Chupeau M.-C.,French National Institute for Agricultural Research |
Granier F.,French National Institute for Agricultural Research |
Pichon O.,French National Institute for Agricultural Research |
Pichon O.,Institut Universitaire de France |
And 4 more authors.
Plant Cell | Year: 2013
The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we present a protocol for the efficient regeneration of plants from Arabidopsis thaliana protoplasts. The specific liquid medium used in our study leads to a high rate of reentry into the cell cycle of most cell types, providing a powerful system to study dedifferentiation/regeneration processes in independent somatic cells. To identify the early events in the establishment of totipotency, we monitored the genome-wide transcript profiles of plantlets and protoplast-derived cells (PdCs) during the first week of culture. Plant cells rapidly dedifferentiated. Then, we observed the reinitiation and reorientation of protein synthesis, accompanied by the reinitiation of cell division and de novo cell wall synthesis. Marked changes in the expression of chromatin-associated genes, especially of those in the histone variant family, were observed during protoplast culture. Surprisingly, the epigenetic status of PdCs and well-established cell cultures differed, with PdCs exhibiting rare reactivated transposons and epigenetic changes. The differentially expressed genes identified in this study are interesting candidates for investigating the molecular mechanisms underlying plant cell plasticity and totipotency. One of these genes, the plant-specific transcription factor ABERRANT LATERAL ROOT FORMATION4, is required for the initiation of protoplast division. © 2013 American Society of Plant Biologists. All rights reserved.
Fernandez V.,Max Planck Institute for Plant Breeding Research |
Takahashi Y.,Max Planck Institute for Plant Breeding Research |
Le Gourrierec J.,Max Planck Institute for Plant Breeding Research |
Le Gourrierec J.,CNRS Research Institute on Horticulture and Seeds |
Coupland G.,Max Planck Institute for Plant Breeding Research
Plant Journal | Year: 2016
Plants detect changes in day length to induce seasonal patterns of flowering. The photoperiodic pathway accelerates the flowering of Arabidopsis thaliana under long days (LDs) whereas it is inactive under short days (SDs), resulting in delayed flowering. This delay is overcome by exposure of plants to high temperature (27°C) under SDs (27°C-SD). Previously, the high-temperature flowering response was proposed to involve either the impaired activity of MADS-box transcription factor (TF) floral repressors or PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) TF-mediated activation of FLOWERING LOCUS T (FT), which encodes the output signal of the photoperiodic pathway. We integrate these observations by studying several PIFs, the MADS-box SHORT VEGETATIVE PHASE (SVP) and the photoperiodic pathway under 27°C-SD. We find that the mRNAs of FT and its paralogue TWIN SISTER OF FT (TSF) are increased at dusk under 27°C-SD compared with 21°C-SD, and that this requires PIF4 and PIF5 as well as CONSTANS (CO), a TF that promotes flowering under LDs. The CO and PIF4 proteins are present at dusk under 27°C-SD, and they physically interact. Although Col-0 plants flower at similar times under 27°C-SD and 21°C-LD the expression level of FT is approximately 10-fold higher under 21°C-LD, suggesting that responsiveness to FT is also increased under 27°C-SD, perhaps as a result of the reduced activity of SVP in the meristem. Accordingly, only svp-41 ft-10 tsf-1 plants flowered at the same time under 21°C-SD and 27°C-SD. Thus, we propose that under non-inductive SDs, elevated temperatures increase the activity and sensitize the response to the photoperiod pathway. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.
Belin E.,University of Notre Dame |
Rousseau D.,University of Lyon |
Boureau T.,CNRS Research Institute on Horticulture and Seeds |
Caffier V.,CNRS Research Institute on Horticulture and Seeds
Computers and Electronics in Agriculture | Year: 2013
Fluorescence imaging has recently been shown to be useful for the detection of apple scab, and thermal imaging for both detection and quantification of apple scab. We undertake a comparison of these two techniques and demonstrate the advantages of thermal imaging compared to fluorescence imaging to detect and quantify the presence of apple scab at the surface of leaves. We demonstrate, in practical environmental conditions of growth chambers, the advantages of thermal imaging compared to fluorescence imaging in terms of detection in the framework of a Neyman-Pearson strategy with the Bhattacharrya distance and ROC curves and in terms of quantification by establishing a linear relationship between percentage of leaf diseased area estimated visually and percentage of leaf area estimated by imaging segmentation. This opens perspectives for quantitative aspect of pathogenicity in the study of apple scab and constitutes a general framework for the comparison of nonconventional optical imaging applied to plant pathology. © 2012 Elsevier B.V.
Arango J.,Albert Ludwigs University of Freiburg |
Arango J.,International Center for Tropical Agriculture |
Jourdan M.,CNRS Research Institute on Horticulture and Seeds |
Geoffriau E.,CNRS Research Institute on Horticulture and Seeds |
And 2 more authors.
Plant Cell | Year: 2014
The typically intense carotenoid accumulation in cultivated orange-rooted carrots (Daucus carota) is determined by a high protein abundance of the rate-limiting enzyme for carotenoid biosynthesis, phytoene synthase (PSY), as compared with white-rooted cultivars. However, in contrast to other carotenoid accumulating systems, orange carrots are characterized by unusually high levels of α-carotene in addition to β-carotene. We found similarly increased α-carotene levels in leaves of orange carrots compared with white-rooted cultivars. This has also been observed in the Arabidopsis thaliana lut5 mutant carrying a defective carotene hydroxylase CYP97A3 gene. In fact, overexpression of CYP97A3 in orange carrots restored leaf carotenoid patterns almost to those found in white-rooted cultivars and strongly reduced α-carotene levels in the roots. Unexpectedly, this was accompanied by a 30 to 50% reduction in total root carotenoids and correlated with reduced PSY protein levels while PSY expression was unchanged. This suggests a negative feedback emerging from carotenoid metabolites determining PSY protein levels and, thus, total carotenoid flux. Furthermore, we identified a deficient CYP97A3 allele containing a frame-shift insertion in orange carrots. Association mapping analysis using a large carrot population revealed a significant association of this polymorphism with both α-carotene content and the α-/β-carotene ratio and explained a large proportion of the observed variation in carrots. © 2014 American Society of Plant Biologists. All rights reserved.
Jaspard E.,CNRS Research Institute on Horticulture and Seeds |
Macherel D.,CNRS Research Institute on Horticulture and Seeds |
Hunault G.,University of Angers
PLoS ONE | Year: 2012
Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. © 2012 Jaspard et al.
Tellier A.,TU Munich |
Lemaire C.,CNRS Research Institute on Horticulture and Seeds
Molecular Ecology | Year: 2014
Population genetics theory has laid the foundations for genomic analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingman coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so-called multiple merger coalescent models are reviewed here (Λ-coalescent, beta-coalescent, Bolthausen-Sznitman, Ξ-coalescent). We explain how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as (i) the skew in offspring production typical of marine species, (ii) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, (iii) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles and (iv) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies. © 2014 John Wiley & Sons Ltd.
Housekeeping gene sequencing and multilocus variable-number tandem-repeat analysis to identify subpopulations within Pseudomonas syringae pv. maculicola and Pseudomonas syringae pv. tomato that correlate with host specificity
Gironde S.,CNRS Research Institute on Horticulture and Seeds |
Manceau C.,CNRS Research Institute on Horticulture and Seeds
Applied and Environmental Microbiology | Year: 2012
Pseudomonas syringae pv. maculicola causes bacterial spot on Brassicaceae worldwide, and for the last 10 years severe outbreaks have been reported in the Loire Valley, France. P. syringae pv. maculicola resembles P. syringae pv. tomato in that it is also pathogenic for tomato and causes the same types of symptoms. We used a collection of 106 strains of P. syringae to characterize the relationships between P. syringae pv. maculicola and related pathovars, paying special attention to P. syringae pv. tomato. Phylogenetic analysis of gyrB and rpoD gene sequences showed that P. syringae pv. maculicola, which causes diseases in Brassicaceae, forms six genetic lineages within genomospecies 3 of P. syringae strains as defined by L. Gardan et al. (Int. J. Syst. Bacteriol. 49[Pt 2]:469-478, 1999), whereas P. syringae pv. tomato forms two distinct genetic lineages. A multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) conducted with eight minisatellite loci confirmed the genetic structure obtained with rpoD and gyrB sequence analyses. These results provide promising tools for fine-scale epidemiological studies on diseases caused by P. syringae pv. maculicola and P. syringae pv. tomato. The two pathovars had distinct host ranges; only P. syringae pv. maculicola strains were pathogenic for Brassicaceae. A subpopulation of P. syringae pv. maculicola strains that are pathogenic for Pto-expressing tomato plants were shown to lack avrPto1 and avrPtoB or to contain a disrupted avrPtoB homolog. Taking phylogenetic and pathological features into account, our data suggest that the DC3000 strain belongs to P. syringae pv. maculicola. This study shows that P. syringae pv. maculicola and P. syringae pv. tomato appear multiclonal, as they did not diverge from a single common ancestral group within the ancestral P. syringae genomospecies 3, and suggests that pathovar specificity within P. syringae may be due to independent genetic events. © 2012, American Society for Microbiology.
Dutheil J.Y.,Max Planck Institute for Terrestrial Microbiology |
Dutheil J.Y.,Montpellier University |
Gaillard S.,CNRS Research Institute on Horticulture and Seeds |
Stukenbrock E.H.,Max Planck Institute for Terrestrial Microbiology
BMC Genomics | Year: 2014
Background: Sequence alignments are the starting point for most evolutionary and comparative analyses. Full genome sequences can be compared to study patterns of within and between species variation. Genome sequence alignments are complex structures containing information such as coordinates, quality scores and synteny structure, which are stored in Multiple Alignment Format (MAF) files. Processing these alignments therefore involves parsing and manipulating typically large MAF files in an efficient way.Results: MafFilter is a command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner. It provides an extensive set of tools which can be parametrized and combined by the user via option files. We demonstrate the software's functionality and performance on several biological examples covering Primate genomics and fungal population genomics. Example analyses involve window-based alignment filtering, feature extractions and various statistics, phylogenetics and population genomics calculations.Conclusions: MafFilter is a highly efficient and flexible tool to analyse multiple genome alignments. By allowing the user to combine a large set of available methods, as well as designing his/her own, it enables the design of custom data filtering and analysis pipelines for genomic studies. MafFilter is an open source software available at http://bioweb.me/maffilter. © 2014 Dutheil et al.; licensee BioMed Central Ltd.
Crespel L.,CNRS Research Institute on Horticulture and Seeds |
Morel P.,CNRS Research Institute on Horticulture and Seeds
Plant Breeding | Year: 2014
Pollen viability and male meiosis in intraspecific hybrids of Hydrangea aspera subsp. aspera Kawakami group (2n = 2x = 36) and subsp. sargentiana (2n = 2x = 34) were investigated. Although it had been assumed that they were sterile, pollen viability was observed; it varied from 2.5% to 12.1%. The production of gametes with different chromosome numbers was implied by the analysis of the dispersion of the diameter distribution of pollen grains. Analysis of male meiosis made it possible to identify the origins with two major categories of meiotic aberrations: abnormal chromosome distribution (early chromosome migration at metaphase, lagging chromosomes at anaphase, micronuclei at telophase), leading to the formation of unbalanced tetrads and/or ones with supernumerary microspores; and abnormal spindle orientation in metaphase II (tripolar, fused and parallel spindles), leading to the formation of dyads or triads. The mode of 2n pollen formation is of the First Division Restitution type. The high level of parental heterozygosity that is normally associated with them should facilitate the transfer of a polygenic trait in breeding programme. © 2014 Blackwell Verlag GmbH.
Candat A.,CNRS Research Institute on Horticulture and Seeds |
Paszkiewicz G.,CNRS Research Institute on Horticulture and Seeds |
Neveu M.,CNRS Research Institute on Horticulture and Seeds |
Gautier R.,University of Nice Sophia Antipolis |
And 3 more authors.
Plant Cell | Year: 2014
Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress. © 2014 American Society of Plant Biologists. All rights reserved.