Mondher Bouzayen

Institut National Polytechnique de Toulouse | INPT · Biotechnology

Ripening is the last stage of the developmental program in fleshy fruits. During this phase, fruits become edible and acquire their unique sensory qualities and post-harvest potential. Although our knowledge of the mechanisms that regulate fruit ripening has improved considerably over the past decades, the processes that trigger the transition to r...

Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in frequency. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of ma...

Malformed fruits depreciate a plant's market value. In tomato (Solanum lycopersicum), fruit malformation is associated with the multi‐locule trait, which involves genes regulating shoot apical meristem (SAM) development. The expression pattern of TOPLESS3 (SlTPL3) throughout SAM development prompted us to investigate its functional significance via...

Understanding the mechanisms underlying differentiation of inflorescence and flower meristems is essential towards enlarging our knowledge of reproductive organ formation and to open new prospects for improving yield traits. Here, we show that SlDOF9 is a new modulator of floral differentiation in tomato. CRISPR/Cas9 knockout strategy uncovered the...

Ethylene Response Factors (ERFs) are downstream components of ethylene-signaling pathways known to play critical roles in ethylene-controlled climacteric fruit ripening, yet little is known about the molecular mechanism underlying their mode of action. Here, we demonstrate that SlERF.F12, a member of the ERF.F subfamily containing EAR motifs, negat...

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 previou...

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...

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...

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‐de...

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 ce...

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...

The apical hook of dark-grown dicotyledonous plants results from asymmetric growth of the inner and outer sides of the upper part of the hypocotyl. This protective structure prevents damage of the shoot apical meristem and the young leaves as the seedling pushes through the soil. HOOKLESS (HLS1) of Arabidopsis was recognised as an ethylene response...

The involvement of ethylene in fruit ripening is well documented, though knowledge regarding the crosstalk between ethylene and other hormones in ripening is lacking. We discovered that AUXIN RESPONSE FACTOR 2A (ARF2A), a recognized auxin signaling component, functions in the control of ripening. ARF2A expression is ripening regulated and reduced i...

Expression levels of ARF2A and fruit phenotypes in different independent ARF2-OX transgenic lines. (A) Relative expression levels of ARF2A analyzed by qRT-PCR in leaves of WT cv. M82 and five independent ARF2-OX transgenic lines; error bars represent SE; statistical significance was evaluated using a student’s t-test with three biological repeats b...

Hierarchical clustering analysis of ARF2-OX microarray data. Hierarchical clustering analysis of differentially expressed genes in ARF2-OX transgenic fruit, compared to WT-42G, as analyzed by microarray analysis. (TIF)

Hierarchical clustering analysis of carotenoid-related genes in ARF2-OX fruit. Hierarchical clustering analysis of carotenoid-related genes in ARF2-OX transgenic fruit, compared to WT-42G, as analyzed by microarray analysis. (TIF)

Hormone analysis during fruit development in two seasons of harvest. Hormone levels were measured in ten fruit developmental stages (immature green to red ripe; 1 to 10) in two sequential growing seasons (2014 and 2015). Error bars represent SD. (TIF)

Expression levels of ARF2 genes and fruit phenotypes in ARF2as transgenic lines. (A) Summary of ARF2A and ARF2B expression changes and fruit phenotypes in seven independent ARF2as transgenic lines. Relative expression levels of (B) ARF2A and (C) ARF2B, analyzed by qRT-PCR in red fruit of WT cv. MicroTom and independent ARF2as transgenic lines; erro...

Gene expression analysis of ARF2as transgenic fruit. Relative expression levels of ripening regulators in ARF2as red fruit, analysed by qRT-PCR. DPA- days post anthesis; cv. MicroTom; * p-value<0.05; * *p-value<0.01 (TIF)

Expression analyses of ARF2 homologs in ARF2-OX patches. Relative gene expression levels of ARF2 homologs (ARF2B, ARF3, ARF4 and ARF9) in WT cv. M82 and ARF2-OX fruit at 39, 42 and 53 dpa. Error bars represent SE; statistical significance was evaluated using an ANOVA test (JMP software, SAS) with three biological repeats based on the average of thr...

Hierarchical clustering analysis of ethylene-related genes in ARF2-OX fruit. Hierarchical clustering analysis of ethylene-related genes in ARF2-OX transgenic fruit, compared to WT-42G, as analyzed by microarray analysis. (TIF)

PCA of untargeted flavonoid analysis in negative mode from UPLC-QTOF-MS analysis of ARF2as. (XLSX)

Significantly different putative metabolites identified to in red ARF2as tomato fruit by UPLC/qTOF-MS in positive and negative modes. (XLSX)

Ethylene- related genes differentially expressed in ARF2-OX fruit. (XLSX)

Isoprenoids, carotenoids and glycoalkaloid in ARF2-OX fruit from HPLC analysis. (XLSX)

ACS4 expression in altered ethylene treated fruit. Relative expression levels of ACS4 in ethylene treated fruit at three developmental stages (MG, Br and R). Error bars represent SE. Statistical significance was evaluated using a student’s t-test, **p-value<0.01 and ***p-value<0.001; dpa: days post anthesis. (TIF)

Alignment of ARF2as fragment with ARF2A and ARF2B sequences. Nucleotide alignment of the ARF2as construct with ARF2A and ARF2B genes, showing putative targeting of both closely related genes. (PDF)

Differentially expressed genes in ARF2-OX transgenic fruit from microarray analysis. (XLSX)

Classification of differentially expressed genes in ARF2-OX transgenic fruit according to biological processes (by Gene Orthology annotation). (XLSX)

Carotenoid-related genes differentially expressed in ARF2-OX fruit. (XLSX)

PCA of untargeted flavonoid analysis in positive mode from UPLC-QTOF-MS analysis of ARF2-OX. (XLSX)

Hormone analysis of ARF2-OX fruit. (XLSX)

PCA of untargeted flavonoid analysis in negative mode from UPLC-QTOF-MS analysis. (XLSX)

Detailed protocol of the hormone analysis. (PDF)

Hormone analysis of ARF2as fruit. (XLSX)

Classification of differentially expressed genes in ARF2-OX transgenic fruit according to molecular function (by Gene Orthology annotation). (XLSX)

List of oligonucleotides used for cloning, qRT-PCR and Fluidigm© analyses in this study. (XLSX)

Meteorological data originate from the Regional Agency for the Environmental Protection of Veneto (ARPAV), Italy. Climatological data of decadal temperatures, rainfall, and temperature excursions for 2011–2012 compared to the period 1992–2012 are reported.

Quantitative RT-PCR analyses on the following VviYUC1, VviTAR4, Vvi ARF25, VviIAA15b, VviGH3-21, and VviGH3-22 performed in flesh and skin of berries sampled from both 1103P/CS (solid bars) and M4/CS (empty bars) graft combination in 2011 growing season. Results are shown as means and SE for two biological replicates. Bars indicate SE. Different le...

(A) Sequencing and alignment statistics. Sample name (Sample), replicate, paired-end Tag, total number of produced reads (Total), filtered reads after trimming (Filtered), good-quality reads (# Good), aligned and percentage of aligned reads (% Aligned), number of alignment (# alignment) are reported. (B) Summary of read number after pairing (F3 + F...

Expression values (mean normalized mRNA-seq counts) of all 56 auxin-related genes. Gene family, V1 12X annotation, gene name are reported. Graft combination (CS/1103P and CS/M4), considered tissue (whole berry, skin, and pulp) and phenological phase (E-L31, E-L36, and E-L38) are also indicated.

Colorimetric results of CS/1103P and CS/M4 berry. Analyses were carried out at four time points corresponding to 45, 72, 86, and 100 DAFB.

Samplings of berries grown in both 1103P/CS and M4/CS graft combinations were performed at different stages of berry development and ripening. Growing season: 2012. (A) Soluble solids content in CS/M4 (squares) and CS/1103P (circles) throughout fruit development. (B) CIRG values of CS/M4 (square) and CS/1103P (circle) graft combinations throughout...

Quantitative RT-PCR analyses on the following flavonoid-related genes: VviPAL3-like (VIT_13s0019g04460, A), VviCHS3 (VIT_05s0136g00260, B), VviLAR2 (VIT_17s0000g04150, C), VviFLS1 (VIT_18s0001g03430, D), and VviUFGT (VIT_16s0039g02230, E). Transcript levels in CS/1103P (black) and CS/M4 (white) berries are shown as means of normalized expression ±S...

Nomenclature of genes belonging to the grapevine ARF, Aux/IAA, and GH3 multigenic families.

Primers used for qPCR analyses. V1 12X identifier (V1 12X ID), gene name, forward (FW sequence) and reverse (RV sequence) sequences are reported.

List of DEGs influenced by Rootstock (R), Tissue (T), and Phenological Phase (PP) components. Numbers of DEG are given in brackets. PN40024 V1 12X annotation (V1 12X ID) and functional annotation (Funct. annot.) of DEGs are reported. Statistical analysis were carried out according to an FDR adjusted p-value lower than 0.05.

Over-enriched GO terms of genes differentially expressed influenced by rootstock (R), tissue (T), and phenological phase (P) factors. For each term, the GO identifier (GO-ID), the complete Gene Ontology term (Description), the p-value and the FDR-corrected P-value (corr p-value) of the Fisher's exact test, the numbers of sequences in the test set (...

In modern viticulture, grafting commercial grapevine varieties on interspecific rootstocks is a common practice required for conferring resistance to many biotic and abiotic stresses. Nevertheless, the use of rootstocks to gain these essential traits is also known to impact grape berry development and quality, although the underlying mechanisms are...

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...

Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2) which encodes...

Auxin related phenotypes displayed by SlARF2A/B-RNAi lines. (A) SlARF2A/B-RNAi lines showing the development of triple cotyledons. (B) SlARF2A/B lines showing root branching phenotypes. (PDF)

List of primers used in the expression studies. (PDF)

Expression of SlARF in SlARF2AB-RNAi fruits assessed by Quantitative RT-PCR. Total RNA was extracted from WT and mutant fruits at the breaker stage. The relative mRNA levels of each SlARF gene in WT were standardized to 1.0, referring to the SlActin gene as internal control. Error bar means ±SD of three biological replicates. Stars indicate statist...

The plant hormone ethylene plays a key role in climacteric fruit ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the ripening-related genes and interacts with other signaling pathways to regulate the...

Water deficit and increasing salinization reduce productivity of wheat, the leading crop for human diet. While the complete genome sequence of this crop has not been deciphered, a BAC library screening allowed the isolation of TdERF1, the first ethylene response factor gene from durum wheat. This gene is putatively involved in mediating salt stress...

Auxin is known to be involved in all the stages of fruit development. Aux/IAAs are regulators of the auxin signaling at the transcription level. In a recent study, using RNAi strategy to limit the expression Sl-IAA17, it was shown that this tomato AuxIAA regulates fruit size mainly through altering the ploidy level of pericarp cells. Indeed, Sl-IAA...

Significance This work shows that active DNA demethylation governs ripening, an important plant developmental process. Our work defines a molecular mechanism, which has until now been missing, to explain the correlation between genomic DNA demethylation and fruit ripening. It demonstrates a direct cause-and-effect relationship between active DNA de...

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 geno...

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 caro...

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...

Auxin plays a pivotal role in various plant growth and development processes, including vascular differentiation. The modulation of auxin responsiveness through the auxin perception and signaling machinery is believed to be a major regulatory mechanism controlling cambium activity and wood formation. To gain more insights into the roles of key Aux/...

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...

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...

Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyp...

Auxin is known to regulate cell division and cell elongation, thus controlling plant growth and development. Part of the auxin signaling pathway depends on the fine-tuned degradation of the auxin/indole acetic acid (Aux/IAA) transcriptional repressors. Recent evidence indicates that Aux/IAA proteins play a role in fruit development in tomato (Solan...

As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat...

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 that Sl-ERF.B.3 is an abiotic stress responsive gene, which is induced by cold, heat, and flooding, but downregulated by salinity and drought. To get mor...

Most land plant species live in symbiosis with arbuscular mycorrhizal (AM) fungi. These fungi differentiate essential functional structures called arbuscules in root cortical cells from which mineral nutrients are released to the plant. We investigated the role of miR393, a microRNA that targets several auxin receptors, in AM root colonization. Exp...