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Species of the genus Coffea accumulate diterpenes of the ent-kaurane family in the endosperm of their seeds, of which cafestol and kahweol are the most abundant. The diterpenes are mainly stored in esterified form with fatty acids, mostly palmitate. In contrast to the numerous studies on their effects on human health and therapeutic applications, nothing was previously known about their biological and ecological role in planta. The antifungal and anti-insect activities of cafestol and cafestol palmitate were thus investigated in this study. Cafestol significantly affected the mycelial growth of five of the six phytopathogenic fungi tested. It also greatly reduced the percentage of pupation of larvae and the pupae and adult masses of one of the two fruit flies tested. By contrast, cafestol palmitate had no significant effect against any of the fungi and insects studied. Using confocal imaging and oil body isolation and analysis, we showed that diterpenes are localized in endosperm oil bodies, suggesting that esterification with fatty acids enables the accumulation of large amounts of diterpenes in a non-toxic form. Diterpene measurements in all organs of seedlings recovered from whole seed germination or embryos isolated from the endosperm showed that diterpenes are transferred from the endosperm to the cotyledons during seedling growth and then distributed to all organs, including the hypocotyl and the root. Collectively, our findings show that coffee diterpenes are broad-spectrum defence compounds that protect not only the seed on the mother plant and in the soil, but also the seedling after germination.

Background and Aims The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. Methods We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. Key Results A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. Conclusions The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.

For millennia, people have harvested fruits from the wild for their alimentation. Gradually, they have started selecting wild individuals presenting traits of interest, protecting and cultivating them. This was the starting point of their domestication. The passage from a wild to a cultivated status is accompanied by a modification of a number of morphological and genetic traits, commonly known as the domestication syndrome. We studied the domestication syndrome in

Background and Aims Oaks are the foundation and dominant tree species of most Mediterranean forests. As climate models predict dramatic changes in the Mediterranean basin, a better understanding of the ecophysiology of seed persistence and germination in oaks could help define their regeneration niches. Tunisian oaks occupy distinct geographical areas, which differ in their rainfall and temperature regimes, and are thus a valuable model to investigate relationships between seed traits and species ecological requirements. Methods Seed morphological traits, desiccation sensitivity level, lethal freezing temperature, embryonic axis and cotyledon sugar and lipid composition, and seed and acorn germination rates at various constant temperatures were measured in Quercus canariensis, Q. coccifera, Q. ilex and Q. suber, using seeds sampled in 22 Tunisian woodlands. Key Results Only faint differences were observed for desiccation sensitivity in the oak species studied. By contrast, the species differed significantly in sensitivity to freezing, germination rates at low temperature and base temperature. Quercus ilex and Q. canariensis, which occur at high elevations where frost events are frequent, showed the lowest freezing sensitivity. A significant correlation was found between hexose contents in the embryonic axis and freezing tolerance. Significant interspecific differences in the time for seeds to germinate and the time for the radicle to pierce the pericarp were observed. The ratio of pericarp mass to acorn mass differed significantly among the species and was negatively correlated with the acorn germination rate. Quercus coccifera, which is frequent in warm and arid environments, showed the highest acorn germination rate and synchrony. Conclusions Seed lethal temperature, seed germination time at low temperatures, the ratio of pericarp mass to acorn mass and the embryonic axis hexose content appeared to be key functional traits that may influence the geographical ranges and ecological requirements of Mediterranean oaks in Tunisia.

Crude palm oil (CPO) is extracted from the mesocarp of oil palm (Elaeis guineensis) fruits. CPO is widely consumed in many African countries. Due to its high provitamin A carotenoid content, it is also widely used in programmes designed to prevent vitamin A deficiency. Elaeis guineensis occurs naturally across a wide geographical range in Africa. We investigated the carotene, tocochromanol (vitamin E) and fatty acid composition of a large set of genotypes representative of this genetic and geographic diversity. We found considerable intraspecific diversity in most lipid traits. Populations from Côte d'Ivoire were distinguished from other origins by their very low palmitate content and high tocochromanol content. Genotypes from Benin, Côte d'Ivoire and Nigeria were characterized by high carotene contents. Finally, hybrids of crosses between genotypes from Côte d'Ivoire and Nigeria produce CPO with exceptionally high provitamin A and vitamin E contents together with low palmitate content.

Lateral root organogenesis plays an essential role in elaborating plant root system architecture. In Arabidopsis , the AP2 family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify potential targets of PUCHI, we analyzed a time course transcriptomic dataset of lateral root formation. We report that multiple genes coding for very long chain fatty acid (VLCFA) biosynthesis enzymes are induced during lateral root development in a PUCHI-dependent manner. Significantly, several mutants perturbed in VLCFA biosynthesis show similar lateral root developmental defects as puchi-1 . Moreover, puchi-1 roots display the same disorganized callus formation phenotype as VLCFA biosynthesis-deficient mutants when grown on auxin-rich callus-inducing medium. Lipidomic profiling of puchi-1 roots revealed reduced VLCFA content compared with WT. We conclude that PUCHI-regulated VLCFA biosynthesis is part of a pathway controlling cell proliferation during lateral root and callus formation.

Background and aims Palms are vital to worldwide human nutrition, in particular as major sources of vegetable oils. However, our knowledge of seed and fruit lipid diversity in the family Arecaceae is limited. We therefore aimed to explore relationships between seed and fruit lipid content, fatty acid composition in the respective tissues, phylogenetic factors and biogeographical parameters. Methods Oil content and fatty acid composition were characterized in seeds and fruits of 174 and 144 palm species respectively. Distribution, linear regression and multivariate analyses allowed an evaluation of the chemotaxonomic value of these traits and their potential relationship with ecological factors. Key Results A considerable intra-family diversity for lipid traits was revealed. Species with the most lipid-rich seeds belonged to the tribe Cocoseae, while species accumulating oil in the mesocarp occurred in all subfamilies and two-thirds of the tribes studied. Seed and fruit lipid contents were not correlated. Fatty acid composition of mesocarp oil was highly variable within tribes. By contrast, within-tribe diversity for seed lipid traits was low, whereas between-tribe variability was high. Consequently, multivariate analyses of seed lipid traits produced groupings of species belonging to the same tribe. Medium-chain fatty acids predominated in seeds of most palm species, but they were also accumulated in the mesocarp in some cases. Seed unsaturated fatty acid content correlated with temperature at the coldest latitude of natural occurrence. Conclusion Several previously uncharacterized palms were identified as potential new sources of vegetable oils for comestible or non-food use. Seed lipid traits reflect genetic drift that occurred during the radiation of the family and therefore are highly relevant to palm chemotaxonomy. Our data also suggest that seed unsaturated fatty acids may provide an adaptive advantage in the coldest environments colonized by palms by maintaining storage lipids in liquid form for efficient mobilization during germination.

In contrast to desiccation-tolerant ‘orthodox’ seeds, so-called ‘intermediate’ seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds, but they show a considerable variability in seed desiccation tolerance (DT), which may help to decipher the molecular basis of seed DT in plants. We performed a comparative transcriptome analysis of developing seeds in three coffee species with contrasting desiccation tolerance. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were up-regulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, we detected up-regulation of numerous genes involved in the metabolism, transport, and perception of auxin in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT are better prepared to cease respiration and avoid oxidative stresses., Seeds of coffee species that are more tolerant to desiccation display a specific late maturation transcriptional program that primes them to better cease respiration and avoid oxidative stress upon dehydration.

The occurrence of somaclonal variants (ca 5%) among populations of somatic embryo-derived oil palms (Elaeis guineensis Jacq.) currently hampers 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 Sssl-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.

Integrative analysis of developing coffee seeds reveals the key cellular, metabolic, and regulatory processes associated with acquisition of desiccation tolerance in intermediate seeds, The ‘intermediate seed’ category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage and has implications for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone contents, and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis, and respiration, and the up-regulation of genes coding for late-embryogenesis abundant (LEA) proteins, heat-shock proteins (HSPs), and antioxidant enzymes. Analysis of the heat-stable proteome in mature coffee seeds confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggested a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ, and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.

The oil palm (Elaeis guineensis), a monocotyledonous species in the family Arecaceae, has an extraordinarily oil rich fleshy mesocarp, and presents an original model to examine the ripening processes and regulation in this particular monocot fruit. Histochemical analysis and cell parameter measurements revealed cell wall and middle lamella expansion and degradation during ripening and in response to ethylene. Cell wall related transcript profiles suggest a transition from synthesis to degradation is under transcriptional control during ripening, in particular a switch from cellulose, hemicellulose, and pectin synthesis to hydrolysis and degradation. The data provide evidence for the transcriptional activation of expansin, polygalacturonase, mannosidase, beta-galactosidase, and xyloglucan endotransglucosylase/hydrolase proteins in the ripening oil palm mesocarp, suggesting widespread conservation of these activities during ripening for monocotyledonous and eudicotyledonous fruit types. Profiling of the most abundant oil palm polygalacturonase (EgPG4) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) transcripts during development and in response to ethylene demonstrated both are sensitive markers of ethylene production and inducible gene expression during mesocarp ripening, and provide evidence for a conserved regulatory module between ethylene and cell wall pectin degradation. A comprehensive analysis of NAC transcription factors confirmed at least 10 transcripts from diverse NAC domain clades are expressed in the mesocarp during ripening, four of which are induced by ethylene treatment, with the two most inducible (EgNAC6 and EgNAC7) phylogenetically similar to the tomato NAC-NOR master-ripening regulator. Overall, the results provide evidence that despite the phylogenetic distance of the oil palm within the family Arecaceae from the most extensively studied monocot banana fruit, it appears ripening of divergent monocot and eudicot fruit lineages are regulated by evolutionarily conserved molecular physiological processes.

International audience; Coffee grown at high elevations fetches a better price than that grown in lowland regions. This study was aimed at determining whether climatic conditions during bean development affected sensory perception of the coffee beverage and combinations of volatile compounds in green coffee. Green coffee samples from 16 plots representative of the broad range of climatic variations in Réunion Island were compared by sensory analysis. Volatiles were extracted by solid phase micro-extraction and the volatile compounds were analysed by GC-MS. The results revealed that, among the climatic factors, the mean air temperature during seed development greatly influenced the sensory profile. Positive quality attributes such as acidity, fruity character and flavour quality were correlated and typical of coffees produced at cool climates. Two volatile compounds (ethanal and acetone) were identified as indicators of these cool temperatures. Among detected volatiles, most of the alcohols, aldehydes, hydrocarbons and ketones appeared to be positively linked to elevated temperatures and high solar radiation, while the sensory profiles displayed major defects (i.e. green, earthy flavour). Two alcohols (butan-1,3-diol and butan-2,3-diol) were closely correlated with a reduction in aromatic quality, acidity and an increase in earthy and green flavours. We assumed that high temperatures induce accumulation of these compounds in green coffee, and would be detected as off-flavours, even after roasting. Climate change, which generally involves a substantial increase in average temperatures in mountainous tropical regions, could be expected to have a negative impact on coffee quality. (Résumé d'auteur)

Depuis le debut des annees 1990, les semences des cafeiers ont ete adoptees par de nombreux laboratoires internationaux comme le systeme modele pour l’etude de la physiologie des semences de type « intermediaire ». A la difference des semences orthodoxes, dont la longevite augmente lorsqu’elles sont deshydratees et placees a basse temperature, les semences intermediaires ne sont que partiellement tolerantes a la dessiccation et au froid. Dans les plages etroites de teneurs en eau et de temperatures qui peuvent ainsi etre utilisees, la longevite des semences intermediaires est tres reduite, ce qui constitue une contrainte majeure pour la conservation de la biodiversite de ces especes. Le developpement de nouvelles techniques de chimie analytique a permis d’imputer la faible longevite des semences de cafeiers a des dommages cellulaires de plusieurs natures : une hydrolyse des lipides neutres conduisant a une accumulation d’acides gras libres destabilisant les membranes ; la perte selective d’une classe de phospholipides ; une perte et une oxydation des deux principaux antioxydants hydrophiles des cellules, l’acide ascorbique et le glutathion. Grâce a ces nouvelles connaissances sur les processus impliques dans le vieillissement des semences de cafeiers, nous proposons pour la premiere fois dans cet article des recommandations techniques tres precises pour la preparation et le stockage a court terme des lots de semences. Parallelement, grâce a des approches biophysiques, utilisant notamment la microcalorimetrie, la comprehension des mecanismes impliques dans la tolerance des semences de cafeiers a une exposition aux tres basses temperatures a progresse de maniere significative. Sur la base de ces connaissances, une technique de cryoconservation tres efficace a ete mise au point pour ces semences, permettant d’envisager desormais la sauvegarde a long terme des ressources genetiques du genre Coffea.

La saveur du cafe implique le developpement d’aromes lors de la torrefaction a partir de precurseurs biochimiques presents dans la graine de cafeier. La caracterisation des voies de biosynthese des principaux composes de reserve de la graine, ainsi que l’identification des genes cles associes, permet donc d’identifier les determinants moleculaires de la qualite. Cette revue decrit le developpement recent des outils moleculaires et des connaissances genomiques chez le cafeier. A travers la description des travaux de recherche cibles sur la regulation du metabolisme des sucres, des acides chlorogeniques et de la cafeine, les differentes approches de genomique fonctionnelle, et leurs complementarites, sont illustrees.

Micropropagation of oil palm by somatic embryogenesis produces a proportion of off-type individuals (approximately 5% overall) displaying a homeotically modified flower structure known as mantled. Transformation of the fertile or sterile androecium into carpel-like structures is observed in staminate and pistillate mantled flowers, respectively, resulting in lower oil yields in affected plantations. Given the epigenetic nature of the mantled condition, a gene expression-based approach was used rather than a genetic one to investigate its molecular basis. Suppression subtractive hybridisation (SSH) and macroarray hybridisation were used to compare transcriptome patterns between normal and mantled inflorescences. Two SSH libraries, enriched for complementary deoxyribonucleic acids (cDNAs) of either true-to-type or somaclonal variant material, were generated. Bioinformatic analysis of these two libraries allowed the identification of 1,350 unique sequences and their annotation by a gene ontology-based approach. Macroarray hybridisation was used to compare gene expression between normal and mantled inflorescences, and 32 genes were found to be differentially expressed. The temporal expression patterns of six genes were further investigated in more detail in relation to male and female inflorescence development. Full-length cDNAs were isolated and characterised for two of these genes, EgFB1 and EgRING1, both of which are down-regulated in the mantled inflorescences and both of which encode proteins associated with proteolytic signalling complexes. Our data shed light on gene expression changes associated with the mantled phenotype and have provided novel transcriptome markers which can help to distinguish the abnormal and wild-type inflorescences.

The fatty acid (FA) composition of Oenocarpus bataua oil from 38 samples collected over a large geographical range (i.e. French Guiana and Peru) was analyzed. Fifteen fatty acids were obtained from the mesocarp of this palm species. Oleic (72.7%) and palmitic (18.1%) acids were the predominant FAs. Minor FAs were cis-vaccenic acid (2.3%), linoleic acid (1.9%), stearic acid (1.7%), palmitoleic (0.9%) and alpha-linolenic acid (0.8%). The mean lipid content of the dry mesocarp was 51.6%. The O. bataua oil samples analyzed were remarkably rich in α-tocopherol. By contrast, the other fractions of the unsaponifiable matter (sterols, carotenoids) did not show any noteworthy specificity in comparison with common vegetable oils. However, the particularly high percentage in Δ5-avenasterol of O. bataua oil could serve as a marker for its authentication. Results are discussed in terms of the potential nutritional value of O. bataua oil.

Coffee (Coffea spp.) is one of the world?s most valuable agricultural export commodities produced by small-scale farmers. Its germplasm, which holds useful traits for crop improvement, has traditionally been conserved in fi eld genebanks, which presents many challenges for conservation. New techniques of in vitro and cryopreservation have been developed to improve the Long-term conservation of coffee. But a question remains as to whether these new techniques are more cost effective than fi eld collections and more effi cient at reducing genetic erosion. This study compared the costs of maintaining one of the world?s largest coffee fi eld collections with those of establishing a coffee cryo-collection at the Centro Agronómico Tropical de Investigación y Enseñanza (CATIE) in Costa Rica. The results indicate that cryopreservation costs less (in perpetuity per accession) than conservation in fi eld genebanks. A comparative analysis of the costs of both methods showed that the more accessions there are in cryopreservation storage, the lower the peraccession cost. In addition to cost, the study examined the advantages of cryopreservation over fi eld collection and showed that for species that are diffi cult to conserve using seeds, and that can only be conserved as live plants, cryopreservation may be the method of choice for long-term conservation of genetic diversity. Made available in DSpace on 2011-04-09T22:27:55Z (GMT). No. of bitstreams: 1 Costefficiency.pdf: 871770 bytes, checksum: 8bd257ccdbf65f45dffbcc9248c7172a (MD5) Previous issue date: 2011-03-10

With the aim of understanding the molecular mechanisms underlying somatic embryogenesis (SE) in oil palm, we examined transcriptome changes that occur when embryogenic suspension cells are initiated to develop somatic embryos. Two reciprocal suppression subtractive hybridization (SSH) libraries were constructed from oil palm embryogenic cell suspensions: one in which embryo development was blocked by the presence of the synthetic auxin analogue 2,4-dichlorophenoxyacetic acid (2,4-D: ) in the medium (proliferation library); and another in which cells were stimulated to form embryos by the removal of 2,4-D: from the medium (initiation library). A total of 1867 Expressed Sequence Tags (ESTs) consisting of 1567 potential unigenes were assembled from the two libraries. Functional annotation indicated that 928 of the ESTs correspond to proteins that have either no similarity to sequences in public databases or are of unknown function. Gene Ontology (GO) terms assigned to the two EST populations give clues to the underlying molecular functions, biological processes and cellular components involved in the initiation of embryo development. Macroarrays were used for transcript profiling the ESTs during SE. Hierarchical cluster analysis of differential transcript accumulation revealed 4 distinct profiles containing a total of 192 statistically significant developmentally regulated transcripts. Similarities and differences between the global results obtained with in vitro systems from dicots, monocots and gymnosperms will be discussed.

International audience; Global demand for vegetable oils is increasing at a dramatic rate, while our understanding of the regulation of oil biosynthesis in plants remains limited. To gain insights into the mechanisms that govern oil synthesis and fatty acid (FA) composition in the oil palm fruit, we used a multilevel approach combining gene coexpression analysis, quantification of allele-specific expression and joint multivariate analysis of transcriptomic and lipid data, in an interspecific backcross population between the African oil palm, Elaeis guineensis, and the American oil palm, Elaeis oleifera, which display contrasting oil contents and FA compositions. The gene coexpression network produced revealed tight transcriptional coordination of fatty acid synthesis (FAS) in the plastid with sugar sensing, plastidial glycolysis, transient starch storage and carbon recapture pathways. It also revealed a concerted regulation, along with FAS, of both the transfer of nascent FA to the endoplasmic reticulum, where triacylglycerol assembly occurs, and of the production of glycerol-3-phosphate, which provides the backbone of triacylglycerols. Plastid biogenesis and auxin transport were the two other biological processes most tightly connected to FAS in the network. In addition to WRINKLED1, a transcription factor (TF) known to activate FAS genes, two novel TFs, termed NF-YB-1 and ZFP-1, were found at the core of the FAS module. The saturated FA content of palm oil appeared to vary above all in relation to the level of transcripts of the gene coding for b-ketoacyl-acyl carrier protein synthase II. Our findings should facilitate the development of breeding and engineering strategies in this and other oil crops.

International audience; Background and Aims : Dominant tree species in northern temperate forests, for example oak and beech, produce desiccation-sensitive seeds. Despite the potentially major influence of this functional trait on the regeneration and distribution of species under climate change, little is currently known about the ecological determinants of the persistence of desiccation-sensitive seeds in transient soil seed banks. Knowing which key climatic and microsite factors favour seed survival will help define the regeneration niche for species whose seeds display extreme sensitivity to environmental stressMethods : Using the Mediterranean Holm oak (Quercus ilex) forest as a model system, an in situ time-course monitoring of seed water status and viability was performed during the unfavourable winter season in two years with contrasting rainfall, at an instrumented site with detailed climate records. In parallel, the characteristics of the microhabitat and their influence on the post-winter water status and viability of seeds were investigated in a regional survey of 33 woodlands representative of the French distribution of the species.Key Results : Time-course monitoring of seed water status in natural conditions confirmed that in situ desiccation is the main abiotic cause of mortality in winter. Critical water contents could be reached in a few days during drought spells. Seed dehydration rates were satisfactorily estimated using integrative climate proxies including vapour pressure deficit and potential evapotranspiration. Seed water status was therefore determined by the balance between water uptake after a rainfall event and water loss during dry periods. Structural equation modelling of microhabitat factors highlighted the major influence of canopy openness and resulting incident radiation on the ground.Conclusions : This study provides part of the knowledge required to implement species distribution models which incorporate their regeneration niche. It is an important step forward in evaluating the ecological consequences of increasing winter drought and environmental filtering due to climate change on the regeneration of the most dominant Mediterranean tree species.

A study was carried out to investigate the influence of desiccation and freezing followed by various presowing rehydration procedures on the desiccation sensitivity of the seed of Citrus suhuiensis cv. limau madu. The freshly harvested seeds of limau madu were desiccated under a broad range of relative humidity (RH) to various equilibrium water contents (g H2O g(-1) dw). The desiccated and desiccated-frozen seeds were either directly sown under germination conditions or subjected to presowing rehydration procedures: seed preheating, prehumidification and osmoconditioning. The hydrated and desiccated seeds were sown in controlled germination conditions and the survival was evaluated 4-6 weeks after sowing. The results showed that desiccation progressively reduced the percentage of normal seedling of the seeds of limau madu and the viability is almost lost at water contents below 0.08 g H2O g(-1) dw. The estimated desiccation sensitivity was substantially high (WC50 = 0. 143 g H2O g(-1) dw) when the desiccated seeds were rapidly rehydrated (uncontrolled rehydration). In contrast, seed prehumidification, preheating and osmoconditioning (controlled rehydration procedures) markedly enhanced normal seedling percentages decreasing the estimated values of WC50 (between 0.08 and 0. 127 g H2O g(-1) dw). While the rapidly rehydrated desiccated-frozen seeds were almost killed at water content of 0. 15 g H2O g(-1) dw, prehumidification and preheating have noticeably increased percentage of frozen seeds survival at the same water content. However, at water content of 0.21 g H2O g(-1) dw preheating significantly (P < 0.05) increased percentage of normal seedling of the frozen seeds. Seed desiccation markedly reduced the percentages of germinated seeds with multiple seedlings. Seed controlled rehydration remarkably increased the survival of polyembryos. The beneficial effect of seed controlled rehydration on the survival of the desiccated seeds was pronounced at medium water contents (0.08-0.25 g H2O g(-1) dw).

Background The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world’s largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. Methods In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. Results Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. Conclusions Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2023-1) contains supplementary material, which is available to authorized users.

International audience; In the perspective of studying lipid biosynthesis in the argan seed, the anatomy, ploidy level and lipid composition of mature seed tissues were investigated using an experimental design including two locations in Algeria and four years of study. Using flow cytometry, we determined that mature argan seeds consist of two well-developed tissues, the embryo and the endosperm. The lipid content of the embryo was higher than that of the endosperm, but the dry weight of the endosperm was higher. Consequently, both tissues contribute equally to seed oil yield. Considerable differences in fatty acid composition were observed between the two tissues. In particular, the endosperm 18:2 percentage was twofold higher than that of the embryo. The tocopherol content of the endosperm was also markedly higher than that of the embryo. In contrast, the endosperm and the embryo had similar sterol and triterpene alcohol contents and compositions.

Polyploidy impacts the diversity of plant species, giving rise to novel phenotypes and leading to ecological diversification. In order to observe adaptive and evolutionary capacities of polyploids, we compared the growth, primary metabolism and transcriptomic expression level in the leaves of the newly formed allotetraploid Coffea arabica species compared with its two diploid parental species (Coffea eugenioides and Coffea canephora), exposed to four thermal regimes (TRs; 18-14, 23-19, 28-24 and 33-29 degrees C). The growth rate of the allopolyploid C. arabica was similar to that of C. canephora under the hottest TR and that of C. eugenioides under the coldest TR. For metabolite contents measured at the hottest TR, the allopolyploid showed similar behavior to C. canephora, the parent which tolerates higher growth temperatures in the natural environment. However, at the coldest TR, the allopolyploid displayed higher sucrose, raffinose and ABA contents than those of its two parents and similar linolenic acid leaf composition and Chl content to those of C. eugenioides. At the gene expression level, few differences between the allopolyploid and its parents were observed for studied genes linked to photosynthesis, respiration and the circadian clock, whereas genes linked to redox activity showed a greater capacity of the allopolyploid for homeostasis. Finally, we found that the overall transcriptional response to TRs of the allopolyploid was more homeostatic compared with its parents. This better transcriptional homeostasis of the allopolyploid C. arabica afforded a greater phenotypic homeostasis when faced with environments that are unsuited to the diploid parental species.

To understand the mechanisms of sucrose-induced acclimation in relation to plant cryopreservation, sugars, sterols, fatty acids of different lipid fractions (neutral lipids, glycolipids and sphingolipids and phospholipids), as well as free fatty acids were analyzed in proliferating meristern cultures of different banana varieties. The four banana varieties that were selected show different post-thaw shoot regeneration rates (0-53.4%). All mentioned parameters were analyzed using (1) control meristems that were cultured on a normal sucrose concentration (0.09 M), which resulted in low survival after cryopreservation; and (2) 2-week sucrose precultured meristems (0.4 M). This sucrose preculture, essential for regeneration after cryopreservation, resulted in a significant increase of each of seven sugars detected. The ratio of stigmasterol/sitosterol (St/Si) in sucrose-pretreated meristems significantly increased. The sucrose pretreatment also resulted in a significant increase of total fatty acid content of the neutral lipid fraction and of the glycolipid and sphingolipid fraction, as well as the total free fatty acid content. The individual fatty acid content of the phospholipids was differently changed by the sucrose pretreatment for the given varieties studied. In most cases, sucrose pretreatment resulted in an increase of the double bond index DBI in the neutral lipids and a decrease of DBI in the glycolipids and sphingolipids, in phospholipids as well as in free fatty acids. Principal component analysis of all collected data revealed that (1) for the control material, sucrose and total sugar contents were closely linked to the post-thaw shoot regeneration, suggesting that sucrose and total sugar may be main limiting factors to survive cryopreservation; (2) accumulation of large quantities of sugars (glucose, fructose, sucrose and total sugar) in sucrose-pretreated material cannot explain the differences in survival after cryopreservation of the four banana varieties. We assume that a minimal amount of sugars is needed in meristern cultures to survive cryopreservation. Still, other limiting factors do influence the survival following the sucrose pretreatment. We observed that the parameters which are closely linked to the post-thaw shoot regeneration are a minimal change in the ratios of St/Si, the minimal change of the DBI of phospholipids and free fatty acids, as well as linoleic acid content (C18:2); and (3) inositol, raffinose, myristic acid (C14:0) and oleic acid (C18:1) were present in small quantities; however, they could be correlated to survival after cryopreservation, suggesting that they may be also involved in cryopreservation process.

The biochemical and physiological basis of intermediate seed storage behaviour was examined by investigating the effects of equilibrium drying under relative humidities (RHs) of 9-81% and of storage at 20 or 5 degrees C on coffee seed viability and antioxidant, lipid and sugar status. Slow drying induced a significant decrease in the concentrations of the pools of two major antioxidants, glutathione and ascorbate, and an increase in the free fatty acid (FFA) content of seeds, independent of the RH employed. Seeds stored at 81% RH and 20 degrees C lost their viability very rapidly and showed an extensive loss and oxidation of antioxidants, an accumulation of FFA and a selective loss of phospholipids, in particular phosphatidylethanolamine (PE). Interestingly, the changes in PE content were not due to fatty acid de-esterification and the increase in FFA levels resulted from neutral lipid hydrolysis. Decreasing the storage temperature to 5 degrees C considerably slowed both the loss of seed viability and the level of oxidative stress as well as the rates of lipid hydrolysis. No decline in seed viability was observed under storage conditions of 45% RH/20 degrees C. After 1 year under 45% RH/5 degrees C, the loss of seed viability was found to be due to imbibitional damage and could be circumvented by pre-humidifying or pre-heating seeds before sowing.

A robust spectroscopic method for determining total antioxidant activity in aqueous extractions has been applied to tissues from diverse woody plant species, including seeds of Coffea arabica and in vitro shoots from Ribes nigrum, Picea sitchensis and Shorea leprosula. The assay involves scavenging of an ABTS [2,2'-azinobis-(3-ethyl-benzothiazoline-6-sulphonic acid)] radical generated by the reaction of potassium persulphate with ABTS to produce an ABTS*(+) chromophore (lambda=734 nm). Antioxidants reduce ABTS*(+) back to ABTS with a concomitant decrease in absorbance. Aqueous extractions from C. arabica and S. leprosula had considerably higher (110-205 micromol Trolox eq. g(-1) FW) total antioxidant activities than P. sitchensis and R. nigrum (6-11 micromol Trolox eq. g(-1) FW). Further studies in two of these species showed that the inclusion of water-insoluble polyvinylpyrrolidone during aqueous tissue extraction enabled the combined phenolic and alkaloid antioxidant activity to be determined. These fractions accounted for 85% and 60% of total antioxidant activity for C. arabica seeds and R. nigrum shoots, respectively. The ABTS radical scavenging assay is presented herein as a robust method for determining total antioxidant activity in germplasm from diverse woody plant tissues and species. Its applicability to study oxidative stress in tissue cultures and germplasm employed in plant biotechnology, breeding and stress physiology programmes is discussed.

Chlorogenic acids, sensu largo (CGA), are secondary metabolites of great economic importance in coffee: their accumulation in green beans contributes to coffee drink bitterness. Previous evaluations have already focussed on wild species of coffee trees, but this assessment included six new taxa from Cameroon and Congo and involved a simplified method that generated more accurate results. Five main results were obtained: (1) Cameroon and Congo were found to be a centre of diversity, encompassing the entire range of CGA content from 0.8% to 11.9% dry matter basis (dmb); (2) three groups of coffee tree species – CGA1, CGA2 and CGA3 – were established on the basis of discontinuities; (3) means were 1.4%, 5.6% and 9.9% dmb, respectively; (4) there was a qualitative relationship between caffeine and ACG content distribution; (5) only a small part of the CGA is trapped by caffeine as caffeine chlorogenate.

Caffeine is a metabolite of great economic importance, especially in coffee. Previous evaluations have already focussed on wild species of coffee trees, but this assessment included six new taxa from Cameroon and Congo and involved a simplified method that generated more accurate results. Two main results were obtained: (1) Cameroon and Congo were found to be a centre of diversity, encompassing the entire range of caffeine content; (2) four groups of coffee tree species – CAF1, CAF2, CAF3 and CAF4 – were established on the basis of discontinuities in the caffeine content range. The trace levels of caffeine in CAF1 is due to an absence of accumulation in beans – a factor that is controlled by a major gene. The other classes, i.e., CAF2, CAF3 and CAF4, were characterized by the extents of their caffeine accumulation. Caffeine content was found to increase twofold from CAF2 (0.55% dmb) to CAF3 (1.1% dmb) and from CAF3 to CAF4 (2.3% dmb). This discontinuous distribution is discussed from an evolutionary standpoint.

Genetic diversity among 40 accessions (Coffea canephora) of robusta coffee genepool available in India was determined in comparison with 14 representative samples from a C. canephora core collection and three accessions of C. congensis, using amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Both these molecular approaches were able to generate unique fingerprints for each of the accessions analysed. All the 12 SSR primers used in the present study were found polymorphic, with an average of six alleles per primer pair. Comparative analysis revealed the higher amount of diversity in representatives from a core collection than in the Indian genepool. Moreover, a total of 205 polymorphic AFLP bands were scored in all the 57 accessions analysed. The genetic relationship among 57 accessions was compared on the basis of SSR and AFLP polymorphisms. Genetic similarity dendrograms showed high correlation between the two marker systems. This study clearly established the high amount of diversity present in core samples, which is not represented in Indian genepool. Furthermore, the three accessions of C. congensis did not exhibit any significant diversity from other robusta accessions supporting the school of thought that C. congensis forms a biotype of C. canephora. The potential use of SSRs and AFLP markers in genetic diversity analysis for better ex situ management and also for exploitation of diversity in breeding programmes is discussed.

• Background and Aims The purpose of this study was to investigate the basis of the optimal hydration status for cryopreservation of intermediate oily seeds using Citrus as a model. • Methods The relationships between equilibrium relative humidity (RH), seed water content, presence of freezable water as determined by DSC analysis, and germination percentage after immersion in liquid nitrogen (LN) were investigated in Citrus aurantifolia, C. grandis, C. madurensis and C. reticulata. The relationship between the lipid content of seeds and their unfrozen water content was also investigated. • Key Results Independent of their level of seed desiccation tolerance, the optimal desiccation RH for seed tolerance to LN exposure was 75–80 % in the four species studied. This optimal hydration status always coincided with that at which presence of frozen water could not be detected in seed tissues during the cooling/thawing process. The unfrozen water content of seeds was variable between species and negatively correlated to seed lipid content. Using the present data, those obtained previously in seven coffee species and those reported by other authors for five other species, a significant linear relationship was found between the lipid content and the unfrozen water content of seeds. • Conclusions This study provides additional evidence that intermediate oily seeds do not withstand the presence of freezable water in their tissues during the cooling/warming process. Moreover, it offers two important applied perspectives: (1) independent of their level of desiccation tolerance, testing germination of seeds of a given oily seed species after equilibration in 75–80 % RH at 25 °C and LN exposure, gives a rapid and reliable evaluation of the possibility of cryopreserving whole seeds of this given species; (2) it is now possible to calculate the interval of water contents in which non-orthodox oily seeds of a given species are likely to withstand LN exposure as a function of their lipid content.

Trigonelline and sucrose are two coffee aroma precursors. Contents of these compounds are higher in Coffea arabica than in Coffea canephora green beans and this could be the main explanation for consumers' preference for C. arabica coffee. This is the first evaluation of sucrose and trigonelline contents involving 14 species and six new taxa not yet botanically characterised. Trigonelline and sucrose contents varied between species from 0.39% to 1.77% dry matter basis (dmb) and from 3.8% to 10.7% dmb, respectively. C. canephora could be improved through both compounds by crosses with Coffea eugenioides.

The genetic determinism of seed desiccation sensitivity was studied using a cross between two coffee species exhibiting a large difference for this trait, Coffea pseudozanguebariae (tolerant) and C. liberica (sensitive). Throughout the whole study, seed desiccation tolerance was quantified both in terms of water content and water activity. Whatever the parameter used, the level of seed desiccation tolerance in F1 hybrids corresponded to that of the mid-parent, thus indicating an additive inheritance of seed desiccation tolerance at the F1 level. A broad variation was observed among hybrids backcrossed to C. liberica (BCs) for seed desiccation tolerance, independent of the parameter used to quantify it. This variation was continuous and BCs showed transgression in the direction of the most desiccation sensitive parent, indicating (i) that desiccation tolerance is a polygenic trait in coffee species, and (ii) that C. pseudozanguebariae does not present the most favourable alleles for all the genes involved in seed desiccation tolerance. No significant difference was observed between the two reciprocal backcrosses, F1xC. liberica and C. libericaxF1, for the level of desiccation tolerance of their seeds, showing the absence of a maternal effect on this trait. There was no significant effect of the number of seeds harvested from each BC on the level of desiccation tolerance of its seeds. Moreover, there was no significant correlation within BCs between seed size, seed viability, and water content before desiccation and desiccation tolerance.

Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution. Science , this issue p. 1181 ; see also p. 1124

Numerous aroma precursor evaluations have been undertaken with green coffee beans of both species of worldwide economic importance: Coffea arabica L. and Coffea canephora P. Efforts have been made to characterise cultivars of these two species. The originality of this study is to present the biochemical diversity of wild accessions originating from Ethiopia and Kenya for C. arabica (38 genotypes) and from five African countries (Cote d'Ivoire, Guinea, Congo, Cameroon and Central African Republik) for C. canephora (38 genotypes). The biochemical aroma parameters assessed by HPLC analysis were: (1) the two alkaloids, caffeine and trigonelline, (2) chlorogenic acids and (3) sucrose. Results reveal that the two species showed significant accession differences for all compounds. Between-species-average-content comparison confirms that C. arabica showed more trigonelline and sucrose and that C. canephora presented more CGA and caffeine. C. canephora diversity was higher than that of C. arabica, except for trigonelline and sucrose. For C. canephora, results showed that: (1) no differences were highlighted between accessions for countries of origin for the alkaloids and sucrose, and (2) the 3-CQA content allowed to accessions to be pooled into two groups.

Large differences in seed desiccation sensitivity have been observed previously among ten coffee species (Coffea arabica, C. brevipes, C. canephora, C. eugenioides, C. humilis, C. liberica, C. pocsii, C. pseudo-zanguebariae, C. sessiliflora and C.stenophylla). Of these species,C. libericaandC. humiliswere the most sensitive to desiccation andC. pseudozanguebariaethe most tolerant. A study was carried out using the same seed lots to investigate if these differences in desiccation tolerance could be correlated with differences in soluble sugar content. Soluble sugars were extracted from dry seeds and analysed using high performance liquid chromatography. The seed monosaccharide (glucose and fructose) content was very low (1.5 to 2 mg g-1dry weight [dw]) in all species studied. The sucrose content ranged from 33 mg g-1dw inC. libericaseeds to 89 mg g-1dw in seeds ofC. pocsii. Raffinose was detected in the seeds of only five species (C.arabica, C.brevipes, C.humilis, C.sessiliflora, C.stenophylla), among which only three species (C.arabica, C.sessilifloraandC.brevipes) also contained stachyose. Both raffinose and stachyose were present in very low quantities (0.3–1.4 mg g-1dw and 0.1–0.7 mg g-1dw, respectively). Verbascose was never detected. No significant relationship was found between seed desiccation sensitivity and: (i) the sugar content; (ii) the presence/absence of oligosaccharides; and (iii) the oligosaccharide:sucrose ratio.

A broad variability for seed desiccation sensitivity, as quantified by the water content and the water activity at which half of the initial viability is lost, has been previously observed within nine African coffee species. In order to investigate if these different degrees of desiccation sensitivity correspond to an adaptive trait, additional data, such as the duration of seed development and seed water content at maturity, were measured for these species, and the relationships between these parameters and some climatic characteristics of their specific native environments were investigated. Since flowering in all coffee species occurs only a few days after the main rainfall marking the end of the dry season, simulations could be made, based on the continuous sequences of rainfall data compiled in databases of nine climatic stations, chosen for their appropriate location in the collecting areas. The simulations revealed a highly significant correlation between the duration of seed development and that of the wet season. Consequently, mature seeds are shed at the beginning of the following dry season. Moreover, the mean number of dry months that seeds have to withstand after shedding was significantly correlated with the parameters used to quantify seed desiccation sensitivity. By contrast, seed moisture content at maturity was not correlated with the level of seed desiccation tolerance. All these results are discussed on the basis of more detailed descriptions of the natural habitats of the coffee species studied.

Nineteen arabica coffee introgression lines (BC1F4) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between #Coffea arabica$ (2n=4x=44) and #C. canephora$ (2n=2x=22) were analysed for the introgression of #C. canephora$ genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of #C. arabica$ and 8 accessions of #C. canephora$. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the Timor Hybrid-derived genotypes from the accessions of #C. arabica$. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection of introgression in #C. arabica$. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in #C. arabica$. Although representing only a small proportion of the genetic diversity available in #C. canephora$, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee introgressed gentotypes were estimated to represent from 9% to 29% of the #C. canephora$ genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should justify the development of adapted breeding strategies. (Résumé d'auteur)

Seed desiccation sensitivity was studied in nine species of the genus Coffeaby measuring seed viability after equilibration over various saturated salt solutions. A quantal response model based on the logistic distribution was developed in order to describe the typical S-shaped patterns observed. The closeness of fit of the desiccation sensitivity model was shown, and the assumption that seed desiccation sensitivity follows a continuous distribution within species was verified. For each species, the water content at which 50% of initial viability was reached, WC50, and a specific parameter describing the intra-specific variability, β, were calculated using a non-linear regression. A simplified water sorption model was developed which allowed easy calculation of water activity and water potential corresponding to WC50 (aw50 and Ψ50) for relative humidities ranging between 10 and 100%. Distribution of WC50and Ψ50 (or aw50) in the genus Coffea was homogeneous within the following intervals: from 0.05 to 0.38 g H2O.g−1dw for WC50 and from −168 to −11 MPa for Ψ50. Different classifications of the coffee species studied as regards to their desiccation sensitivity were obtained depending on whether WC50 or Ψ50was used for classification. The continuum for desiccation sensitivity observed within the nine species studied confirmed that coffee is an appropriate material for studying desiccation sensitivity.

International audience; The seed of Coffea arabica accumulates large amounts of cell wall storage polysaccharides (CWSPs) of the mannan family in the cell walls of the endosperm. The variability induced by the growing environment and extensive pairwise correlation analysis with stringent significance thresholds was used to investigate transcript-transcript and transcript-metabolite relationships among 26 sugar-related genes, and the amount of CWSPs and seven soluble low molecular weight carbohydrates in the developing coffee endosperm. A dense module of nine quantitatively co-expressed genes was detected at the mid-developmental stage when CWSPs accumulate. This module included the five genes of the core galactomannan synthetic machinery, namely genes coding for the enzymes needed to assemble the mannan backbone (mannan synthase, ManS), and genes that introduce the galactosyl side chains (galactosyltransferase, GMGT), modulate the post-depositional degree of galactose substitution (?-galactosidase), and produce the nucleotide sugar building blocks GDP-mannose and UDP-galactose (mannose-1P guanyltransferase and UDP-glucose 4'-epimerase, respectively). The amount of CWSPs stored in the endosperm at the onset of their accumulation was primarily and quantitatively modulated at the transcriptional level (i.e. positively correlated with the expression level of these key galactomannan biosynthetic genes). This analysis also suggests a role for sorbitol and raffinose family oligosaccharides as transient auxiliary sources of building blocks for galactomannan synthesis. Finally, a microarray-based analysis of the developing seed transcriptome revealed that all genes of the core galactomannan synthesis machinery grouped in a single cluster of 209 co-expressed genes. Analysis of the gene composition of this cluster revealed remarkable functional coherence and identified transcription factors that putatively control galactomannan biosynthesis in coffee. (Résumé d'auteur)

Phosphoenolpyruvate Carboxylase (PEPC; EC: 4.1.1.31) and Ribulose 1,5-bisphosphate Carboxylase/Oxygenase (RubisCO; EC: 4.1.1.39) enzyme specific activities were measured during the in vitro development of coconut (Cocos nucifera L.) zygotic mature embryos into plantlets and compared with those of palms produced by conventional seed germination. At the time of initiation of germination, high PEPC and low RubisCO activities were measured in both cultured and conventionally germinated embryos, thus indicating an anaplerotic CO2 fixation. During both in vitro and in planta development, RubisCO progressively took over and became the main route for inorganic carbon fixation. The in vitro-grown coconut plantlets showed a faster decrease in their PEPC:RubisCO ratio than the seedlings, suggesting that an earlier transition from a heterotrophic to an autotrophic mode of carbon fixation takes place in the in vitro-derived material. Just before acclimatization, the RubisCO activity in in vitro-derived plantlets (2.83 µmol CO2h−1mg−1 TSP) was lower than that in seedlings (6.98 µmol CO2h−1mg−1 TSP) of the same age. Nevertheless, after acclimatization, RubisCO activities were comparable in both in vitro and in planta germinated material

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 subdivided into three independent subclonal lines. Once established, cultures proliferated for 12 months and genomic DNA was sampled 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.

UMR AGAP - équipe ID - Intégration des données; Oil palm (Elaeis guineensis) produces two oils of major economic importance, commonly referred to as palm oil and palm kernel oil, extracted from the mesocarp and the endosperm, respectively. While lauric acid predominates in endosperm oil, the major fatty acids (FAs) of mesocarp oil are palmitic and oleic acids. The oil palm embryo also stores oil, which contains a significant proportion of linoleic acid. In addition, the three tissues display high variation for oil content at maturity. To gain insight into the mechanisms that govern such differences in oil content and FA composition, tissue transcriptome and lipid composition were compared during development. The contribution of the cytosolic and plastidial glycolytic routes differed markedly between the mesocarp and seed tissues, but transcriptional patterns of genes involved in the conversion of sucrose to pyruvate were not related to variations for oil content. Accumulation of lauric acid relied on the dramatic up-regulation of a specialized acyl-acyl carrier protein thioesterase paralog and the concerted recruitment of specific isoforms of triacylglycerol assembly enzymes. Three paralogs of the WRINKLED1 (WRI1) transcription factor were identified, of which EgWRI1-1 and EgWRI1-2 were massively transcribed during oil deposition in the mesocarp and the endosperm, respectively. None of the three WRI1 paralogs were detected in the embryo. The transcription level of FA synthesis genes correlated with the amount of WRI1 transcripts and oil content. Changes in triacylglycerol content and FA composition of Nicotiana benthamiana leaves infiltrated with various combinations of WRI1 and FatB paralogs from oil palm validated functions inferred from transcriptome analysis.

In the present study, the efficiency of two cryopreservation strategies for oil palm (Elaeis guineensis Jacq.) was compared. If extracted from rehydrated kernels, 65% of the embryos desiccated to around 0.3 g H2O/g DW developed into plantlets after cryopreservation. In contrast, only 25% of embryos (0.12 g H2O/g DW) extracted from cryopreserved dry kernels developed into plantlets. However, this value was increased to 63% if kernels were partially rehydrated before freezing until the water content of embryos reached 0.3 g H2O/g DW. This study emphasizes the importance of partial rehydration of oil palm embryos before cryopreservation.