Biology subjects

Denoyes, B.

Publications and source records attributed to Denoyes, B..

8 recordsLinked to original sources

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↗

bioRxiv2025

Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry

Floral initiation is required for sexual reproduction in angiosperm plants, and has a significant impact on crop yields. In cultivated strawberry, the molecular basis of floral initiation is poorly understood and most studies have focused on a single genotype grown under controlled conditions. To gain more insight into this process, we conducted a study under natural conditions in two countries using two seasonal flowering cultivars. We focused on the early steps of floral initiation by using samples spanning key developmental stages of the shoot apical meristem. The analysis of differential gene expression in leaf and terminal bud tissues revealed enrichment for genes involved in carbohydrate metabolism and phytohormone pathways in leaves. Other protein classes that were enriched during early floral initiation were associated with cytoskeleton organization, cell cycle regulation, and chromatin structure. We also identified genes associated with the photoperiodic pathway, well-characterized floral integrators such as TFL1 and SOC1, and several linked to phytohormone regulation, such as XTH23, PP2 and EIN3.

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↗

bioRxiv2023

Epigenetic and transcriptional landscape of heat-stress memory in woodland strawberry (Fragaria vesca)

We have previously reported that different stresses can lead to substantial DNA methylation changes in strawberry. Here, we wanted to assess the heritability of heat-stress induced DNA methylation and transcriptional changes following asexual and sexual reproduction in a plant. Woodland strawberry (Fragaria vesca) is an ideal model to study epigenetic inheritance in plants because it presents two modes of reproduction: sexual and asexual. Here we wanted to assess if heat-stress induced DNA methylation changes can be transmitted via asexual reproduction and whether past stresses can also affect sexually propagated progenies. Our genome-wide study provides evidence for a memory acquisition and maintenance in F. vesca. We found that certain DNA methylation changes can stably be transmitted over at least three asexual generations. Finally, the first sexual generation by selfing from stressed maternal and their respective non-stressed asexual daughter plants showed both shared and unique stress responses. This suggests that an acquired molecular memory from the previous heat-stress event was transmitted. This molecular memory might be involved in functional plasticity and stress adaption, an important aspects that will have to be investigated in future studies. Finally, these findings may contribute to novel approaches that may contribute to the breeding of climate-ready plants. IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSWith ongoing climate change, natural plant populations and crops are facing stress situations more frequently and at higher intensity. These unfavorable growing conditions force plants to develop strategies to adapt to persist. One of these strategies involves epigenetic mechanisms which can affect the activity of genes without altering the actual DNA sequence. These molecular modifications can be retained by plants as a molecular "memory" which might be used later to better respond to a stressful event. QuestionIs there multi-generational persistence of heat-stress induced epigenetic patterns in strawberry and are heritable epigenetic changes associated with stress adaptation? FindingsWe found that the strawberry methylome and transcriptome respond with a high level of flexibility to heat-stress. In addition, we took advantage of the two reproductive modes of strawberry (asexual and sexual) to evaluate the acquisition and maintenance of molecular stress memory. We showed how specific DNA methylation and gene expression changes can persist for a long time in progeny plants. We found that the asexual, and seemingly also sexual progenies can retain information in the genome of a past stressful condition that was encountered by its progenitor. Next stepsOur work presents valuable epigenetic and transcriptional screening data to understand plant memory maintenance and transmission over generations. The most important next step will be to assess if heritable stress-induced epigenetic changes can contribute to stress adaptation through a plant competition experiment in natural environments. One sentence summaryStrawberry can transmit molecular stress-memory at the DNA methylation and transcriptional level over multiple generations which may play an important role in stress adaptation.

plant biology↗

bioRxiv2022

DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)

O_LIEnvironmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes especially at the level of DNA methylation. DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. C_LIO_LIWe investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable environmental conditions at DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. C_LIO_LIThese findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses. C_LI

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

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↗