J. Verdeil, L. Alemanno, N. Niemenak, and T. J. Tranbarger, Pluripotent versus totipotent plant stem cells: Dependence versus autonomy?, Trends Plant Sci, vol.12, pp.245-252, 2007.

, Int. J. Mol. Sci, vol.20, p.4665, 2019.

M. Ikeuchi, A. Iwase, B. Rymen, H. Harashima, M. Shibata et al., PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis

F. Zeng, X. Zhang, S. Jin, L. Cheng, S. Liang et al., Chromatin reorganization and endogenous auxin/cytokinin dynamic activity during somatic embryogenesis of cultured cotton cell, Plant Cell Tissue Organ Cult, vol.90, pp.63-70, 2007.

J. Reinert, Morphogenese und ihre Kontrolle an Gewebekulturen aus Carotten, Naturwissenschaften, vol.45, pp.344-345, 1958.

F. C. Steward, M. O. Mapes, and K. Mears, Growth and Organized Development of Cultured Cells. II. Organization in Cultures Grown from Freely Suspended Cells, Am. J. Bot, vol.45, pp.705-708, 1958.

X. Yang, X. Zhang, D. Yuan, F. Jin, Y. Zhang et al., Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton, BMC Plant Biol, vol.12, 2012.

Y. Indoliya, P. Tiwari, A. S. Chauhan, R. Goel, M. Shri et al., Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies, Sci. Rep, 2016.

M. D. Gaj, S. Zhang, J. J. Harada, and P. G. Lemaux, Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis, Planta, vol.222, pp.977-988, 2005.

M. Lelu-walter, D. Thompson, L. Harvengt, L. Sanchez, M. Toribio et al., Somatic embryogenesis in forestry with a focus on Europe: State-of-the-art, benefits, challenges and future direction, Tree Genet. Genomes, vol.9, pp.883-899, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268045

H. Etienne, Somatic embryogenesis protocol: Coffee (Coffea arabica L. and C. canephora P.). In Protocols for Somatic Embryogenesis in Woody Plants

S. M. Jain and P. K. Gupta, , pp.167-179, 2005.

S. N. Maximova, L. Alemanno, A. Young, N. Ferriere, A. Traore et al., Efficiency, genotypic variability, and cellular origin of primary and secondary somatic embryogenesis of Theobroma cacao L, In Vitro Cell. Dev. Biol. Plant, vol.38, pp.252-259, 2002.

I. A. Montalbán, N. De-diego, and P. Moncaleán, Enhancing initiation and proliferation in radiata pine (Pinus radiata D. Don) somatic embryogenesis through seed family screening, zygotic embryo staging and media adjustments, Acta Physiol. Plant, vol.34, pp.451-460, 2012.

E. Corredoira, A. Ballester, M. Ibarra, and A. M. Vieitez, Induction of somatic embryogenesis in explants of shoot cultures established from adult Eucalyptus globulus and E. saligna × E. maidenii trees, Tree Physiol, vol.35, pp.678-690, 2015.

E. Corredoira, S. Valladares, and A. M. Vieitez, Morphohistological analysis of the origin and development of somatic embryos from leaves of mature Quercus robur, In Vitro Cell. Dev. Biol. Plant, vol.42, pp.525-533, 2006.

A. F. Ribas, E. Dechamp, A. Champion, B. Bertrand, M. Combes et al., Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures, BMC Plant Biol, vol.11, 2011.

M. Ikeuchi, Y. Ogawa, A. Iwase, and K. Sugimoto, Plant regeneration: Cellular origins and molecular mechanisms, Development, vol.143, pp.1442-1451, 2016.

K. Boutilier, G. C. Angenent, M. S. Castan, L. H. Hui, and . Embryogenesis, , 2016.

X. Yang and X. Zhang, Regulation of Somatic Embryogenesis in Higher Plants, Crit. Rev. Plant Sci, vol.29, pp.36-57, 2010.

S. Jayasankar, B. R. Bondada, Z. Li, and D. J. Gray, Comparative Anatomy and Morphology of Vitis vinifera (Vitaceae) Somatic Embryos from Solid-and Liquid-Culture-Derived Proembryogenic Masses, Am. J. Bot, vol.90, pp.973-979, 2003.

V. Raghavan, Role of 2,4-dichlorophenoxyacetic acid (2,4-D) in somatic embryogenesis on cultured zygotic embryos of Arabidopsis: Cell expansion, cell cycling, and morphogenesis during continuous exposure of embryos to 2,4-D, Am. J. Bot, vol.91, pp.1743-1756, 2004.

, Int. J. Mol. Sci, vol.20, pp.4665-4691, 2019.

S. L. Florez, R. L. Erwin, S. N. Maximova, M. J. Guiltinan, and W. R. Curtis, Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor, BMC Plant Biol, vol.15, 2015.

N. A. Campos, B. Panis, and S. C. Carpentier, Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities. Front, Plant Sci, vol.8, 1460.

J. M. Bonga, K. K. Klimaszewska, and P. Von-aderkas, Recalcitrance in clonal propagation, in particular of conifers, Plant Cell Tissue Organ Cult, vol.100, pp.241-254, 2010.

H. Etienne, D. Breton, J. Breitler, B. Bertrand, E. Déchamp et al., Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones from the Two Cultivated Species? Front, Plant Sci, vol.9, 1630.

V. Aguilar-hernández and V. M. Loyola-vargas, Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis. Front, Plant Sci, vol.9, 1658.

M. S. Pais, Somatic Embryogenesis Induction in Woody Species: The Future After OMICs Data Assessment, Front. Plant Sci, vol.10, p.240, 2019.

O. Fiehn, J. Kopka, P. Dörmann, T. Altmann, R. N. Trethewey et al., Metabolite profiling for plant functional genomics, Nat. Biotechnol, vol.18, pp.1157-1161, 2000.

E. Businge, K. Brackmann, T. Moritz, and U. Egertsdotter, Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies), Tree Physiol, vol.32, pp.232-244, 2012.

A. R. Robinson, R. Dauwe, N. K. Ukrainetz, I. F. Cullis, R. White et al., Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics, Plant Biotechnol. J, vol.7, pp.952-963, 2009.

I. Dobrowolska, E. Businge, I. N. Abreu, T. Moritz, and U. Egertsdotter, Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies), Tree Physiol, vol.37, pp.1752-1766, 2017.

Z. Vondrakova, P. I. Dobrev, B. Pesek, L. Fischerova, M. Vagner et al., Profiles of Endogenous Phytohormones Over the Course of Norway Spruce Somatic Embryogenesis. Front, Plant Sci, vol.9, 1283.

F. Gautier, P. Label, K. Eliá?ová, J. Leplé, V. Motyka et al., Biochemical and Molecular Events of the Embryogenic State in Douglas-fir (Pseudotsuga menziesii, Front. Plant Sci, vol.10, 2019.

B. Bertrand, C. Montagnon, F. Georget, P. Charmetant, and H. Etienne, Création et diffusion de variétés de caféiers Arabica: Quelles innovations variétales? Cah, vol.21, pp.77-88, 2012.

J. P. Ducos, G. Labbe, C. Lambot, and V. Pétiard, Pilot scale process for the production of pre-germinated somatic embryos of selected robusta (Coffea canephora) clones, In Vitro Cell. Dev. Biol. Plant, vol.43, pp.652-659, 2007.

H. Etienne, B. Bertrand, C. Montagnon, R. Bodadilla-landey, E. Dechamp et al., Un exemple de transfert de technologie réussi dans le domaine de la micropropagation: La multiplication de Coffea arabica par embryogenèse somatique, Cah. Agric, vol.21, pp.115-124, 2012.

J. P. Ducos, R. Alenton, J. F. Reano, C. Kanchanomai, A. Deshayes et al., Agronomic performance of Coffea canephora P. trees derived from large-scale somatic embryo production in liquid medium, Euphytica, vol.131, pp.215-223, 2003.

R. B. Landey, A. Cenci, F. Georget, B. Bertrand, G. Camayo et al., High Genetic and Epigenetic Stability in Coffea arabica Plants Derived from Embryogenic Suspensions and Secondary Embryogenesis as Revealed by AFLP, MSAP and the Phenotypic Variation Rate, PLoS ONE, issue.8, p.56372, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268002

F. Georget, P. Courtel, E. M. Garcia, M. Hidalgo, E. Alpizar et al., Somatic embryogenesis-derived coffee plantlets can be efficiently propagated by horticultural rooted mini-cuttings: A boost for somatic embryogenesis, Sci. Hortic, vol.216, pp.177-185, 2017.

, Int. J. Mol. Sci, vol.20, pp.4665-4692, 2019.

J. Verdeil, V. Hocher, C. Huet, F. Grosdemange, J. Escoute et al., Ultrastructural changes in coconut calli associated with the acquisition of embryogenic competence, Ann. Bot, vol.88, pp.9-18, 2001.

P. Talamond, J. Verdeil, and G. Conéjéro, Secondary metabolite localization by autofluorescence in living plant cells, Molecules, vol.20, pp.5024-5037, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01141100

C. Díaz-sala, Molecular Dissection of the Regenerative Capacity of Forest Tree Species: Special Focus on Conifers, Front. Plant Sci, vol.9, 1943.

K. Sugimoto, L. Xu, U. Paszkowski, and M. Hayashi, Multifaceted Cellular Reprogramming at the Crossroads Between Plant Development and Biotic Interactions, Plant Cell Physiol, vol.59, pp.651-655, 2018.

L. Tao, Y. Zhao, Y. Wu, Q. Wang, H. Yuan et al., Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim, Gene, vol.578, pp.17-24, 2016.

J. Trontin, K. Klimaszewska, A. Morel, C. Hargreaves, and M. Lelu-walter, Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights, Methods Mol. Biol, vol.1359, pp.167-207, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01269052

K. Nowak, B. Wójcikowska, and M. Gaj, ERF022 impacts the induction of somatic embryogenesis in Arabidopsis through the ethylene-related pathway, Planta, vol.241, pp.967-985, 2015.

M. A. Zavattieri, A. M. Frederico, M. Lima, R. Sabino, and B. Arnholdt-schmitt, Induction of somatic embryogenesis as an example of stress-related plant reactions, Electro. J. Biotech, vol.13, pp.12-13, 2010.

G. I. Nic-can, R. M. Galaz-Ávalos, C. De-la-peña, A. Alcazar-magaña, K. Wrobel et al., Somatic Embryogenesis: Identified Factors that Lead to Embryogenic Repression. A Case of Species of the Same Genus, PLoS ONE, vol.10, 2015.

A. Gomez-garay, J. A. Lopez, E. Camafeita, M. A. Bueno, and B. Pintos, Proteomic perspective of Quercus suber somatic embryogenesis, J. Proteom, vol.93, pp.314-325, 2013.

R. De-carvalho-silva, L. S. Carmo, Z. G. Luis, L. P. Silva, J. E. Scherwinski-pereira et al., Proteomic identification of differentially expressed proteins during the acquisition of somatic embryogenesis in oil palm, Elaeis guineensis Jacq.). J. Proteom, vol.104, pp.112-127, 2014.

C. Xu, H. Cao, E. Xu, S. Zhang, and Y. Hu, Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation, Plant Cell Physiol, vol.59, pp.744-755, 2018.

A. M. Gatica-arias, G. Arrieta-espinoza, and A. M. Espinoza-esquivel, Plant regeneration via indirect somatic embryogenesis and optimisation of genetic transformation in Coffea arabica L. cvs. Caturra and Catuaí, Electron. J. Biotechnol, vol.11, pp.1-12, 2008.

M. S. Pádua, L. V. Paiva, L. C. Silva, K. G. Livramento, E. Alves et al., Morphological characteristics and cell viability of coffee plants calli, Ciênc. Rural, vol.44, pp.660-665, 2014.

A. T. Silva, D. Barduche, K. G. Do-livramento, W. Ligterink, and L. V. Paiva, Characterization of a Putative Serk-Like Ortholog in Embryogenic Cell Suspension Cultures of Coffea arabica L, Plant Mol. Biol. Rep, vol.32, pp.176-184, 2014.

N. Neves, M. Segura-nieto, M. A. Blanco, M. Sánchez, A. González et al., Biochemical characterization of embryogenic and non-embryogenic calluses of sugarcane, In Vitro Cell. Dev. Biol. Plant, vol.39, pp.343-345, 2003.

M. Jeyaseelan and M. V. Rao, Biochemical studies of embryogenic and non-embryogenic callus of Cardiospermum halicacabum L, Indian J. Exp. Biol, vol.43, pp.555-560, 2005.

D. Vestman, E. Larsson, D. Uddenberg, J. Cairney, D. Clapham et al., Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression, BMC Proc, vol.5, 2011.

C. Guillou, A. Fillodeau, E. Brulard, D. Breton, S. De-faria-maraschin et al., Indirect somatic embryogenesis of Theobroma cacao L. in liquid medium and improvement of embryo-to-plantlet conversion rate, In Vitro Cell. Dev. Biol. Plant, vol.54, pp.377-391, 2018.

X. Liang, L. Zhang, S. K. Natarajan, and D. F. Becker, Proline mechanisms of stress survival, Antioxid. Redox Signal, vol.19, pp.998-1011, 2013.

E. Magnani, J. M. Jiménez-gómez, L. Soubigou-taconnat, L. Lepiniec, and E. Fiume, Profiling the onset of somatic embryogenesis in Arabidopsis, vol.18, 2017.

V. Aderkas, P. Lelu, M. Label, and P. , Plant growth regulator levels during maturation of larch somatic embryos, Plant Physiol. Biochem, vol.39, pp.495-502, 2001.

Y. Su, Y. Liu, and X. Zhang, Auxin-Cytokinin Interaction Regulates Meristem Development, Mol. Plant, vol.4, pp.616-625, 2011.

P. R. White, Potentially Unlimited Growth of Excised Plant Callus in an Artificial Nutrient, Am. J. Bot, vol.26, pp.59-64, 1939.

F. Skoog and C. O. Miller, Chemical regulation of growth and organ formation in plant tissues cultured in vitro, Symp. Soc. Exp. Biol, vol.11, pp.118-130, 1957.

F. Bourgaud, A. Gravot, S. Milesi, and E. Gontier, Production of plant secondary metabolites: A historical perspective, Plant Sci, vol.161, pp.839-851, 2001.

Y. Guan, S. Li, X. Fan, and Z. Su, Application of Somatic Embryogenesis in Woody Plants, Front. Plant Sci, vol.7, p.938, 2016.

V. G. Ladygin, N. I. Bondarev, G. A. Semenova, A. A. Smolov, O. V. Reshetnyak et al., Chloroplast ultrastructure, photosynthetic apparatus activities and production of steviol glycosides in Stevia rebaudiana in vivo and in vitro, Biol. Plant, vol.52, pp.9-16, 2008.

A. M. Ali, M. E. El-nour, and S. M. Yagi, Total phenolic and flavonoid contents and antioxidant activity of ginger (Zingiber officinale Rosc.) rhizome, callus and callus treated with some elicitors, J. Genet. Eng. Biotechnol, vol.16, pp.677-682, 2018.

F. Ge, H. Hu, X. Huang, Y. Zhang, Y. Wang et al., Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo

H. Svobodová, J. Albrechtová, L. Kumstý?ová, H. Lipavská, M. Vágner et al., Somatic embryogenesis in Norway spruce: Anatomical study of embryo development and influence of polyethylene glycol on maturation process, Plant Physiol. Bioch, vol.37, pp.209-221, 1999.

L. Fischerova, L. Fischer, Z. Vondrakova, and M. Vagner, Expression of the gene encoding transcription factor PaVP1 differs in Picea abies embryogenic lines depending on their ability to develop somatic embryos, Plant Cell Rep, vol.27, pp.435-441, 2008.

D. Iraqi and F. M. Tremblay, Analysis of carbohydrate metabolism enzymes and cellular contents of sugars and proteins during spruce somatic embryogenesis suggests a regulatory role of exogenous sucrose in embryo development, J. Exp. Bot, vol.52, pp.2301-2311, 2001.

V. L. Dodeman, G. Ducreux, and M. Kreis, Zygotic embryogenesis versus somatic embryogenesis, J. Exp. Bot, vol.48, pp.1493-1509, 1997.

M. C. Pedroso, N. Primikirios, K. A. Roubelakis-angelakis, and M. S. Pais, Free and conjugated polyamines in embryogenic and non-embryogenic leaf regions of camellia leaves before and during direct somatic embryogenesis, Physiol. Plant, vol.101, pp.213-219, 1997.

S. C. Grace and B. A. Logan, Energy dissipation and radical scavenging by the plant phenylpropanoid pathway, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.355, pp.1499-1510, 2000.

S. S. Gill and N. Tuteja, Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants, Plant Physiol. Biochem, vol.48, pp.909-930, 2010.

M. Ikeda-iwai, M. Umehara, S. Satoh, and H. Kamada, Stress-induced somatic embryogenesis in vegetative tissues of Arabidopsis thaliana, Plant J, vol.34, pp.107-114, 2003.

F. Dethloff, A. Erban, I. Orf, J. Alpers, I. Fehrle et al., Profiling methods to identify cold-regulated primary metabolites using gas chromatography coupled to mass spectrometry, Methods Mol. Biol, vol.1166, pp.171-197, 2014.

A. Erban, N. Schauer, A. R. Fernie, and J. Kopka, Nonsupervised construction and application of mass spectral and retention time index libraries from time-of-flight gas chromatography-mass spectrometry metabolite profiles, Methods Mol. Biol, vol.358, pp.19-38, 2007.

A. Luedemann, K. Strassburg, A. Erban, and J. Kopka, TagFinder for the quantitative analysis of gas chromatography-Mass spectrometry (GC-MS)-based metabolite profiling experiments, Bioinformatics, vol.24, pp.732-737, 2008.

J. Kopka, N. Schauer, S. Krueger, C. Birkemeyer, B. Usadel et al., DB: The Golm Metabolome Database, Bioinformatics, vol.21, pp.1635-1638, 2005.

, Int. J. Mol. Sci, vol.20, pp.4665-4694, 2019.

N. Strehmel, J. Hummel, A. Erban, K. Strassburg, and J. Kopka, Retention index thresholds for compound matching in GC-MS metabolite profiling, J. Chromatogr. B, vol.871, pp.182-190, 2008.

C. Campa, L. Urban, L. Mondolot, D. Fabre, S. Roques et al., Juvenile Coffee Leaves Acclimated to Low Light Are Unable to Cope with a Moderate Light Increase. Front
URL : https://hal.archives-ouvertes.fr/ird-01599877

N. R. Canada, Plant Hormone Profiling, p.20, 2019.

M. M. Lulsdorf, H. Y. Yuan, S. M. Slater, A. Vandenberg, X. Han et al., Endogenous hormone profiles during early seed development of C. arietinum and C. anatolicum. Plant Growth Regul, vol.71, pp.191-198, 2013.

N. Chauvaux, W. Van-dongen, E. L. Esmans, and H. A. Van-onckelen, Quantitative analysis of 1-aminocyclopropane-1-carboxylic acid by liquid chromatography coupled to electrospray tandem mass spectrometry, J. Chromatogr. A, vol.775, pp.143-150, 1997.

. R-core-team, R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing, 2019.

C. Cheadle, M. P. Vawter, W. J. Freed, and K. G. Becker, Analysis of Microarray Data Using Z Score Transformation, J. Mol. Diagn, vol.5, pp.73-81, 2003.

Z. Gu, R. Eils, and M. Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data, Bioinformatics, vol.32, pp.2847-2849, 2016.

. Cran-package and . Pvclust, , p.20, 2019.

R. Suzuki and H. Shimodaira, Pvclust: An R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.22, pp.1540-1542, 2006.

. Metaboanalyst, , p.19, 2019.