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International audience; Ethanol is known to accumulate in various plant organs under various environmental conditions. However, there are very scarce data about ethanol sensing by plants. We observed that ethanol accumulates up to 3.5 mM during tomato seed imbibition, particularly when seeds were stacked. Stacked seeds germinated less than spread out seeds suggesting ethanol inhibits germination. In support of this, exogenous ethanol at physiological concentrations, ranging from 1 to 10 mM, inhibited germination of wild type tomato seeds. However, the germination pattern over the whole ethanol concentration range tested was modified in an ethylene insensitive mutant, never-ripe (nr). The effects of exogenous ethanol were not linked to differences in ethylene production by imbibed seeds. But, we observed that exogenous ethanol at a concentration as low as 0.01 mM down regulated the expression of some ethylene receptors. Moreover, the triple response induced by ethylene in tomato seedlings was partially alleviated by 1 mM ethanol. Similar observations were made on Arabidopsis seeds. These results show there are interactions between ethylene sensing and ethanol in plants.

International audience; MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3 , both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling high-lighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development.

WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat (Triticum turgidum L. subsp. Durum). A PCR-based screening of a T. turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands within oceans of TEs. Each BAC clone harbored a TdWRKY gene. The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum. The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4, TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, and IIc, respectively. Enrichment of cis-regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles in mediating plant responses to a wide variety of environmental stresses. The four TdWRKY genes displayed different expression patterns in response to the salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation in tolerant genotype leaves. The TdWRKY transcripts levels in roots increased in tolerant genotype compared to sensitive genotype. The present results indicate that these genes might play some functional role in the salt tolerance in durum wheat.

International audience; Two transgenic lines of 'Cantaloupe' melon derived from the same wild type genotype were previouslygenerated using ACC oxidase antisense constructs from melon (pMEL1AS) and apple (pAP4AS). Both linesyielded fruit with reduced ethylene production and low ACC oxidase (ACCO) expression. ACCO antisensefruit also exhibited lower expression of ACC synthase genes, ACCS1 and ACCS3, indicating that these genesare positively regulated by ethylene and participate in the autocatalytic ethylene production process. Incontrast, a higher expression of ACCS5 was observed in antisense lines when compared to the wild typeindicating a negative feedback regulation of ACCS5 by ethylene. Fruit of both transformed lines exhibiteddelayed ripening and reduction in ester volatile production but differed in their response to exogenousethylene supply. While postharvest ethylene application fully restored the ripening process in pMEL1ASmelon, it only restored flesh softening of pAP4AS melon but not rind color change or aroma volatile pro-duction. Up-regulation of lipoxygenase pathway associated genes (hydroxyperoxide lyase, lipoxygenase,and alcohol acyl transferases 1, 3 and 4) occurred in ethylene-treated pMEL1AS fruit but not in pAP4ASmelons. Polygalacturonase1 gene transcript accumulation increased in pMEL1AS and pAP4AS fruit uponethylene supply. Zeatin and zeatin riboside content of roots and fruit (rind and flesh) of pAP4AS plantswere 5-fold higher than the wild type and pMEL1AS counterparts. Higher relative transcript accumula-tion of a gene involved in the cytokinin synthesis and a gene involved in cytokinin response were alsofound in the roots and fruit of pAP4AS. In addition, polyamines, which are known to reduce sensitiv-ity to ethylene, remained unchanged in all fruit. Collectively the results suggest a putative role for theincreased endogenous cytokinin content in counteracting ethylene action in some aspects of the fruitripening process.

SPE EA BIOME IPM UB INRA; International audience; Pyoverdines are siderophores synthesized by fluorescent Pseudomonas spp. Under iron-limiting conditions, these high-affinity ferric iron chelators are excreted by bacteria in the soil to acquire iron. Pyoverdines produced by beneficial Pseudomonas spp. ameliorate plant growth. Here, we investigate the physiological incidence and mode of action of pyoverdine from Pseudomonas fluorescens C7R12 on Arabidopsis (Arabidopsis thaliana) plants grown under iron-sufficient or iron-deficient conditions. Pyoverdine was provided to the medium in its iron-free structure (apo-pyoverdine), thus mimicking a situation in which it is produced by bacteria. Remarkably, apo-pyoverdine abolished the iron-deficiency phenotype and restored the growth of plants maintained in the iron-deprived medium. In contrast to a P. fluorescens C7R12 strain impaired in apo-pyoverdine production, the wild-type C7R12 reduced the accumulation of anthocyanins in plants grown in iron-deficient conditions. Under this condition, apo-pyoverdine modulated the expression of around 2,000 genes. Notably, apo-pyoverdine positively regulated the expression of genes related to development and iron acquisition/redistribution while it repressed the expression of defense-related genes. Accordingly, the growth-promoting effect of apo-pyoverdine in plants grown under iron-deficient conditions was impaired in iron-regulated transporter1 and ferric chelate reductase2 knockout mutants and was prioritized over immunity, as highlighted by an increased susceptibility to Botrytis cinerea This process was accompanied by an overexpression of the transcription factor HBI1, a key node for the cross talk between growth and immunity. This study reveals an unprecedented mode of action of pyoverdine in Arabidopsis and demonstrates that its incidence on physiological traits depends on the plant iron status.

International audience; Most of the world’s wine-producing regions are subjected to seasonal drought,and,in the light of the dramatic climate-change events occurring in recent years, the selection of resistant rootstocks is becoming a crucial factor for the development of sustainable agricultural models to ensure optimal grape berry development and ripening. In this study, roots and leaves of 101.14 (drought-susceptible) and M4 (drought-tolerant) rootstocks were sampled in progressive drought and mRNA-seq profiles were evaluated. Physiological characterization indicated that only M4 was able to maintain high leaf transpiration and net assimilation rates under severe stress conditions. Statistical analyses, carried out on mRNA-seq data, highlighted that “treatment” (water stress) and “genotype” (rootstock-genotype) seem to be the main variables explaining differential gene expression in roots and leaves tissues, respectively. Upon water-stress, roots and leaves of the tolerant genotype M4 exhibit a higher induction of stilbenes (i.e., STS) and flavonoids (e.g., CHS, F3H, FLS) biosynthetic genes. Moreover, the higher expression of STS genes in M4 is coupled with an up-regulation of WRKYs transcription factors. STS genes promoter regions, extracted from whole genome of M4 and 101.14, highlighted a higher number of WBOX cis elements (binding site for WRKYs) in the tolerant genotype.

International audience; Our knowledge of the factors mediating ethylene-dependent ripening of climacteric fruit remains limited. The transcription of ethylene-regulated genes is mediated by ethylene response factors (ERFs), but mutants providing information on the specific role of the ERFs in fruit ripening are still lacking, likely due to functional redundancy among this large multigene family of transcription factors. We present here a comprehensive expression profiling of tomato (Solanum lycopersicum) ERFs in wild-type and tomato ripening-impaired tomato mutants (Never-ripe [Nr], ripening-inhibitor [rin], and non-ripening [nor]), indicating that out of the 77 ERFs present in the tomato genome, 27 show enhanced expression at the onset of ripening while 28 display a ripeningassociated decrease in expression, suggesting that different ERFs may have contrasting roles in fruit ripening. Among the 19 ERFs exhibiting the most consistent up-regulation during ripening, the expression of 11 ERFs is strongly down-regulated in rin, nor, and Nr tomato ripening mutants, while only three are consistently up-regulated. Members of subclass E, SlERF.E1, SlERF.E2, and SlERF.E4, show dramatic down-regulation in the ripening mutants, suggesting that their expression might be instrumental in fruit ripening. This study illustrates the high complexity of the regulatory network connecting RIN and ERFs and identifies subclass E members as the most active ERFs in ethylene- and RIN/NOR-dependent ripening.

Highlights Drought tolerance in the M4 grapevine rootstock genotype could be associated with a higher capability to counteract oxidative stresses by enhancing the accumulation of resveratrol in roots., In light of ongoing climate changes in wine-growing regions, the selection of drought-tolerant rootstocks is becoming a crucial factor for developing a sustainable viticulture. In this study, M4, a new rootstock genotype that shows tolerance to drought, was compared from a genomic and transcriptomic point of view with the less drought-tolerant genotype 101.14. The root and leaf transcriptome of both 101.14 and the M4 rootstock genotype was analysed, following exposure to progressive drought conditions. Multifactorial analyses indicated that stress treatment represents the main factor driving differential gene expression in roots, whereas in leaves the genotype is the prominent factor. Upon stress, M4 roots and leaves showed a higher induction of resveratrol and flavonoid biosynthetic genes, respectively. The higher expression of VvSTS genes in M4, confirmed by the accumulation of higher levels of resveratrol in M4 roots compared with 101.14, was coupled to an up-regulation of several VvWRKY transcription factors. Interestingly, VvSTS promoter analyses performed on both the resequenced genomes highlighted a significantly higher number of W-BOX elements in the tolerant genotype. It is proposed that the elevated synthesis of resveratrol in M4 roots upon water stress could enhance the plant’s ability to cope with the oxidative stress usually associated with water deficit.

Background Tomato fruit ripening is controlled by ethylene and is characterized by a shift in color from green to red, a strong accumulation of lycopene, and a decrease in β-xanthophylls and chlorophylls. The role of other hormones, such as auxin, has been less studied. Auxin is retarding the fruit ripening. In tomato, there is no study of the carotenoid content and related transcript after treatment with auxin. Results We followed the effects of application of various hormone-like substances to “Mature-Green” fruits. Application of an ethylene precursor (ACC) or of an auxin antagonist (PCIB) to tomato fruits accelerated the color shift, the accumulation of lycopene, α-, β-, and δ-carotenes and the disappearance of β-xanthophylls and chlorophyll b. By contrast, application of auxin (IAA) delayed the color shift, the lycopene accumulation and the decrease of chlorophyll a. Combined application of IAA + ACC led to an intermediate phenotype. The levels of transcripts coding for carotenoid biosynthesis enzymes, for the ripening regulator Rin, for chlorophyllase, and the levels of ethylene and abscisic acid (ABA) were monitored in the treated fruits. Correlation network analyses suggest that ABA, may also be a key regulator of several responses to auxin and ethylene treatments. Conclusions The results suggest that IAA retards tomato ripening by affecting a set of (i) key regulators, such as Rin, ethylene and ABA, and (ii) key effectors, such as genes for lycopene and β-xanthophyll biosynthesis and for chlorophyll degradation. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0495-4) contains supplementary material, which is available to authorized users.

International audience; Ultraviolet-C (UV-C) radiation is used as a postharvest treatment to prolong the shelf life of fruit.However, this stressful process may also affect ethylene production and, consequently, the expression of genes encoding ethylene response factors (ERFs). To test this hypothesis, MicroTom tomatoes harvested at the breaker stage were subjected to: 1 – application of 3.7 kJ m-2 UV-C radiation, 2 – application of 2 µLL-1 1-methylcyclopropene (1-MCP) followed by UV-C radiation; and 3 – without 1-MCP or UV-C (control treatment). After treatment all fruit were stored for 12 d at 21 +/- 2C° and 80 +/- 5% relative humidity (RH). Although UV-C radiation increased ACC oxidase transcripts and stimulated ethylene production, the ripening evolution was delayed. Fruit treated with UV-C showed lower accumulation of lycopene, b-carotene, lutein + zeaxanthin and d-tocopherol; but retained higher levels of chlorogenic acid, r-coumaric acid and quercetin after 6 d. Additionally, UV-C treated fruit had higher contents of polyamines (putrescine and spermidine). Among the 14 ERFs studied, 11 (Sl-ERF A.1, Sl-ERF A.3,Sl-ERF B.1, Sl-ERF B.2, Sl-ERF B.3, Sl-ERF C.6, Sl-ERF D.1, Sl-ERF D.3, Sl-ERF E.1, Sl-ERF F.5, Sl-ERF G.2) exhibited increased transcript accumulation, 2 ERFs (Sl-ERF E.2 and Sl-ERF E.4) showed decreased transcript accumulation and only 1 ERF (Sl-ERF E.3) was not significantly affected by UV-C treatment. As expected, the transcript profiles of 1-MCP and/or UV-C-treated tomatoes demonstrate that ethylene plays an important role in the expression of ERFs. The delay in fruit ripening may be caused by the activation of ERFs that could act as regulators of metabolic pathways during ripening. However, this hypothesis needs to be better tested. In conclusion, a relationship has been established between UV-C treatment and ripening delay, correlated to changes in 13 ERF transcripts evaluated during postharvest treatment.

International audience; Parthenocarpy is a desired trait in fruit crops; it enables fruit set under environmental conditions suboptimal for pollination, and seedless fruits represent a valuable consumer product. We employed TILLING-based screening of a mutant tomato population to find genetic lesions in Aux/IAA9, a negative regulator of the auxin response involved in the control of fruit set. We identified three mutations located in the coding region of this gene, including two singlebase substitutions and one single-base deletion, which leads to a frame shift and premature stop codon. The transcription of IAA9 was strongly reduced in the frame-shift mutant, and partial loss of mutated protein activity was evidenced by an in vitro transactivation assay. Whereas missense mutations were predicted to be tolerated and did not cause mutant phenotypes, the frame-shift mutation-induced phenotypes expected for a loss of IAA9 function, including altered axillary shoot growth, reduced leaf compoundness and a strong tendency to produce parthenocarpic fruits. Mutant flowers showed pleiotropic anther cone defects, a phenotype frequently associated with parthenocarpy in tomato and other species. Mutant fruits were larger than those of the seeded control, with higher brix

[EN] All-flesh tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Here, we show that SlMBP3 is a master regulator of locular tissue in tomato fruit and that a deletion at the gene locus underpins the All-flesh trait. Intriguingly, All-flesh varieties lack the deleterious phenotypes reported previously for SlMBP3 under-expressing lines and which preclude any potential commercial use. We resolve the causal factor for this phenotypic divergence through the discovery of a natural mutation at the SlAGL11 locus, a close homolog of SlMBP3. Misexpressing SlMBP3 impairs locular gel formation through massive transcriptomic reprogramming at initial phases of fruit development. SlMBP3 influences locule gel formation by controlling cell cycle and cell expansion genes, indicating that important components of fruit softening are determined at early pre-ripening stages. Our findings define potential breeding targets for improved texture in tomato and possibly other fleshy fruits. The all-flesh type of tomato fruits is caused by mutation of the MBP3 gene, however, knocking down MBP3 in certain genotypes also affect plant and fruit development. Here, the authors show that a natural mutation of AGL11, a close homolog of MBP3, is responsible for the phenotypic divergence., The authors are grateful to L. Lemonnier and D. Saint-Martin for transformation and cultivation of tomato plants and GeT-PlaGe core facility (INRAe Toulouse) for ChIP deep sequencing. The authors also want to thank Dr. Christian Chevalier (INRAE et Univsersite de Bordeaux) for helping in analyzing genes related to cell cycle, cell division, and endoreduplication in tomato. This research was supported by the EU H2020 TomGEM 679796 and HARNESSTOM 101000716 projects.

Highlight text A mutation in the plum auxin-receptor encoded by PslAFB5, which acts as a negative regulator of auxin responses, results in inactive Pslafb5 protein causing accelerated fruit-ontogeny events associated with auxin hypersensitivity., Ethylene has long been considered the key regulator of ripening in climacteric fruit. Recent evidence showed that auxin also plays an important role during fruit ripening, but the nature of the interaction between the two hormones has remained unclear. To understand the differences in ethylene- and auxin-related behaviours that might reveal how the two hormones interact, we compared two plum (Prunus salicina L.) cultivars with widely varying fruit development and ripening ontogeny. The early-ripening cultivar, Early Golden (EG), exhibited high endogenous auxin levels and auxin hypersensitivity during fruit development, while the late-ripening cultivar, V98041 (V9), displayed reduced auxin content and sensitivity. We show that exogenous auxin is capable of dramatically accelerating fruit development and ripening in plum, indicating that this hormone is actively involved in the ripening process. Further, we demonstrate that the variations in auxin sensitivity between plum cultivars could be partially due to PslAFB5, which encodes a TIR1-like auxin receptor. Two different PslAFB5 alleles were identified, one (Pslafb5) inactive due to substitution of the conserved F-box amino acid residue Pro61 to Ser. The early-ripening cultivar, EG, exhibited homozygosity for the inactive allele; however, the late cultivar, V9, displayed a PslAFB5/afb5 heterozygous genotype. Our results highlight the impact of auxin in stimulating fruit development, especially the ripening process and the potential for differential auxin sensitivity to alter important fruit developmental processes.

Sl-ERF.B.3 (Solanum lycopersicum ethylene response factor B.3)gene encodes for a tomato transcription factor of the ERF (ethylene responsive factor) family. Our results of real-time RT-PCR showed thatSl-ERF.B.3is an abiotic stress responsive gene, which is induced by cold, heat, and flooding, but downregulated by salinity and drought. To get more insight into the role ofSl-ERF.B.3in plant response to separate salinity and cold, a comparative study between wild type and twoSl-ERF.B.3antisense transgenic tomato lines was achieved. Compared with wild type,Sl-ERF.B.3antisense transgenic plants exhibited a salt stress dependent growth inhibition. This inhibition was significantly enhanced in shoots but reduced in roots, leading to an increased root to shoot ratio. Furthermore, the cold stress essay clearly revealed that introducing antisenseSl-ERF.B.3in transgenic tomato plants reduces their cell injury and enhances their tolerance against 14 d of cold stress. All these results suggest thatSl-ERF.B.3gene is involved in plant response to abiotic stresses and may play a role in the layout of stress symptoms under cold stress and in growth regulation under salinity.

Glycosides are an important potential source of aroma and flavour compounds for release as volatiles in flowers and fruit. The production of glycosides is catalysed by UDP-glycosyltransferases (UGTs) that mediate the transfer of an activated nucleotide sugar to acceptor aglycones. A screen of UGTs expressed in kiwifruit (Actinidia deliciosa) identified the gene AdGT4 which was highly expressed in floral tissues and whose expression increased during fruit ripening. Recombinant AdGT4 enzyme glycosylated a range of terpenes and primary alcohols found as glycosides in ripe kiwifruit. Two of the enzyme's preferred alcohol aglycones, hexanol and (Z)-hex-3-enol, contribute strongly to the 'grassy-green' aroma notes of ripe kiwifruit and other fruit including tomato and olive. Transient over-expression of AdGT4 in tobacco leaves showed that enzyme was able to glycosylate geraniol and octan-3-ol in planta whilst transient expression of an RNAi construct in Actinidia eriantha fruit reduced accumulation of a range of terpene glycosides. Stable over-expression of AdGT4 in transgenic petunia resulted in increased sequestration of hexanol and other alcohols in the flowers. Transgenic tomato fruit stably over-expressing AdGT4 showed changes in both the sequestration and release of a range of alcohols including 3-methylbutanol, hexanol and geraniol. Sequestration occurred at all stages of fruit ripening. Ripe fruit sequestering high levels of glycosides were identified as having a less intense, earthier aroma in a sensory trial. These results demonstrate the importance of UGTs in sequestering key volatile compounds in planta and suggest a future approach to enhancing aromas and flavours in flowers and during fruit ripening. Yauk YK1, Ged C, Wang MY, Matich AJ, Tessarotto L, Cooney JM, Chervin C, Atkinson RG.

International audience; The problem of finding a template function that represents the common pattern of a sample of curves is considered. To address this issue, a novel algorithm based on a robust version of the isometric featuring mapping (Isomap) algorithm is developed. When the functional data lie on an unknown intrinsically low-dimensional smooth manifold, the corresponding empirical Frechet median function is chosen as an intrinsic estimator of the template function. However, since the geodesic distance is unknown, it has to be estimated. For this, a version of the Isomap procedure is proposed, which has the advantage of being parameter free and easy to use. The feature estimated with this method appears to be a good pattern for the data, capturing the inner geometry of the curves. Comparisons with other methods, with both simulated and real datasets, are provided.

International audience; Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30 degrees C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.

It has been established that drought-responsive element binding (DREB) proteins correspond to transcription factors which play important regulatory roles in plant response to abiotic and biotic stresses. In this study, a novel cDNA encoding DREB transcription factor, designated StDREB1, was isolated from potato (Solanum tuberosum L.). This protein was classified in the A-4 group of DREB subfamily based on multiple sequence alignments and phylogenetic characterization. Semi-quantitative RT-PCR showed that StDREB1 is expressed in leaves, stems, and roots under stress conditions and it is greatly induced by NaCl, drought, low temperature, and abscisic acid (ABA) treatments. Overexpression of StDREB1 cDNA in transgenic potato plants exhibited an improved salt and drought stress tolerance in comparison to the non-transformed controls. The enhanced stress tolerance may be associated with the increase in P5CS-RNA expression (δ 1-pyrroline-5-carboxylate synthetase) and the subsequent accumulation of proline osmoprotectant in addition to a better control of water loss. Overexpression of StDREB1 also activated stress-responsive genes, such as those encoding calcium-dependent protein kinases (CDPKs), in transgenic potatoes under standard and high salt conditions. These data suggest that the StDREB1 transcription factor is involved in the regulation of salt stress tolerance in potato by the activation of different downstream gene expression.

International audience; The impact of organic fertilizers on plant behaviour under andosol conditions is not well understood. A field experiment was conducted on a silty and slightly acidic andosol, very poor in phosphorous (3 mg kg- 1of soil) and potassium (0.13 meq/100g of soil), with an imbalance Ca:Mg:K ratio of 74.0:25.0:0.7. The effect of integrated mineral fertilization (using N, P, K, Ca and Mg), dry poultry manure (organic), the association of the two (organo-mineral) fertilizers and non-integrated mineral fertilization has been studied on yield and nutrient allocation of two varieties of tomato (Solanum lycopersicum L. var. Roma VF and Tima). Yields of red tomatoes from organo-mineral fertilized plants (39.27-34.38 t ha-1) werethree times higher than the yields from plants fertilized with non-integrated minerals (12.97-11.59 t ha-1).Allocation of macronutrients (P, K and Ca) was high in fruits from plants fertilized with organic, organomineraland integrated mineral fertilizers. Fruit calcium increased mostly at the fruit ripening stage, while phosphorus and potassium accumulated mainly before the fruit ripening stage. This trend was by far more pronounced under organo-mineral and organic fertilization. Overall, the kinetics of nutrient allocation indicate a clear positive impact of poultry manure and organo-mineral fertilizers in improving tomato production on andosol.

International audience; As a consequence of the non-climacteric status of grapes (Vitis vinifera), ethylene biosynthesis and signal transduction have scarcely been studied in this fruit. In spite this drawback, the available information suggests a role for ethylene in ripening grape berries. In this work, we report the identification of three homologous genes that encode 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), a key component of ethylene biosynthesis. A comparison of protein sequences revealed that all three VvACOs harbor a 2OG-Fe(II) oxygenase domain, which is typical of the ACO gene family; however, VvACO1 showed a higher amino acid sequence homology with VvACO2 than with VvACO3. The expression pattern of VvACOs and the effect of exogenous ethylene on their transcript accumulation were evaluated during table grape berry development in the "Thompson Seedless" cultivar. A peak in VvACO1 transcript accumulation levels was registered around veraison that was 4-fold higher than at harvest, and this peak was confirmed during a second season in grapes that were harvested from three different vineyards. An enhancement in ethylene production and VvACO genes transcript levels was observed in grapes sprayed with ethephon during berry development. However, VvACO1 transcripts reached the highest accumulation earlier than VvACO2 and VvACO3. Altogether, these data confirmed that ethylene may have a role in some aspects of the grape ripening process, and they also highlighted the potential use of some VvACO genes as molecular markers for identifying grape veraison stages in grapes.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Auxin-binding protein1 (ABP1) is an active element involved in auxin signaling and plays critical roles in auxin-mediated plant development. Here, we report the isolation and characterization of a putative sequence from Prunus salicina L., designated PslABP1. The expected protein exhibits a similar molecular structure to that of well-characterized maize-ABP1; however, PslABP1 displays more sequence polarity in the active-binding site due to substitution of some crucial amino-acid residues predicted to be involved in auxin-binding. Further, PslABP1 expression was assessed throughout fruit ontogeny to determine its role in fruit development. Comparing the expression data with the physiological aspects that characterize fruit-development stages indicates that PslABP1 up-regulation is usually associated with the signature events that are triggered in an auxin-dependent manner such as floral induction, fruit initiation, embryogenesis, and cell division and elongation. However, the diversity in PslABP1 expression profile during the ripening process of early and late plum cultivars seems to be due to the variability of endogenous auxin levels among the two cultivars, which consequently can change the levels of autocatalytic ethylene available for the fruit to co-ordinate ripening. The effect of auxin on stimulating ethylene production and in regulating PslABP1 was investigated. Our data suggest that auxin is involved in the transition of the mature green fruit into the ripening phase and in enhancing the ripening process in both auxin- and ethylene-dependent manners thereafter.

Ethylene plays a critical regulatory role in climacteric fruit ripening, and its biosynthesis is fine-tuned at the transcriptional and posttranslational levels. Nevertheless, the mechanistic link between transcriptional and posttranslational regulation of ethylene biosynthesis during fruit ripening is largely unknown. This study uncovers a coordinated transcriptional and posttranslational mechanism of controlling ethylene biosynthesis during banana (Musa acuminata) fruit ripening. NAC (NAM, ATAF, and CUC) proteins MaNAC1 and MaNAC2 repress the expression of MaERF11, a protein previously known to negatively regulate ethylene biosynthesis genes MaACS1 and MaACO1. A RING E3 ligase MaXB3 interacts with MaNAC2 to promote its ubiquitination and degradation, leading to the inhibition of MaNAC2-mediated transcriptional repression. In addition, MaXB3 also targets MaACS1 and MaACO1 for proteasome degradation. Further evidence supporting the role of MaXB3 is provided by its transient and ectopic overexpression in banana fruit and tomato (Solanum lycopersicum), respectively, which delays fruit ripening via repressing ethylene biosynthesis and thus ethylene response. Strikingly, MaNAC1 and MaNAC2 directly repress MaXB3 expression, suggesting a feedback regulatory mechanism that maintains a balance of MaNAC2, MaACS1, and MaACO1 levels. Collectively, our findings establish a multilayered regulatory cascade involving MaXB3, MaNACs, MaERF11, and MaACS1/MaACO1 that controls ethylene biosynthesis during climacteric ripening.

International audience; One irreversible consequence of acidic pH for roots is cell death. Growing evidence suggests the role of hormones and cell wall-related enzymes in response to acidic pH that could possibly avoid cell mortality. Here, we have investigated the role of ethylene and class III peroxidases (CIII Prxs) activity on sensitivity to further low pH treatment. Seedlings of Arabidopsis thaliana were pretreated with ethylene, at various concentrations for various times, and then exposed to low pH. In contrast to non-treated roots, roots pretreated with ethylene for 3 h became tolerant to subsequent low pH, with negligible cell mortality in meristematic (MZ), transition (TZ), and early elongation (EZ) zones. This effect of ethylene was time dependent since it was achieved only when seedlings were pre-incubated with ethylene for at least 3 h. This tolerance induced by ethylene was not observed in the gain-of-function mutation etr1-1 (insensitive to ethylene 1–1). Besides, it was prevented by salicylhydroxamic acid (SHAM) which is an inhibitor of CIII Prxs activity. In late EZ, the decrease in cell expansion due to low pH was dependent on both ethylene signaling and a SHAM-sensitive process. The responses mediated by ethylene signaling might involve CIII Prxs-dependent cell wall modifications, leading to tolerance to low pH and arrest in cell expansion during stress.

International audience; RIN-deficient fruits generated by CRISPR/Cas9 initiated partial ripening at a similar time to wild-type (WT) fruits but only 10% WT levels of carotenoids and ethylene were synthesised. RIN-deficient fruit never ripened completely, even when supplied with exogenous ethylene. The low amount of endogenous ethylene that they did produce was sufficient to enable ripening initiation and this could be suppressed by the ethylene perception inhibitor 1-MCP. The reduced ethylene production by RIN-deficient tomatoes was due to an inability to induce autocatalytic system-2 ethylene synthesis, a characteristic feature of climacteric ripening. Production of volatiles and transcripts of key volatile biosynthetic genes were also greatly reduced in the absence of RIN. In contrast, the initial extent and rates of softening in the absence of RIN were similar to WT fruits, although detailed analysis showed the expression of some cell wall modifying enzymes was delayed and others increased in the absence of RIN.These results support a model where RIN and ethylene, via ERFs, are required for fullexpression of ripening genes. Ethylene initiates ripening of mature green fruit, upregulates. RIN expression and other changes, including system-2 ethylene production. RIN, ethylene andother factors are required for completion of the full fruit ripening program.

International audience; Facultative parthenocarpy is of great practical value. However, the molecular mechanism underlying facultative parthenocarpy remains elusive. Transcriptional co-repressors (TPL) act as a central regulatory hub controlling all nine phytohormone pathways. Previously, we proved that SlTPLs participate in the auxin signaling pathway by interacting with auxin/indole acetic acid (Aux/IAAs) in tomato; however, their function in fruit development has not been studied. In addition to their high expression levels during flower development, the interaction between SlTPL1 and SlIAA9 stimulated the investigation of its functional significance via RNA interference (RNAi) technology, whereby the translation of a protein is prevented by selective degradation of its encoded mRNA. Down-regulation of SlTPL1 resulted in facultative parthenocarpy. Plants of SlTPL1-RNAi transgenic lines produced similar fruits which did not show any pleiotropic effects under normal conditions. However, they produced seedless fruits upon emasculation and under heat stress conditions. Furthermore, SlTPL1-RNAi flower buds contained higher levels of cytokinins and lower levels of abscisic acid. To reveal how SlTPL1 regulates facultative parthenocarpy, RNA-seq was performed to identify genes regulated by SlTPL1 in ovaries before and after fruit set. The results showed that down-regulation of SlTPL1 resulted in reduced expression levels of cytokinin metabolism-related genes, and all transcription factors such as MYB, CDF, and ERFs. Conversely, down-regulation of SlTPL1 induced the expression of genes related to cell wall and cytoskeleton organization. These data provide novel insights into the molecular mechanism of facultative tomato parthenocarpy and identify SlTPL1 as a key factor regulating these processes.

Auxin response factors (ARFs) play important roles in various plant physiological processes, however, knowledge of the exact role of ARFs in plant responses to water deficit is limited. In this study, SlARF4, a member of the ARF family, was functionally characterized under water deficit. Real-time fluorescence quantitative polymerase chain reaction (PCR) and β-glucuronidase (GUS) staining showed that water deficit and abscisic acid (ABA) treatment reduced the expression of SlARF4. SlARF4 was expressed in the vascular bundles and guard cells of tomato stomata. Loss of function of SlARF4 (arf4) by using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 (CRISPR/Cas 9) technology enhanced plant resistance to water stress and rehydration ability. The arf4 mutant plants exhibited curly leaves and a thick stem. Malondialdehyde content was significantly lower in arf4 mutants than in wildtype plants under water stress, furthermore, arf4 mutants showed higher content of antioxidant substances, superoxide dismutase, actual photochemical efficiency of photosystem II (PSII), and catalase activities. Stomatal and vascular bundle morphology was changed in arf4 mutants. We identified 628 differentially expressed genes specifically expressed under water deficit in arf4 mutants, six of these genes, including ABA signaling pathway-related genes, were differentially expressed between the wildtype and arf4 mutants under water deficit and unlimited water supply. Auxin responsive element (AuxRE) elements were found in these genes’ promoters indicating that SlARF4 participates in ABA signaling pathways by regulating the expression of SlABI5/ABF and SCL3, thereby influencing stomatal morphology and vascular bundle development and ultimately improving plant resistance to water deficit.

International audience; Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodeling associated with the flower‐to‐fruit transition remains poor.We investigated the epigenetic and transcriptomic reprogramming underlying pollination‐dependent and auxin‐induced flower‐to‐fruit transitions in the tomato (Solanum lycopersicum L.) using combined genome‐wide transcriptomic profiling, global ChIP‐sequencing and whole genomic DNA bisulfite sequencing (WGBS).Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone post translational modifications rather than DNA methylation are associated with the remodeling of the epigenetic landscape underpinning the flower‐to‐fruit transition.Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.

International audience; Soluble sugars, organic acids and volatiles are important components that determine unique fruit flavor and consumer preferences. However, the metabolic dynamics and underlying regulatory networks that modulate overall flavor formation during fruit development and ripening remain largely unknown for most fruit species. In this study, by integrating flavor-associated metabolism and transcriptome data from 12 fruit developmental and ripening stages of Actinidia chinensis cv Hongyang, we generated a global map of changes in the flavor-related metabolites throughout development and ripening of kiwifruit. Using this dataset, we constructed complex regulatory networks allowing to identify key structural genes and transcription factors that regulate the metabolism of soluble sugars, organic acids and important volatiles in kiwifruit. Moreover, our study revealed the regulatory mechanism involving key transcription factors regulating flavor metabolism. The modulation of flavor metabolism by the identified key transcription factors was confirmed in different kiwifruit species providing the proof of concept that our dataset provides a suitable tool for clarification of the regulatory factors controlling flavor biosynthetic pathways that have not been previously illuminated. Overall, in addition to providing new insight into the metabolic regulation of flavor during fruit development and ripening, the outcome of our study establishes a foundation for flavor improvement in kiwifruit.

International audience; The usual definition of the difference between climacteric and non-climacteric fruit relies on the fact that climacteric fruit ripens with concomitant increases of respiration and ethylene production, whereas barely any change in these two metabolisms occurs in non-climacteric fruit (Cherian et al., 2014). These authors list a series of climacteric fruit, such as tomato, banana, apple and mango, and a series of non-climacteric fruit such as strawberry, melon and grape. I think melon is a particular case, with climacteric and non-climacteric cultivars (Obando-Ulloa et al., 2009; Saladié et al., 2015), and this will not be detailed here. Other fruits have such climacteric and non-climacteric cultivars within a same species, for example Asian pears (Itai and Fujita, 2008) and plums (Minas et al., 2015). There have been many other reviews and articles over the last decade, regarding the differences between climacteric and non-climacteric fruit classes (Paul et al., 2012; Osorio et al., 2013; Saladié et al., 2015; Farcuh et al., 2017; Fuentes et al., 2019), but none pointed out that starch accumulation or breakdown could be a cornerstone in the definition of these two fruit classes. A quick data review, as detailed below, shows that most climacteric fruit accumulate starch before the onset of ripening, then starch is broken down to soluble sugars after the inception of ripening, whereas in the non-climacteric fruit the starch content drops very rapidly after anthesis, and they accumulate mainly soluble sugars throughout development and ripening. This big difference leads to different harvest strategies: climacteric fruit can be picked early, and the starch reserve will be converted to sugars over postharvest stages, whereas the non-climacteric fruit should be picked when the desired soluble sugar level is reached. However, starch metabolism is rarely mentioned as a key difference between climacteric and non-climacteric fruit. Osorio et al. (2012) suggested that the regulation of starch synthesis may be part of this difference, when comparing climacteric (tomato) and non-climacteric (pepper) fruit transcripts around the onset of ripening. Thus, I will first list starch contents in some climacteric and non-climacteric fruit, then I will review rapidly the starch synthesis and the starch breakdown metabolisms in plants, and finally I will discuss research perspectives.

International audience; 3-isobutyl-2-methoxypyrazine (IBMP) is a grape-derived aroma compound responsible for the bell pepper character of wine. It is still unclear whether this molecule is always negatively perceived by consumers. The objective of this study was to establish a consumer rejection threshold (CRT) for IBMP in French white and red wines from the Gaillac area made from Sauvignon and Fer respectively. The best estimate thresholds (BET) were determined by carrying out three-alternative forced choice (3-AFC) tests: 5.5 ng/L for Sauvignon and 16.8 ng/L for Fer. For the estimation of the CRT, consumers (n = 48) received pairs of samples consisting of a base wine and a base wine spiked with an ascending concentration of IBMP. They were asked to indicate which sample they preferred, and the CRT was calculated as the concentration for which the spiked sample was significantly rejected. CRTs were determined at 50 ng/L and 30 ng/L for Sauvignon and Fer respectively. Our findings indicate that IBMP is more acceptable in white wine than in red wine. As IBMP concentrations reported in the literature for Sauvignon and Fer are generally below CRT concentrations, IBMP appears to be neutrally perceived by consumers at usual concentrations in wines from Gaillac made from these two cultivars. Our findings tend to contradict the belief in the wine industry that consumers systematically reject 'vegetative' styles of wines, and our results do not encourage local winegrowers and winemakers to necessarily implement viticultural or enological practices to minimise IBMP concentrations in wine. consumer rejection threshold (CRT), Sauvignon white wine, Fer red wine, 3-isobutyl-2-methoxypyrazine (IBMP), protected designation of origin Gaillac

Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants. High-resolution metabolome and transcriptome data were used to explore the metabolic landscape of 20 major tissues and developmental stages of MicroTom tomato. The MicroTom Metabolic Network dataset provides a global map of the tomato metabolic regulatory network throughout its life cycle and can be used to identify novel transcription factors that regulate important metabolic pathways.

This work provides new insight into the regulation of trichome formation by gibberellin which has not previously been described in tomato., Trichomes are epidermal protuberances on aerial parts of plants known to play an important role in biotic and abiotic stresses. To date, our knowledge of the regulation of trichome formation in crop species is very limited. Through phenotyping of the Solanum pennellii×S. lycopersicum (cv. M82) introgression population, we identified the SlbHLH95 transcription factor as a negative regulator of trichome formation in tomato. In line with this negative role, SlbHLH95 displayed a very low expression in stems where trichomes are present at high density. Overexpression of SlbHLH95 resulted in a dramatically reduced trichome density in stems and a significant down-regulation of a set of trichome-related genes. In addition to the lower trichome density, overexpressing lines also showed pleiotropic alterations affecting both vegetative and reproductive development. While most of these phenotypes were reminiscent of gibberellin (GA)-deficient phenotypes, expression studies showed that two GA biosynthesis genes, SlGA20ox2 and SlKS5, are significantly down-regulated in SlbHLH95-OE plants. Moreover, in line with a decrease in active GA content, the glabrous and dwarf phenotypes were rescued by exogenous GA treatment. In addition, yeast one-hybrid and transactivation assays revealed that SlbHLH95 represses the expression of SlGA20ox2 and SlKS5 via direct binding to their promoters. Taken together, our study established a link between SlbHLH95, GA, and trichome formation, and uncovered the role of this gene in modulating GA biosynthesis in tomato.

International audience

Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). This study focuses on the involvement of SlARF4 in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of SlARF4 promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore, ARF4-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced SlARF4 mutant showed similar growth and stomatal responses as ARF4-as plants, which suggest that arf4-cr can tolerate salt and osmotic stresses. Our data support the involvement of ARF4 as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.

International audience; Polycomb group (PcG) proteins play vital roles in plant development via epigenetically repressing the transcription of target genes. However, to date, their function in fruit ripening is largely unknown.Combining reverse genetic approaches, physiological methods, yeast two-hybrid, co-immunoprecipitation, and chromatin immunoprecipitation assays, we show that Like Heterochromatin Protein 1b (SlLHP1b), a tomato Polycomb Repressive Complex 1 (PRC1)-like protein with a ripening-related expression pattern, represses fruit ripening via colocalization with epigenetic mark H3K27me3.RNA interference (RNAi)-mediated downregulation of SlLHP1b advanced ripening initiation, climacteric ethylene production, and fruit softening, whereas SlLHP1b overexpression delayed these events. Ripening-related genes were significantly upregulated in SlLHP1b RNAi fruits and downregulated in overexpressing fruits compared with wild-type. Furthermore, SlLHP1b protein interacts with ripening regulator MSI1, a subunit of the PRC2 complex. Moreover, SlLHP1b also binds the epigenetic histone mark H3K27me3 in vivo and chromatin immunoprecipitation-quantitative PCR results showed binding occurs preferentially to regions of ripening-associated chromatin marked by histone H3K27me3. Furthermore, the H3K27me3 levels in chromatin of ripening-related genes is negatively correlated with accumulation of their transcripts in SlLHP1b down or upregulated fruits during ripening.Our findings reveal a novel regulatory function of SlLHP1b in fruit and provide new insights into the PcG-mediated epigenetic regulation of climacteric fruit ripening.

International audience; Fleshy fruits are major sources of necessary nutrients in many diets worldwide. Most fruit quality attributes emerge during ripening making the fruit more attractive to consumers. Understanding the molecular regulatory network underpinning fleshy fruit ripening is important not only for fruit quality improvement but also for postharvest shelf life. The phytohormone ethylene plays an essential role in climacteric fruit ripening and a number of studies have demonstrated that ethylene signaling components and related transcription factors are involved in the regulation of fruit ripening. However, the transcriptional network by which ethylene interacts with other signaling pathways to regulate the ripening process is not fully understood. In this review, focusing on the tomato as a reference species, the key points regarding the role of ethylene in coordinating the ripening process at the molecular and physiological levels are described. The interplay between ethylene and ripening‐related regulators and its crosstalk with other phytohormones and present recent data on ripening‐related epigenetic modifications are also discussed. Overall, the paper summarizes the most advanced research progress in this area to help facilitate its future development.

International audience; Tomato (Solanum lycopersicum L.) plants are cold sensitive and the fruit are susceptible to postharvest chilling injury when stored at low-temperature. However, the mechanisms underlying cold stress responses in tomato are poorly understood. We demonstrate that SlGRAS4, encoding a transcription factor induced by low temperature, promotes chilling tolerance in tomato leaves and fruit. Combined genome-wide ChIP-seq and RNA-seq approaches identified among cold stressassociated genes those being direct targets of SlGRAS4 and protein studies revealed that SlGRAS4 forms a homodimer to self-activate its own promoter. SlGRAS4 can also directly bind tomato SlCBF promoters to activate their transcription without inducing any growth retardation. The study identifies the SlGRAS4-regulon as a new cold response pathway conferring cold stress tolerance in tomato independently of the ICE1-CBF pathway. This provides new track for breeding strategies aiming to improve chilling tolerance of cultivated tomatoes and to preserve sensory qualities of tomato fruit often deteriorated by storage at low temperatures.

Ethylene regulates many aspects of plant growth and development. It is perceived by a family of ethylene receptors (ETRs) that have been well described. However, a full understanding of ETR function is complicated by functional redundancy between the receptor isoforms. Here, we characterize a new ETR, SlETR7, that was revealed by tomato genome sequencing. SlETR7 expression in tomato fruit pericarp increases when the fruit ripens and its expression is synchronized with the expression of SlETR1, SlETR2, and SlETR5 which occurs later in the ripening phase than the increase observed for SlETR3, SlETR4, and SlETR6. We uncovered an error in the SlETR7 sequence as documented in the ITAG 3 versions of the tomato genome which has now been corrected in ITAG 4, and we showed that it belongs to sub-family II. We also showed that SlETR7 specifically binds ethylene. Overexpression (OE) of SlETR7 resulted in earlier flowering, shorter plants, and smaller fruit than wild type. Knock-out (KO) mutants of SlETR7 produced more ethylene at breaker (Br) and Br + 2 days stages compared to wild type (WT), but there were no other obvious changes in the plant and fruit in these mutant lines. We observed that expression of the other SlETRs is upregulated in fruit of SlETR7 KO mutants, which may explain the absence of obvious ripening phenotypes. Globally, these results show that SlETR7 is a functional ethylene receptor. More work is needed to better understand its specific roles related to the six other tomato ETRs.

International audience; Aim : Grape growers sometimes use cyanamides (calcium or hydrogen) to release bud dormancy in warm climate regions, where the chilling requirement has not been met during winter. However, these products can cause damage to plants and are dangerous to handle, so alternatives would be welcomed by growers. Connections between metabolisms of ethanol, ethylene and cyanide revealed by previous studies led us to test the potential of ethanol sprays on bud break and early shoot growth.Methods and results : Trials were performed over three years on Vitis vinifera grapevines trained in Guyot or cordon, and on cuttings in growth chambers. Cultivars used in the studies included Cabernet-Sauvignon, Syrah and Ugni blanc. The results show that ethanol can advance bud break of all three cultivars at concentrations ranging from 2.5 to 10 % ethanol in water. Ethanol stimulates bud development in both Guyot and cordon training systems. However, the timing of ethanol application is crucial, and late spring season applications reduce the effectiveness of the treatment.Conclusions : Observations were performed over three different seasons. The trials revealed that ethanol sprays can advance bud break of different Vitis vinifera vines, trained with cane or spur systems.Significance and impact of the study : Climate change impacts dormancy release, making it an increasingly important issue over the next few decades. An alternative to the dangerous use of cyanamides to promote bud break would greatly help growers. These preliminary results with ethanol are promising but should lead to trials in various growing areas and with various cultivars in order to confirm their potential for viticulture.

International audience; A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cyclic adenosine 30,50-monophosphate (cAMP) cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction.

Glutathione-dependent root growth in Arabidopsis is linked to polar auxin transport (PAT). Arabidopsis mutants with reduced glutathione (GSH) levels also show reduced PAT. To gain an insight into the relationship between PAT and GSH level, we analysed tomato polycotyledon mutant, pct1-2, which has enhanced PAT. Microarray analysis of gene expression in pct1-2 mutant revealed underexpression of several genes related to glutamate and glutathione metabolism. In consonance with microarray analysis, enzymatic as well as in-vivo assay revealed higher glutathione level in the early phase of pct1-2 seedling growth than WT. The inhibition of auxin transport by 2,3,5-triiodobenzoic acid (TIBA) reduced both GSH level and PIN1 expression in pct1-2 root tips. The reduction of in vivo GSH accumulation in pct1-2 root tips by buthionine sulfoximine (BSO) stimulated elongation of the short root of pct1-2 mutant akin to TIBA. The rescue of short root phenotype of pct1-2 mutant was restricted to TIBA and BSO. The other auxin transport inhibitors 1-N-naphthylphthalamic acid (NPA), 2-[4-(diethylamino)-2-hydroxybenzoyl] benzoic acid (BUM), 3-chloro-4-hydroxyphenylacetic acid (CHPAA), brefeldin and gravacin inhibited root elongation in both WT and pct1-2 mutant. Our results indicate a relationship between PAT and GSH level in tomato akin to Arabidopsis. Our work also highlights that TIBA rescues short root phenotype of the pct1-2 mutant by acting on a PAT component distinct from the site of action of other PAT inhibitors.

Ethylene regulates fruit ripening and several plant functions (germination, plant growth, plant-microbe interactions). Protein quantification of ethylene receptors (ETRs) is essential to study their functions, but is impaired by low resolution tools such as antibodies that are mostly nonspecific, or the lack of sensitivity of shotgun proteomic approaches. We developed a targeted proteomic method, to quantify low-abundance proteins such as ETRs, and coupled this to mRNAs analyses, in two tomato lines: Wild Type (WT) and Never-Ripe (NR) which is insensitive to ethylene because of a gain-of-function mutation in ETR3. We obtained mRNA and protein abundance profiles for each ETR over the fruit development period. Despite a limiting number of replicates, we propose Pearson correlations between mRNA and protein profiles as interesting indicators to discriminate the two genotypes: such correlations are mostly positive in the WT and are affected by the NR mutation. The influence of putative post-transcriptional and post-translational changes are discussed. In NR fruits, the observed accumulation of the mutated ETR3 protein between ripening stages (Mature Green and Breaker + 8 days) may be a cause of NR tomatoes to stay orange. The label-free quantitative proteomics analysis of membrane proteins, concomitant to Parallel Reaction Monitoring analysis, may be a resource to study changes over tomato fruit development. These results could lead to studies about ETR subfunctions and interconnections over fruit development. Variations of RNA-protein correlations may open new fields of research in ETR regulation. Finally, similar approaches may be developed to study ETRs in whole plant development and plant-microorganism interactions.

International audience; Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to the initiation of the ripening process remain elusive, although the presumed role of active hormone interplay has often been postulated. To unravel the putative role of auxin in the unripe-to-ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl-SAUR69, previously identified as a RIN target gene, using reverse genetics approaches. Auxin signalling undergoes dramatic decline at the onset of ripening in wild-type fruit, but not in the nonripening rin mutant. Sl-SAUR69 exhibits reduced expression in rin and its up-regulation results in premature initiation of ripening, whereas its down-regulation extends the time to ripening. Overexpression of Sl-SAUR69 reduces proton pump activity and polar auxin transport, and ectopic expression in Arabidopsis alters auxin transporter abundance, further arguing for its active role in the regulation of auxin transport. The data support a model in which Sl-SAUR69 represses auxin transport, thus generating auxin minima, which results in enhanced ethylene sensitivity. This defines a regulation loop, fed by ethylene and auxin as the main hormonal signals and by RIN and Sl-SAUR69 as modulators of the balance between the two hormones.

Genetic manipulation of genes to upregulate specific branches of metabolic pathways is a method that is commonly used to improve fruit quality. However, the use of a single gene to impact several metabolic pathways is difficult. Here, we show that overexpression of the single gene SlMYB75 (SlMYB75-OE) is effective at improving multiple fruit quality traits. In these engineered fruits, the anthocyanin content reached 1.86 mg g−1 fresh weight at the red-ripe stage, and these SlMYB75-OE tomatoes displayed a series of physiological changes, including delayed ripening and increased ethylene production. In addition to anthocyanin, the total contents of phenolics, flavonoids and soluble solids in SlMYB75-OE fruits were enhanced by 2.6, 4, and 1.2 times, respectively, compared to those of wild-type (WT) fruits. Interestingly, a number of aroma volatiles, such as aldehyde, phenylpropanoid-derived and terpene volatiles, were significantly increased in SlMYB75-OE fruits, with some terpene volatiles showing more than 10 times higher levels than those in WT fruits. Consistent with the metabolic assessment, transcriptomic profiling indicated that the genes involved in the ethylene signaling, phenylpropanoid and isoprenoid pathways were greatly upregulated in SlMYB75-OE fruits. Yeast one-hybrid and transactivation assays revealed that SlMYB75 is able to directly bind to the MYBPLANT and MYBPZM cis-regulatory elements and to activate the promoters of the LOXC, AADC2 and TPS genes. The identification of SlMYB75 as a key regulator of fruit quality attributes through the transcriptional regulation of downstream genes involved in several metabolic pathways opens new avenues towards engineering fruits with a higher sensory and nutritional quality., Genetics: one small tweak, one giant leap for tomatoes A single gene has been identified in tomatoes that regulates multiple aspects of fruit quality, including levels of health-promoting anthocyanins, opening the door to engineering more nutritious and better-tasting tomatoes. Fruit breeders have long-manipulated genes to enhance traits like yield or disease resistance, but it is rare to find a single gene that can improve multiple aspects of fruit quality. In this study, Zhengguo Li at Chongquing University in China and colleagues show that over-expressing a transcription factor called SIMYB75 results in striking deep purple tomatoes enriched in anthrocyanins–antioxidants thought to be protective against various diseases - which tomatoes are usually devoid of. They also had higher levels of other health-promoting phytochemicals and enhanced production of aroma volatiles, which can influence the taste and flavor of fruit.

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes., Measurement(s) genome • RNA • sequence_assembly • transcriptome Technology Type(s) digital curation • RNA sequencing • sequence assembly process Factor Type(s) cultivar Sample Characteristic - Organism Solanum tuberosum Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12562733

Nanotechnology is currently undergoing rapid development partly due to the increasing use of carbon-based nanoparticles, such as Few Layer Graphene (FLG). Owing to its numerous applications, its industrial production is likely to lead to environmental release, including into aquatic ecosystems. In this study, a transcriptomic approach was used to assess the effect of FLG at low (0.1 mg L-1) and high (50 mg L-1) concentrations on the benthic freshwater diatom Nitzschia palea after 48 h of exposure. Direct contact with FLG and induced shading were distinguished to compare the transcriptomic responses. Genes that were differentially expressed after exposure compared with control conditions were identified, and their functional descriptions are discussed. A slight transcriptomic response related to cell wall repair was observed in diatoms exposed to the low FLG concentration. Exposure to the high FLG concentration induced a strong response involving 1907 transcripts. Notably, 16 transcripts involved in the chlorophyll biosynthesis process were under-expressed (log2 fold change between -3 and -1.2), suggesting a down-regulation of the photosynthetic metabolism. Diatoms exposed to the high FLG concentration over-expressed about 13 transcripts encoding for extracellular proteins that play a role in cellular adhesion, and two transcripts involved in cell wall repair were highly up-regulated. Light deprivation caused by shading induced a downregulation of genes involved in the energetic metabolism of N. palea. Overall, these results revealed that metabolic pathways impacted by FLG exposure are concentration and contact dependent. Moreover, this study suggests that a low FLG concentration, close to that in environmental conditions, will have a minor impact on diatom biofilms whereas a high FLG concentration, mimicking accidental release, might be critical for ecosystems.

International audience; The molecular dialogue between the Arbuscular Mycorrhizal Fungi (AMF) and their host regulates symbiosis establishment. It involves strigolactone, a phythormone released by host roots, and Mycfactors released by fungal spores. Other phytohormones are involved in the development of this symbiosis as well, but they are always examined from the plant point of view. Recently, AMF cytokinins and ethylene receptors were identified in silico. It is therefore tempting to speculate that AMF perceive cytokinines or ethylene produced by plants as well. Furthermore, many ectomycorrhizal fungi are reported to produce phytohormones, but there is no strong evidence for AMF. We thus wonder whether AMF may perceive phytohormones imported from root-fungus exchange, or metabolized by AMF themselves. We therefore developed biochemical strategies to detect phytohormones in AMF. A global extraction and enrichment protocol for soluble phytohormones was adapted to different matrixes, like Germination Spores Exudates (GSE) and double compartment culture. In parallel, their detection and identification by liquid chromatography coupled to mass spectrometry was optimized. Ethylene production by fungal spore was investigated by gas chromatography, to decipher its biosynthesis pathways. We have been able to detect for the first time several phytohormones released by spores and extra-radical mycelium. Their metabolic origins, as well as their effect on AMF development still remain unknown and will be further investigated through this project.

International audience; Background: “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog genes. However, the spreading of sequenced genome, often endowed with still preliminary annotations, requires suitable bioinformatics to be appropriately exploited in this framework. Results: We presented here a multilevel comparative approach to investigate on genome evolutionary relationships and peculiarities of two fleshy fruit species of relevant agronomic interest, Solanum lycopersicum (tomato) and Vitis vinifera (grapevine). We defined 17,823 orthology relationships between tomato and grapevine reference gene annotations. The resulting orthologs are associated with the detected paralogs in each species, permitting the definition of gene networks, useful to investigate the different relationships. The reconciliation of the compared collections in terms of an updating of the functional descriptions was also exploited. All the results were made accessible in ComParaLogs, a dedicated bioinformatics platform available at http://biosrv.cab.unina.it/comparalogs/gene/search Conclusions: The aim of the work was to suggest a reliable approach to detect all similarities of gene loci between two species based on the integration of results from different levels of information, such as the gene, the transcript and the protein sequences, overcoming possible limits due to exclusive protein versus protein comparisons. This to define reliable ortholog and paralog genes, as well as species specific gene loci in the two species, overcoming limits due to the possible draft nature of preliminary gene annotations. Moreover, reconciled functional descriptions, as well as common or peculiar enzymatic classes and protein domains from tomato and grapevine, together with the definition of species-specific gene sets after the pairwise comparisons, contributed a comprehensive set of information useful to comparatively exploit the two species gene annotations and investigate on differences between species with climacteric and non-climacteric fruits. In addition, the definition of networks of ortholog genes and of associated paralogs, and the organization of web-based interfaces for the exploration of the results, defined a friendly computational bench-work in support of comparative analyses between two species.

International audience; Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate fungal spore germination and hyphal branching, and promote the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We detected the presence of a cytokinin (iso-pentenyl adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellin A 4) in spore extracts. We also used gas chromatography to show that R. irregu-laris produces ethylene from methionine and the α-keto γ-methylthio butyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.

International audience; With the forecasted fast increase in world population and global climate change, providing sufficient amounts of quality food becomes a major challenge for human society. Seed and fruit crop yield is determined by developmental processes including flower initiation, pollen fertility and fruit set. Fruit set is defined as the transition from flower to young fruit, a key step in the development of sexually reproducing higher plants. Plant hormones have important roles during flower pollination and fertilization, leading to fruit set. Moreover, it is well established that fruit set can be triggered by phytohormones like auxin and gibberellins (GAs), in the absence of fertilization, both hormones being commonly used to produce parthenocarpic fruits and to increase fruit yield. Additionally, a number of studies highlighted the role of ethylene in plant reproductive organ development. The present review integrates current knowledge on the roles of auxin and ethylene in different steps of the fruit set process with a specific emphasis on the interactions between the two hormones. A deeper understanding of the interplay between auxin and ethylene may provide new leads towards designing strategies for a better control of fruit initiation and ultimately yield.