Biology subjects

Rothan, C.

Publications and source records attributed to Rothan, C..

12 recordsLinked to original sources

bioRxiv2025

Shedding light on cuticle formation: phytochrome B and downstream signaling events controlling cuticle deposition in tomato fruits

The cuticle is a hydrophobic barrier limiting water loss and pathogen entry. Although light influences cuticle formation, the underlying mechanisms remain poorly understood, particularly in fruits. Here, we show that fruits from tomato (Solanum lycopersicum) plants grown under far-red-enriched light conditions displayed increased cuticle load due to the up-regulation of cutin and wax biosynthetic genes. Both tomato PHYB-encoding genes (SlPHYB1 and SlPHYB2) were implicated as negative regulators of fruit cuticle formation, as revealed by the thinner cuticles, reduced abundance of cutin monomers and cuticular waxes, and downregulation of cuticle-related genes detected in fruits from transgenic plants overexpressing constitutively active alleles of SlPHYB1/B2 (SlYHB1OE and SlYHB2OE). The impaired cuticle of SlYHB1/B2OE fruits resulted in increased susceptibility to Botrytis cinerea, despite their markedly enhanced flavonoid accumulation in the peel. PHYTOCHROME-INTERACTING FACTORs (SlPIF3, SlPIF4) and the B-box protein SlBBX28 were identified as downstream factors of SlPHYB1/B2-mediated regulation of cuticle deposition, synergistically activating the expression of cuticle-related genes. Additionally, SlPHYB1/B2 signaling also downregulated multiple central carbon metabolism-related genes in the fruit peel, likely reducing the pool of activated fatty acids (FAs) feeding into cutin and wax biosynthetic pathways. Together, our results uncover a novel regulatory layer of light signaling in fleshy fruits, revealing that, besides controlling fruit nutritional traits, the PHYB-PIF-BBX regulatory module also shapes the fruit cuticle formation. HighlightsPhytochrome-dependent light signaling regulates cuticle deposition in tomato fruits by controlling downstream transcription factors and the supply of precursors feeding into cutin/wax biosynthetic pathways, thereby affecting postharvest water loss and pathogen susceptibility.

plant biology↗

bioRxiv2025

Role of the tomato MARS1/ROUGH gene encoding a LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 in adventitious root and fruit skin formation

In contrast to animals, plants have a high regenerative capacity, and they can form new organs and even complete individuals from a few cells present in adult tissues, either in response to injury or to the alteration of their environment. In this study, we describe the isolation and characterization of the more adventitious roots1-1 (mars1-1) mutant, which exhibits enhanced regenerative potential upon wounding in tomato hypocotyl explants. Additionally, the mars1-1 fruits exhibited a rough surface due to the ectopic proliferation of subepidermal cells, which formed callus-like structures on the cuticle. The MARS1/ROUGH gene encodes a conserved lysine-specific histone demethylase, SlLSD1, which regulates a variety of processes in metazoans, including cell proliferation, stem cell pluripotency, and embryogenesis. Two CRISPR/Cas9 null alleles, mars1-2 and mars1-3, were generated and their pleiotropic phenotype was characterized. We found elevated levels of H3K4me1 in mars1/rough seedlings, which suggests that SlLSD1 is required for the demethylation of this histone mark. To ascertain the impact of altered epigenetic marks in the mars1/rough mutants on gene expression regulation, we conducted a transcriptome analysis using a variety of RNA-Seq studies on tomato hypocotyls. By employing specific bioinformatic workflows and leveraging on the resolution of directional RNA-Seq data, we have identified over several dozen distinct genomic regions that exhibit de novo expression in the mars1/rough mutants. One such region includes a novel B-type cyclin gene, which is upregulated in the mars1/rough mutants and may account for the observed phenotypes. Our findings indicate that SlLSD1 plays a role in the establishment and maintenance of silencing in specific genomic regions that are essential for tissue-specific reprogramming.

plant biology↗

bioRxiv2025

Molecular mechanisms underlying the determination of axillary bud fate and outgrowth into branch crown in strawberry

{blacksquare} In strawberry, the axillary bud (AXB) can produce either an elongated stem called stolon giving a daughter-plant (asexual reproduction) or an inflorescence-bearing branch crown (BC) (sexual reproduction). The fate of the AXB depends on node position on the axis and on genetic and environmental factors. Here, in Fragaria vesca, we addressed the largely unanswered question of how molecular factors determine AXB fate. {blacksquare}To get insights into the mechanisms already at play in a morphologically indistinguishable (undifferentiated) AXB, depending on its fate, we combined (1) the phenotypic characterization of AXB development throughout plant growth with (2) the RNA-seq analysis of undifferentiated AXBs, using three different genotypes producing either BCs or stolons (fvetfl1 and fvega20ox mutants, FveFT3 overexpressor). {blacksquare}Results allowed the identification of genes regulating AXB fate and outgrowth, among which FveBRC1. The analysis of FveBRC1 expression in genotypes combining various traits (perpetual/seasonal flowering; runnering/runneless) and the generation of CRISPR/Cas9 brc1 mutants further demonstrated that FveBRC1 plays a central role in the determination of AXB fate in strawberry, in addition to its well-known function in BC outgrowth. {blacksquare}These original results provide new insights into the determination of AXB fate and, consequently, the control of fruit yield in strawberry.

plant biology↗

bioRxiv2024

Targeting the tomato fruit cuticle by gene overexpression and editing with the fruit epidermis-preferential nsLTP promoter

The thick cuticle covering and embedding epidermal cells of tomato (Solanum lycopersicum) fruit, a model for cuticle studies, plays important roles in fruit protection and quality. To further our understanding of the influence of cuticle components on cuticle architecture and properties, the next step is to engineer cuticle composition. Ideally, to avoid indirect effects at whole-plant level, a fruit-and epidermis-specific promoter should be used. Here, to overexpress and edit target genes in tomato, we selected a non-specific Lipid Transfer Protein 2 promoter (pronsLTP) with preferential activity in fruit epidermis, as shown by NLS-GFP fluorescence analysis. Overexpression of SlMYB75 driven by pronsLTP induced anthocyanin accumulation specifically in the growing fruit epidermis, consistent with the cuticle deposition pattern. In keeping with changes in anthocyanins, the cuticle composition in flavonoids and phenolic acids was altered, as shown by Raman microspectroscopy, as were several cuticle properties. We then edited the carotenoid PSY1 gene with a pronsLTP-driven CRISPR/Cas9 system. Different PSY1 knock-out alleles were detected predominantly in fruit exocarp and mesocarp of color-impaired pronsLTP::Cas9-Psy1 mutants, and very little in the leaf. A mutant carrying a heritable knock-out mutation in both fruit and leaf was also detected, indicating that mutants obtained with pronsLTP may require screening before being studied. Altogether, our results indicate that pronsLTP2 can efficiently result in gene overexpression and editing in fruit epidermis. Implications of these findings are important for the functional analysis and genetic engineering of cuticle-related genes in tomato.

plant biology↗

bioRxiv2024

The Zinc Finger protein SlZFP2 is essential for tomato fruit locular tissue morphogenesis

In tomato (Solanum lycopersicum L.) fruit, the locular tissue (LT) is a unique jelly-like tissue that differentiates from the central axis of the fruit after ovule fertilization. LT is essential for seed development and dispersal by preventing early germination and initiating fruit ripening. In this work, we studied a "gel-less" mutant and identified the underlying mutation in the coding sequence of the C2H2 zinc finger transcription factor (TF) SlZFP2. Histological, cytological and molecular characterization from knockout-CRISPR/Cas9 lines for this gene revealed the strong and early impact of zfp2 mutation on cell cycle and endocycle in LT. Additionally, model-based analysis of cellular data revealed that cell cycle was the main altered process, explaining the zfp2 mutant phenotype. Further laser capture microdissection coupled with RNA-Seq analysis of young LT highlighted global expression changes between WT and zfp2 mutant and led to a preliminary list of potential direct targets of the SlZFP2 TF. This multifaceted approach not only uncovered a new role for SlZFP2 TF as an essential regulator of LT morphogenesis, but also provides a foundation for future works aimed at deciphering the intricate regulatory networks governing fruit tissue development in tomato. One sentence summaryAlteration of cell division and endoreduplication in a gel-less mutant reveals the role of the transcription factor SlZFP2 in tomato locular tissue morphogenesis

plant biology↗

bioRxiv2024

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria x ananassa). Taking into account the requirements of both growers and consumers when selecting high quality cultivars is a real challenge. Here, we used an original diversity panel enriched with unique European accessions and the 50K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by GWAS, and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition and appearance occurred simultaneously in European and American populations. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosome regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new QTL, demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf-life. Moreover, major QTL for firmness, glossiness, skin resistance and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness and skin resistance. Overall, our study provides a potential avenue for extending shelf-life without compromising flavor and color as well as the genetic markers needed to achieve this goal.

genetics↗

bioRxiv2023

Strawberry phenotypic plasticity in flowering time is driven by interaction between genetic loci and temperature

The flowering time, which determines when the fruits or seeds can be harvested, is known to be sensitive to plasticity, i.e. the ability of a genotype to display different phenotypes in response to environmental variations. In the context of climate change, strawberry breeding can take advantage of phenotypic plasticity to create high-performing varieties adapted either to local conditions or to a wide range of climates. To decipher how the environment affects the genetic architecture of flowering time in cultivated strawberry (Fragaria xananassa) and modify its QTL effects, we used a bi-parental segregating population grown for two years at widely divergent latitudes (5 European countries) and combined climatic variables with genomic data (Affymetrix(R) SNP array). We detected 10 unique flowering time QTL and demonstrated that temperature modulates the effect of plasticity-related QTL. We propose candidate genes for the three main plasticity QTL, including FaTFL1 which is the most relevant candidate in the interval of the major temperature-sensitive QTL (6D_M). We further designed and validated a genetic marker for the 6D_M QTL which offers great potential for breeding programs, for example for selecting of early-flowering strawberry varieties well adapted to different environmental conditions. HighlightsA GXE study of a segregating strawberry population in Europe showed that temperature is the main driver of flowering time plasticity. A genetic marker was designed for the main QTL.

genetics↗

bioRxiv2022

Cuticle architecture and mechanical properties: a functional relationship delineated through correlated multimodal imaging

O_LICuticle are multifunctional hydrophobic biocomposites that protect aerial organs of plants. Along plant development, plant cuticle must accommodate different mechanical constraints combining extensibility and stiffness, the corresponding structure-function relationships are unknown. Recent data showed a fine architectural tuning of the cuticle architecture and the corresponding chemical clusters along fruit development which raise the question of their impact on the mechanical properties of the cuticle. C_LIO_LIWe investigated the in-depth nanomechanical properties of tomato fruit cuticle from early development to ripening, in relation to chemical and structural heterogeneities by developing a correlative multimodal imaging approach. C_LIO_LIUnprecedented sharps heterogeneities were evidenced with the highlighting of an in-depth mechanical gradient and a soft central furrow that were maintained throughout the plant development despite the overall increase in elastic modulus. In addition, we demonstrated that these local mechanical areas are correlated to chemical and structural gradients. C_LIO_LIThis study shed light on a fine tuning of mechanical properties of cuticle through the modulation of their architecture, providing new insight for our understanding of structure-function relationships of plant cuticle and for the design of biosinpired material. C_LI

plant biology↗

bioRxiv2022

Blue light promotes ascorbate synthesis by deactivating the PAS/LOV photoreceptor that inhibits GDP-L-galactose phosphorylase

Ascorbate (vitamin C) is one of the most essential antioxidants in fresh fruits and vegetables. To get insights into the regulation of ascorbate metabolism in plants, a mutant producing ascorbate-enriched fruits was studied. The causal mutation, identified by a mapping-by-sequencing strategy, corresponded to a knock-out recessive mutation in a new class of photoreceptor named PAS/LOV protein (PLP, Solyc05g07020), which acts as a negative regulator of ascorbate biosynthesis in tomato. This trait was confirmed by CRISPR/Cas9 gene editing, and further found in all plant organs, including fruit that accumulated 2-3 times more ascorbate than in the WT. The functional characterization revealed that PLP interacted with the two isoforms of GDP-L-galactose phosphorylase (GGP), known as the controlling step of the L-galactose pathway of ascorbate synthesis. The interaction with GGP occurred in the cytoplasm and the nucleus, but was abolished when PLP was mutated. These results were confirmed by an optogenetic approach using an animal cell system, which additionally demonstrated that blue light modulated the PLP-GGP interaction. Assays performed in vitro with heterologously expressed GGP and PLP showed that PLP is a non-competitive inhibitor of GGP that is inactivated after blue light exposure. This discovery sheds light on the light-dependent regulation of ascorbate metabolism in plants.

plant biology↗

bioRxiv2020

The genetic architecture of fruit colour in strawberry (Fragaria x ananassa) uncovers the predominant contribution of the F. vesca subgenome to anthocyanins and reveals underlying genetic variations

Fruit colour, which is central to the sensorial and nutritional quality of the fruit, is a major breeding target in cultivated strawberry (Fragaria x ananassa). Red fruit colour is caused by the accumulation of anthocyanins, which are water-soluble flavonoids. Here, using pseudo F1 progeny derived from the cv. Capitola and the advanced line CF1116 and taking advantage of the available high density SNP array, we delineated fruit flavonoids mQTLs (13 compounds: anthocyanin, flavonols and flavan-3-ols) and colour-related QTLs (total anthocyanins and fruit colour) to narrow genomic regions corresponding to specific subgenomes of the cultivated strawberry. Findings showed that the overwhelming majority of the anthocyanin mQTLs and other colour-related QTLs are specific to F. vesca subgenome but that other subgenomes also contribute to colour variations. We then focused on two major homoeo-mQTLs for pelargonidin-3-glucoside (PgGs) localized on both male and female maps on linkage group LG3a (F. vesca subgenome). Combined high-resolution mapping of PgGs mQTLs and colour QTLs, transcriptome analysis of selected progeny individuals and whole genome sequencing of the parents led to the identification of several INDELS in the cis-regulatory region of a MYB102-like ODORANT gene and of the deletion of a putative MADS box binding motif in the 5UTR upstream region of an anthocyanidin reductase (ANR) gene, which likely underlie significant colour variations in strawberry fruit. The implications of these findings are important for the functional analysis and genetic engineering of colour-related genes and for the breeding by Marker-Assisted-Selection of new strawberry varieties with improved colour and health-benefits.

genetics↗

bioRxiv2020

Novel ionic liquids-based extraction method that preserves molecular structure from cutin

The biopolyester cutin is ubiquitous in land plants, building the polymeric matrix of the plants outermost defensive barrier - the cuticle. Cutin influences many biological processes in planta however due to its complexity and highly branched nature, the native structure remains partially unresolved. Our aim was to define an original workflow for the purification and systematic characterisation of the molecular structure of cutin. To purify cutin we tested the ionic liquids cholinium hexanoate and 1-butyl-3-methyl-imidazolium acetate. The ensuing polymers are highly esterified, amorphous and have the typical monomeric composition as demonstrated by solid state NMR, complemented by spectroscopic (GC-MS), thermal (DSC) and x-ray scattering (WAXS) analyses. A systematic study by solution-state NMR of cryogenically milled cutins extracted from Micro-Tom tomatoes (the wild type and the gpat6 and cus1 mutants) was undertaken. Their molecular structures, relative distribution of ester aliphatics, free acid end-groups and free hydroxyl groups, differentiating between those derived from primary and secondary esters, were solved. The acquired data demonstrate the existence of free hydroxyl groups in cutin and reveal novel insights on how the mutations impact the esterification arrangement of cutin. Compared to conventional approaches, the usage of ionic liquids for the study of plant polyesters opens new avenues since simple modifications can be applied to recover a biopolymer carrying distinct types/degrees of modifications (e.g. preservation of esters or cuticular polysaccharides), which in combination with the solution NMR methodologies developed here, constitutes now essential tools to fingerprint the multi-functionality and the structure of cutin in planta.

plant biology↗

bioRxiv2020

Metabolite Quantitative Trait Loci for flavonoids provide new insights into the genetic architecture of strawberry (Fragaria x ananassa) fruit quality

Flavonoids are products from specialized metabolism that contribute to fruit sensorial (colour) and nutritional (antioxidant properties) quality. Here, using a pseudo full-sibling F1 progeny previously studied for fruit sensorial quality of cultivated strawberry (Fragaria x ananassa), we explored over two successive years the genetic architecture of flavonoid-related traits using LC-ESI-MS (13 compounds including anthocyanins, flavonols and flavan-3-ols) and colorimetric assays (anthocyanins, flavonoids, phenolics, FRAP and TEAC antioxidant capacity). Network correlation analysis highlighted the high connectivity of flavonoid compounds within each chemical class and low correlation with colorimetric traits except anthocyanins. Mapping onto the female and male linkage maps of 152 flavonoid metabolic QTLs (mQTLs) and of 26 colorimetric QTLs indicated co-localization on few linkage groups of major flavonoid- and taste-related QTLs previously uncovered. These results pave the way for the discovery of genetic variations underlying flavonoid mQTLs and for marker-assisted selection of strawberry varieties with improved sensorial and nutritional quality.

genetics↗