Identification et analyse des bases moléculaires du processus d’abscission du fruit chez le palmier à huile (Elaeis guineensis)

Plant organ abscission is a complex developmental process that involves cell separation regulated by the environment, stress, pathogens and the physiological status of the plant. In particular, seed and fruit abscission play a central role in seed dispersion and plant reproductive success, and are common domestication traits with important agronomic consequences for many crop species. Oil palm (Elaeis guineensis) is cultivated throughout the tropical regions as one of the most economically important oil crop species in the world. The unsynchronized ripening of the oil palm fruit bunch leads to the abscission of the ripest fruit and consequently high labor cost for harvest and loss of yield. In this context, the control of oil palm ripe fruit abscission is an important agricultural concern for the cultivation of oil palm in a sustainable and cost effective way. In the present study, a protocol to phenotype the oil palm fruit abscission process was developed and used to identify a tree in the field that does not undergo ripe fruit abscission. In parallel, transcriptome and proteome analyses of the oil palm ripe fruit abscission zone (AZ) during abscission induced experimentally by ethylene compared to the AZ undergoing natural abscission in the field was performed. A total of 1,957 candidate genes were identified statistically as differentially expressed in the ripe fruit AZ during ethylene-induced abscission. Furthermore, a total of 64 of these differentially abundant candidates were statistically specific or enriched at least during one time point of the ethylene induced abscission, compared to their profiles in the AZ of immature fruit and the pedicel of ripe fruit, where cell separation is not observed. The profiles of these gene candidates were examined in the ripe fruit AZ undergoing natural abscission in the field to validate their potential role during abscission. Finally, the profiles of selected candidate genes were then examined in the AZ of the tree observed not to undergo fruit abscission in the field. The combined approaches provide evidence of wide scale conservation of the molecular components involved in organ abscission of this monocot compared with the model dicot plants tomato and Arabidopsis. For example, the identification of polygalacturonases very similar to those that function during Arabidopsis floral organ abscission suggests a conservation of the components for pectin disassembly despite the phylogenetic distance between these species. In addition, the data from the global analysis and complementary molecular, cellular and biochemical approaches suggest novel components and provide a robust list of genes and processes important for AZ function during ripe fruit abscission of this important monocot crop species.L’abscission des organes chez les végétaux est hautement régulée au cours du développement. Ce processus physiologique qui consiste à diminuer l’adhésion entre deux cellules adjacentes dépend de l’environnement, du stress, de l’attaque de pathogènes ou encore de l’état physiologique de la plante. L’abscission du fruit et de la graine jouent un rôle déterminant dans le cycle de vie de la plante et en particulier, un rôle central dans la dispersion des graines. C’est également un caractère commun de domestication avec des conséquences économiques pour la plus part des espèces cultivées. Le palmier à huile (Elaeis guineensis) est largement cultivé dans toutes les zones tropicales et l’huile de palme représente aujourd’hui plus d’un tiers des huiles végétales produites dans le monde. La maturation des fruits au sein des régimes est asynchrone. Ainsi, les fruits les plus murs tombent avant le murissement complet du régime, entrainant une baisse du rendement d’une part et rendant leur collecte manuelle fastidieuse et couteuse d’autre part. Dans ce context, le contrôle ou la réduction de la chute des fruits permettrait une meilleure gestion de la récolte à des couts réduits. Dans le cadre de cette étude, un protocole de phénotypage du processus d’abscission du fruit du palmier à huile a été développé et utilisé pour identifier des génotypes à faible ou retard d’abscision des fruits arrivés à maturité. En parallèle, des analyses comparatives de transcriptomes et de protéomes issus de la zone d’abscission (ZA) du fruit ont été conduites tout au long du processus de séparation cellulaire, déclenché au laboratoire par un traitement à l’éthylène ou bien de manière naturelle au champ. Au total 1957 gènes présentent une expression différentielle significative dans la ZA du fruit au cours du processus d’abscission induit par l’éthylène. Parmi ces gènes, 64 sont spécifiquement (ou majoritairement) exprimés dans la ZA des fruits arrivés à maturité par comparaison avec les tissus où le processus de séparation cellulaire n’est pas observé (pédicelle et mésocarpe des fruits murs ; ZA non fonctionnelle des fruits immatures). Le profil d’expression de ces 64 gènes candidats a été également analysé dans la ZA des fruits mûrs prélevés au champ, afin de conforter leur rôle potentiel au cours de l’abscission déclenchée naturellement. Ainsi, en utilisant les nouvelles technologies de séquençage du transcriptome et du protéome, couplées à une analyse biochimique et cellulaire des modifications de la paroi dans la ZA, ce travail a permis de mettre en évidence la conservation de certains processus moléculaires associés à l’abscission des organes chez les monocotylédones par comparaison avec les espèces modèles dicotylédones, telles que la tomate et Arabidopsis. Par exemple, l’identification de gènes codant des polygalacturonases très proches de celles qui sont impliquées dans l’abscission de la fleur chez Arabidopsis suggère la conservation de leur fonction dans l’hydrolyse de la pectine des cellules des ZA, malgré la divergence phylogénétique entre les espèces. Enfin, ce travail a permis également d’identifier de nouveaux régulateurs associés au processus de séparation cellulaire et fournir une liste de gènes associés à des processus biologiques étroitement liés à la fonction de la ZA chez le fruit du palmier à huile

Conservation of the abscission signaling peptide IDA during Angiosperm evolution: withstanding genome duplications and gain and loss of the receptors HAE/HSL2

International audienceThe peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species

Transcriptome Analysis of Cell Wall and NAC Domain Transcription Factor Genes during Elaeis guineensis Fruit Ripening: Evidence for Widespread Conservation within Monocot and Eudicot Lineages

International audienceThe oil palm (Elaeis guineensis), a monocotyledonous species in the familyArecaceae, 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 inducedby 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 appearsripening of divergent monocot and eudicot fruit lineages are regulated by evolutionarily conserved molecular physiological processes

Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

International audienceBackground: Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Results: Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. Conclusions: The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process