybrids have a range of morphological abnormalities caused by uniparental MMR deficiency; these mutant phenotypes include: dwarf or gigantic plants; bushiness; curled, small, large or abnormal leaves; a deterioration in chloroplast structure; small deep-purple tubers and early dehiscent flowers. Forty percent of the viable somatic hybrids planted in a greenhouse, (10 out of 25 genotypes) had mutant phenotypes accompanied by MSI. The majority of the hybrids with ‘mutator’ phenotypes cultured on media containing kanamycin developed roots so sustaining the presence of selectable marker gene nptII, from the initial constructs. Here for the first time, MMR deficiency combined with somatic hybridization, are used to induce new phenotypes in plants, which supports the role of MMR deficiency in increasing introgressions between two related species

Light strongly promotes gene transfer from Agrobacterium tumefaciens to plant cells

Abstract Light conditions during Agrobacterium-based plant transformation, the most routinely used method in plant genetic engineering, differ widely and, to our knowledge, have not been studied systematically in relation to transformation efficiency. Here, light effects were examined in two already optimized transformation procedures: coculture of Agrobacterium tumefaciens with callus from two genotypes of the crop plant Phaseolus acutifolius (tepary bean) and coculture of root segments from two ecotypes of Arabidopsis thaliana. Except for the light conditions during coculture, all steps followed established procedures. Coculture was done either under continuous darkness, under a commonly used photoperiod of 16 h light/8 h darkness or under continuous light. b-glucuronidase (GUS) production due to the transient expression of an intron-containing uidA gene in the binary vector was used to evaluate T-DNA transfer. In all situations, uidA expression correlated highly and positively with the light period used during coculture; it was inhibited severely by darkness and enhanced more under continuous light than under a 16 h light/8 h dark photoperiod. The promotive effect of light was observed with Agrobacterium strains harboring either a nopaline-, an octopine-or an agropine/succinamopine-type nononcogenic helper Ti plasmid. The observed positive effect of light has obvious implications for developing and improving transient and stable transformation protocols, specifically those involving dark coculture conditions

Thirty years of transgenic research in plants

In 1983, the first transgenic tissues and plants were generated by means of disarmed Agrobacterium tumefaciens strains, in which the oncogenes had been replaced by antibiotic resistance markers. Hence, this Special Issue of The International Journal of Developmental Biology celebrates 30 years of transgenic research in plants! Eminent scientists working in the field of plant transformation or plant biotechnology have contributed to this publication and reviewed the state of the art of their particular subdomain or summarized the importance of transgenic research in the discovery of new mechanisms and the establishment of an entirely new field, such as epigenetics