Going mainstream: how is the body axis of plants first initiated in the embryo?, Dev Biol, vol.419, pp.78-84, 2016. ,
Totipotency: what it is and what it is not, Stem Cells Dev, vol.23, issue.8, pp.796-812, 2014. ,
Molecular features of cellular reprogramming and development, Nat Rev Mol Cell Biol, vol.17, issue.3, pp.139-54, 2016. ,
Cell totipotency: molecular features, induction, and maintenance, Natl Sci Rev, vol.2, issue.2, pp.217-242, 2015. ,
Somatic embryogenesis: life and death processes during apical-basal patterning, J Exp Bot, vol.65, issue.5, pp.1343-60, 2014. ,
Somatic embryogenesis and plant regeneration in the culture of Arabidopsis Thaliana (L.) Heynh. Immature zygotic embryos, Methods Mol Biol, vol.710, pp.257-65, 2011. ,
A protocol for obtaining embryogenic cell lines from Arabidopsis, Plant J, vol.9, issue.4, pp.573-580, 1996. ,
Somatic embryogenesis in cultured immature zygotic embryos and leaf protoplasts of Arabidopsis Thaliana ecotypes, Planta, vol.202, issue.3, pp.387-96, 1997. ,
The Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1 gene is expressed in developing ovules and embryos and enhances embryogenic competence in culture, Plant Physiol, vol.127, issue.3, pp.803-819, 2001. ,
The multiple roles of arabinogalactan proteins in plant development, Plant Physiol, vol.122, issue.1, pp.3-10, 2000. ,
The role of cell wall in plant embryogenesis, Cell Mol Biol Lett, vol.7, pp.1137-51, 2002. ,
Auxin-induced WUS expression is essential for embryonic stem cell renewal during somatic embryogenesis in Arabidopsis, Plant J, vol.59, issue.3, pp.448-60, 2009. ,
Gene regulation by the AGL15 transcription factor reveals hormone interactions in somatic embryogenesis, Plant Physiol, vol.172, issue.4, pp.2374-87, 2016. ,
The role of chromatin modifications in somatic embryogenesis in plants, Front Plant Sci, vol.6, p.635, 2015. ,
PRC2 represses hormone-induced somatic embryogenesis in vegetative tissue of Arabidopsis Thaliana, PLoS Genet, vol.13, issue.1, p.1006562, 2017. ,
The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis Thaliana, Nat Protoc, vol.6, issue.1, pp.56-68, 2011. ,
Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles, Nat Protoc, vol.12, issue.2, pp.238-54, 2017. ,
LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development, Proc Natl Acad Sci U S A, vol.98, issue.20, pp.11806-11817, 2001. ,
Embryogenic potential and expression of embryogenesis-related genes in conifers are affected by treatment with a histone deacetylase inhibitor, Planta, vol.234, issue.3, pp.527-566, 2011. ,
The Theobroma Cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation, BMC Plant Biol, vol.14, p.106, 2014. ,
Induced expression of AtLEC1 and AtLEC2 differentially promotes somatic embryogenesis in transgenic tobacco plants, PLoS One, vol.8, issue.8, p.71714, 2013. ,
Classification and clustering of sequencing data using a Poisson model, Ann Appl Stat, vol.5, issue.4, pp.2493-518, 2011. ,
Global scale transcriptome analysis of Arabidopsis embryogenesis in vitro, BMC Genomics, vol.16, p.301, 2015. ,
Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells, Cell, vol.93, issue.7, pp.1195-205, 1998. ,
Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: implications for somatic embryogenesis, Proc Natl Acad Sci U S A, vol.105, issue.8, pp.3151-3157, 2008. ,
Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis, Proc Natl Acad Sci, vol.103, issue.9, pp.3468-73, 2006. ,
Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth, Plant Cell, vol.14, issue.8, pp.1737-1786, 2002. ,
Arabidopsis EMBRYOMAKER encoding an AP2 domain transcription factor plays a key role in developmental change from vegetative to embryonic phase, Plant Mol Biol, vol.73, issue.4-5, pp.481-92, 2010. ,
The BABY BOOM transcription factor activates the LEC1-ABI3-FUS3-LEC2 network to induce somatic embryogenesis, Plant Physiol, vol.175, pp.848-57, 2017. ,
The AP2/ERF transcription factor WIND1 controls cell dedifferentiation in Arabidopsis, Curr Biol, vol.21, issue.6, pp.508-522, 2011. ,
PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis, Nat Plants, vol.1, p.15089, 2015. ,
Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation, Plant Sci, vol.238, pp.251-61, 2015. ,
Mechanisms of pattern formation in plant embryogenesis, Annu Rev Genet, vol.38, pp.587-614, 2004. ,
Comparative transcriptome analysis between somatic embryos (SEs) and zygotic embryos in cotton: evidence for stress response functions in SE development, Plant Biotechnol J, vol.12, issue.2, pp.161-73, 2014. ,
Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos, Nature, vol.482, issue.7383, pp.94-101, 2012. ,
Modulation of embryo-forming capacity in culture through the expression of Brassica genes involved in the regulation of the shoot apical meristem, J Exp Bot, vol.61, issue.14, pp.4069-85, 2010. ,
Ectopic expression of the Brassica SHOOTMERISTEMLESS attenuates the deleterious effects of the auxin transport inhibitor TIBA on somatic embryo number and morphology, Plant Sci, vol.180, issue.2, pp.383-90, 2011. ,
Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium Hirsutum L.) tissues cultured in vitro, Plant Cell Rep, vol.32, issue.5, pp.675-86, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01004075
Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem, Cell, vol.95, issue.6, pp.805-820, 1998. ,
The development of apical embryonic pattern in Arabidopsis, Development, vol.125, issue.16, pp.3027-3062, 1998. ,
Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo, Development, vol.135, issue.17, pp.2839-2882, 2008. ,
Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis Thaliana, Development, vol.131, issue.3, pp.657-68, 2004. ,
A molecular framework for the embryonic initiation of shoot Meristem stem cells, Dev Cell, vol.40, issue.3, pp.264-77, 2017. ,
Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes, Curr Biol, vol.13, issue.20, pp.1768-74, 2003. ,
Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots, Nature, vol.411, issue.6838, pp.709-722, 2001. ,
Gene expression map of the Arabidopsis shoot apical meristem stem cell niche, Proc Natl Acad Sci U S A, vol.106, issue.12, pp.4941-4947, 2009. ,
Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems, Science, vol.283, issue.5409, pp.1911-1915, 1999. ,
Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities, Development, vol.131, issue.12, pp.2997-3006, 2004. ,
Establishment of polarity in lateral organs of plants, Curr Biol, vol.11, issue.16, pp.1251-60, 2001. ,
, Curr Opin Plant Biol, vol.12, issue.5, pp.593-601, 2009.
Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication, PLoS Genet, vol.11, issue.2, p.1004980, 2015. ,
Arabidopsis JAGGED LATERAL ORGANS acts with ASYMMETRIC LEAVES2 to coordinate KNOX and PIN expression in shoot and root meristems, Plant Cell, vol.24, issue.7, pp.2917-2950, 2012. ,
AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks, Trends Plant Sci, vol.19, issue.3, pp.146-57, 2014. ,
Three Arabidopsis AIL/PLT genes act in combination to regulate shoot apical meristem function, Plant J, vol.71, issue.1, pp.108-129, 2012. ,
Arabidopsis regeneration from multiple tissues occurs via a root development pathway, Dev Cell, vol.18, issue.3, pp.463-71, 2010. ,
A high-resolution root spatiotemporal map reveals dominant expression patterns, Science, vol.318, issue.5851, pp.801-807, 2007. ,
The NAC domain transcription factors FEZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells, Dev Cell, vol.15, issue.6, pp.913-935, 2008. ,
SOMBRERO, BEARSKIN1, and BEARSKIN2 regulate root cap maturation in Arabidopsis, Plant Cell, vol.22, issue.3, pp.640-54, 2010. ,
Conservation and diversification of the SHR-SCR-SCL23 regulatory network in the development of the functional endodermis in Arabidopsis shoots, Mol Plant, vol.9, issue.8, pp.1197-209, 2016. ,
AtWuschel promotes formation of the embryogenic callus in Gossypium Hirsutum, PLoS One, vol.9, issue.1, p.87502, 2014. ,
Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo, Dev Biol, vol.341, issue.1, pp.95-113, 2010. ,
The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis, Plant J, vol.30, issue.3, pp.349-59, 2002. ,
Conserved factors regulate signalling in Arabidopsis Thaliana shoot and root stem cell organizers, Nature, vol.446, issue.7137, pp.811-815, 2007. ,
Reconstructing regulatory network transitions, Trends Cell Biol, vol.21, issue.8, pp.442-51, 2011. ,
WOX5 is shining in the root stem cell niche, Trends Plant Sci, vol.20, issue.10, pp.601-604, 2015. ,
Divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms, Regeneration, vol.4, issue.3, pp.132-141, 2017. ,
Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27, Plant Cell, vol.23, issue.11, pp.4065-78, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01000017
Plant callus: mechanisms of induction and repression, Plant Cell, vol.25, issue.9, pp.3159-73, 2013. ,
A demonstration of the recovery of the crown-gall tumor cell with the use of complex tumors of single-cell origin, Proc Natl Acad Sci, vol.45, issue.7, pp.932-940, 1959. ,
Floral dip: a simplified method for Agrobacteriummediated transformation of Arabidopsis Thaliana, Plant J, vol.16, issue.6, pp.735-778, 1998. ,
A gateway cloning vector set for highthroughput functional analysis of genes in planta, Plant Physiol, vol.133, issue.2, pp.462-471, 2003. ,
Analysis of relative gene expression data using real-time quantitative PCR and the 2(?Delta Delta C(T)) method, Methods, vol.25, issue.4, pp.402-410, 2001. ,
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, issue.24, pp.3211-3218, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00748990
Fast gapped-read alignment with bowtie 2, Nat Methods, vol.9, issue.4, pp.357-366, 2012. ,
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res, vol.40, issue.10, pp.4288-97, 2012. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, issue.12, p.550, 2014. ,
The antagonistic development of endosperm and nucellus in Arabidopsis seeds, Plant Cell, vol.28, pp.1343-60, 2016. ,