ORCID Profile
0000-0002-9252-5271
Current Organisations
CIRAD Département Systèmes biologiques
,
CIRAD
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Publisher: Springer Science and Business Media LLC
Date: 06-2002
DOI: 10.1007/S00122-002-0906-4
Abstract: The occurrence of "mantled" somaclonal variants (approx. 5%), which display alterations in floral organ structure, among populations of somatic embryo-derived oil palms ( Elaeis guineensis Jacq.) currently h ers any scaling-up of clonal plant micropropagation. As a first step towards the identification of abnormality-discriminating markers, we have screened a set of 27 oil palm cDNA probes for methylation-sensitive restriction fragment length polymorphisms (RFLPs) using callus genomic DNA digested with the isoschizomeric enzymes MspI and HpaII. Only two probes (CPHO62 and -63) were found to differentiate reproducibly in two different genotypic backgrounds between nodular compact calli (NCC) and fast-growing calli (FGC), which generate 5% and 100% "mantled" plantlets, respectively. Comparative analyses were then conducted on DNA from inflorescences and leaves of normal and abnormal adult regenerants. With both probes, the observed methylation patterns were strongly clone-dependent and monomorphic with respect to the phenotype of the regenerants, except for the type-specific banding pattern obtained with the CPHO62 probe on material from the LMC3 clonal offspring. The results presented here mirror the higher difference in genomic DNA methylation observed between normal and abnormal embryogenic calli when compared to more differentiated plant material. Moreover, they reinforce the paramount interest of NCC and FGC callus lines as a material of choice in the search for early epigenetic markers of the "mantled" somaclonal variation. The potential use of methylation-sensitive RFLPs for the early detection of somaclonal variation at early stages of the micropropagation process is discussed.
Publisher: Oxford University Press (OUP)
Date: 17-07-2008
DOI: 10.1093/JXB/ERN178
Abstract: In oil palm (Elaeis guineensis Jacq.), approximately 5% of somatic embryo-derived regenerants show homeotic changes during floral development, involving an apparent feminization of male parts in flowers of both sexes, called the 'mantled' phenotype. This variant phenotype is associated with a reduction in the level of global DNA methylation. To explore possible relationships between DNA methylation level and accumulation of DNA-(cytosine-5) methyltransferase (DNMT) transcripts, the full-length coding sequences corresponding to three different DNMT families in oil palm, namely the MET, CMT, and DRM classes, have been isolated and characterized. The corresponding genes were designated as EgMET1, EgCMT1, and EgDRM1, and encode predicted polypeptides of 1543, 925, and 591 amino acid residues, respectively. Expression of oil palm DNMTs was compared between normal and variant calli and inflorescence tissues using quantitative reverse-transcription PCR. A consistent increase in transcript levels of EgMET1 and EgCMT1 was found in variant fast-growing calli relative to nodular-compact calli. Nodular-compact calli give rise to about 5% of abnormal regenerants whereas fast-growing calli generate 95% of 'mantled' palms in their clonal offspring and were previously demonstrated as having markedly hypomethylated DNA. In immature abnormal inflorescences only EgMET1 transcript levels were increased, while no changes in relative abundance of the EgCMT1 or EgDRM1 transcripts were observed. Therefore, the genome-wide hypomethylation previously described in 'mantled' material cannot be explained by a decrease in expression levels of the de novo or maintenance DNMTs, a paradox which has been previously reported in tumour cells, where there is evidence for global hypomethylation of DNA.
Publisher: Cold Spring Harbor Laboratory
Date: 30-01-2020
DOI: 10.1101/2020.01.30.926626
Abstract: In Sub-Saharan Africa, the fan palm Borassus aethiopum Mart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic ersity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic ersity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled lification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated a B. aethiopum -specific genomic dataset through high-throughput sequencing and used it for the de novo detection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic ersity in nine B. aethiopum populations. Our results show that genetic ersity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that s led B. aethiopum populations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Savè (which also has the highest He) and populations from the North. In light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic ersity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.
Publisher: Springer Science and Business Media LLC
Date: 13-06-2000
Abstract: Jacq.) currently h ers the scaling-up of clonal plant production. In order to investigate the relationship between the "mantled" somaclonal variant and possible alterations in genomic DNA methylation rate, two complementary approaches have been used. HPLC quantification of relative amounts of 5-methyl-deoxycytidine has shown that global methylation in leaf DNA of abnormal regenerants is 0.5-2.5% lower than in their normal counterparts (20.8% vs 22%, respectively). When comparing nodular compact calli and fast growing calli, yielding respectively 5% and 100% of "mantled" plantlets, this decrease was up to 4.5% (from 23.2 to 18.7%). An alternative method, the SssI-methylase accepting assay, based on the enzymatic saturation of CG sites with methyl groups, gave convergent results. This work demonstrates that a correlation exists between DNA hypomethylation and the "mantled" somaclonal variation in oil palm.
Publisher: EMBO
Date: 07-2005
Publisher: Cold Spring Harbor Laboratory
Date: 28-12-2018
DOI: 10.1101/504092
Abstract: In this paper, we describe the implementation of the MooSciTIC summer schools, a capacity-building initiative targeting West African research scientists and higher education teachers. Throughout the three years of the project, we provided on-site courses and practicals on cross-disciplinary aspects such as scientific writing, communication and integrity, in the aim of improving the self-reliance of researchers and upgrading research practices throughout the sub-region. We explain how the program was designed and implemented and we show the positive outcomes it generated for our former trainees within a relatively short period, hoping to inspire similar initiatives to follow our steps.
Publisher: Springer Science and Business Media LLC
Date: 14-08-2010
Publisher: Springer Science and Business Media LLC
Date: 29-05-2005
DOI: 10.1038/NG1580
Abstract: RNA-directed DNA methylation, one of several RNA interference-mediated pathways in the nucleus, has been documented in plants and in human cells. Despite progress in identifying the DNA methyltransferases, histone-modifying enzymes and RNA interference proteins needed for RNA-directed DNA methylation, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups. DRD1 is a SNF2-like protein required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally ersified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.
Publisher: CABI Publishing
Date: 25-01-2012
Abstract: The amazing ability of epigenetic mechanisms to respond to a wide range of developmental and environmental signals in eukaryotes has earned them a lot of attention. Indeed, epigenetically regulated gene expression (variations in gene expression obtained without permanent alteration of the DNA sequence) is involved in differentiation, organogenesis and acclimation, and, as such, is hypothesized to participate in both phenotypic ersity and the plasticity of living organisms. While the importance of epigenetic mechanisms in the understanding of such vital processes is now widely recognized, many questions remain to be elucidated. Foremost is the point of transmission of epigenetic marks on (methylated cytosines) and around (modified histone tails) DNA, since research is still needed to explain the inheritance of an epigenetic character and which mechanisms are involved. The present review is aimed at illustrating key concepts when considering the exploitation of epigenetic changes for plant breeding, through both its environmentally responsive character and its potential heritability. In doing so, we have avoided developments relating to complex molecular pathways so as to give a glimpse to the interested but non-expert reader on the current debates and on the experimental challenges still ahead.
Publisher: Canadian Science Publishing
Date: 2004
DOI: 10.1139/G03-085
Abstract: The methylation-sensitive lification polymorphism (MSAP) technique has been employed on somatic embryo-derived oil palms (Elaeis guineensis Jacq.) to identify methylation polymorphisms correlated with the "mantled" somaclonal variation. The variant phenotype displays an unstable feminization of male organs in both male and female flowers. Using MSAP, the methylation status of CCGG sites was compared in three normal versus three mantled regenerants s led in clonal populations obtained through somatic embryogenesis from four genotypically distinct mother palms. Overall, 64 selective primer combinations were used and they have lified 23 markers exhibiting a differential methylation pattern between the two phenotypes. Our results indicate that CCGG sites are poorly affected by the considerable decrease in global DNA methylation that has been previously associated with the mantled phenotype. Each of the 23 markers isolated in the present study could discriminate between the two phenotypes only when they were from the same genetic origin. This result h ers at the moment the direct use of MSAP markers for the early detection of variants, even though valuable information on putative target sequences will be obtained from a further characterization of these polymorphic markers.Key words: DNA methylation, epigenetics, MSAP, oil palm, somaclonal variation.
Publisher: Public Library of Science (PLoS)
Date: 17-03-2014
Publisher: Oxford University Press (OUP)
Date: 10-01-2011
DOI: 10.1093/AOB/MCQ266
Publisher: Blackwell Publishing Ltd
Date: 2005
Publisher: Springer Science and Business Media LLC
Date: 15-10-2015
Publisher: Public Library of Science (PLoS)
Date: 07-06-2019
Publisher: Wiley
Date: 07-10-2005
Publisher: Springer Science and Business Media LLC
Date: 23-11-2012
DOI: 10.1007/S00299-012-1369-Y
Abstract: KEY MESSAGE : The long-term proliferation of embryogenic cell suspensions of oil palm is associated with changes in both genomic methylation rates and embryogenic capacities. In the aim of exploring the relationship between epigenetic stability and the long-term in vitro proliferation of plant tissues, we have studied changes in genomic DNA methylation levels in embryogenic suspensions of oil palm (Elaeis guineensis Jacq.). Five embryogenic callus lines were obtained from selected hybrid seeds and then proliferated as suspension cultures. Each clonal line obtained from a single genotype was sub ided into three independent subclonal lines. Once established, cultures proliferated for 12 months and genomic DNA was s led at 4 months intervals for the estimation of global DNA methylation rates through high performance liquid chromatography (HPLC) quantitation of deoxynucleosides. Our results show that in vitro proliferation induces DNA hypermethylation in a time-dependent fashion. Moreover, this trend is statistically significant in several clonal lines and shared between subclonal lines originating from the same genotype. Interestingly, the only clonal line undergoing loss of genomic methylation in the course of proliferation has been found unable to generate somatic embryos. We discuss the possible implications of genome-wide DNA methylation changes in proliferating cells with a view to the maintenance of genomic and epigenomic stability.
Location: Austria
Location: France
Location: France
Start Date: 2016
End Date: 2019
Funder: Agropolis Fondation
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