Biology subjects

Martin-Pizarro, C.

Publications and source records attributed to Martin-Pizarro, C..

6 recordsLinked to original sources

bioRxiv2025

Uncovering the genetic basis of fruit volatiles in Fragaria vesca through GWAS reveals FvJMT2 as a methyl benzoate biosynthesis gene with insect-repellent function

Strawberry aroma is a key component of fruit quality, influencing consumer preferences and playing important ecological roles, including plant defense. However, the genetic basis of volatile organic compound (VOC) biosynthesis remains only partially understood, particularly in the wild woodland strawberry Fragaria vesca, which has enormous potential to uncover genetic diversity within the genus for improving the commercial strawberries. Here, we performed Genome-Wide Association Studies (GWAS) across a diverse European collection of F. vesca accessions. We identified multiple novel candidate genes involved in the biosynthesis of diverse volatile esters, lactones, terpenoids, and methyl ketones. Among them, we characterized FvJMT2, a SABATH family methyltransferase which we found associated with natural variation in benzenoid esters content. Transient expression in Nicotiana benthamiana and strawberry fruit confirmed its role in methyl benzoate biosynthesis, while enzymatic assays demonstrated that FvJMT2 encodes a promiscuous enzyme capable of methylating not only benzoic acid, but also cinnamic, salicylic, and jasmonic acids. Behavioral assays revealed that methyl benzoate at physiologically relevant concentrations significantly reduced the attraction of Drosophila suzukii flies, supporting a dual role of this VOC in both flavor and pest deterrence. Finally, natural variation analyses in wild Fragaria species and F. x ananassa cultivars showed that benzenoid esters have been largely lost in modern cultivars but retained in ancient and wild accessions. Altogether, this study provides novel insights into the genetics and ecological relevance of strawberry volatiles and identifies candidate loci and alleles for future studies.

genomics↗

bioRxiv2025

Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

Ascorbate is the most abundant water-soluble antioxidant in plants, and it is an essential molecule for normal plant development. It is present in all green plants, with very different concentrations in different plant species. While ascorbate accumulation is a trait of nutritional, and therefore, agronomical interest, the impact of different concentrations over cellular homeostasis remains elusive. In order to shed light over this question, we leveraged Arabidopsis lines with very low ascorbate (vtc2 mutant with 20% of WT ascorbate levels), and low ascorbate concentration (vtc4 mutant with 65% of WT levels), and we generated a line that accumulates 165% of WT levels (vtc2/OE-VTC2). An 80% reduction of ascorbate increased the expression of genes implicated in defense against pathogens, but repressed genes associated with abiotic stress responses. Unexpectedly, lines with increased (165% of WT) and decreased (65% of WT) ascorbate levels shared 85% of induced transcription factors and the GO terms associated with their transcriptional programs. Among the group of genes whose expression is positively correlated with ascorbate content, we identified TAA1/WEI8, a gene encoding a tryptophan aminotransferase that catalyzes the first step of auxin biosynthesis. Using a combination of genetic and pharmacological approaches in fluorescent and histochemical reporter lines for auxin biosynthesis and signaling activity, we revealed that TAA1- and TAA1-RELATED2 (TAR2)-mediated auxin biosynthesis is necessary for plants to cope with increased ascorbate concentration in a light-dependent manner, revealing a new layer of complexity in the regulatory landscape of redox homeostasis.

plant biology↗

bioRxiv2025

Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry

Transposable elements (TEs) are major components of plant genomes and powerful drivers of regulatory and phenotypic diversity, yet their mechanistic contributions to gene regulation in non-model crops remain poorly understood. Here, we generate a comprehensive and curated TE annotation for woodland strawberry (Fragaria vesca), revealing that TEs comprise [~]30% of the genome and uncovering an exceptional enrichment of gene-proximal miniature inverted-repeat transposable elements (MITEs) and short inverted repeats (IRs). Integrating small RNA, DNA methylation and transcriptomic data across tissues and fruit developmental stages, we show that most gene-associated MITEs and IRs are epigenetically active, producing 24-nt siRNAs and displaying dynamic CHH methylation patterns during fruit ripening. Genome-wide analyses reveal that MITE- and IR-proximal genes occupy a distinct regulatory landscape compared to genes associated with other TE classes, consistent with a role in context-dependent transcriptional regulation. As a mechanistic proof of concept, we demonstrate that a Mutator-like MITE located near FvAAT1, encoding a key alcohol acyltransferase required for aroma ester biosynthesis, modulates gene expression through siRNA-dependent DNA methylation and ripening-stage-specific chromatin reorganization. Transient perturbation of this MITE epigenetic state alters FvAAT1 expression, and chromatin conformation capture reveals MITE-associated looping at this locus. Notably, this regulatory MITE is conserved in commercial strawberry species, suggesting an evolutionarily preserved function in fruit quality traits. Extending these findings to natural variation, we characterize thousands of TE insertion and deletion polymorphisms across 210 European F. vesca accessions and show that TE-based variation recapitulates population structure. A TE-informed genome-wide association analysis identifies significant associations between MITE and IR polymorphisms and fruit volatile compounds, including key aroma determinants. Together, our results establish MITEs and short IRs as widespread, epigenetically active regulatory elements that shape gene expression, chromatin architecture and phenotypic diversity in strawberry. This work provides a conceptual and methodological framework to integrate TE-driven regulatory variation into population genomics, breeding and genome-editing strategies aimed at improving fruit quality.

genomics↗

bioRxiv2025

FaRIF at the Core of Strawberry Fruit Ripening: Deciphering its Targets and Interaction Networks

Ripening Inducing Factor (RIF) is a key NAC transcription factor regulating strawberry fruit ripening. Previous studies using RIF-RNAi and overexpression lines in Fragaria x ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIFs transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF-RNAi transcriptome data. These analyses revealed FaRIFs direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related transcription factors, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC transcription factors. Among these, FaNAC034 was found to synergistically enhance FaRIFs transcriptional activity. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our knowledge of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular mechanisms underlying strawberry fruit ripening regulation by this transcription factor.

plant biology↗

bioRxiv2020

Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit

Anthocyanins are the principal color-producing compounds synthesized in developing fruits of strawberry (Fragaria spp.). Substantial natural variation in color have been observed in fruits of diploid and octoploid accessions, resulting from distinct accumulation and distribution of anthocyanins in fruits. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. xananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon insertion in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, residing in the F. iinumae-derived subgenome, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression and anthocyanin accumulation. Our findings suggest that putative cis regulatory elements provided by FaEnSpm-2 are required for high and ectopic MYB10-2 expression and induction of anthocyanin biosynthesis in fruit flesh. We developed MYB10-2 (sub-genome) specific DNA markers for marker-assisted selection that accurately predicted anthocyanin phenotypes in octoploid segregating populations.

plant biology↗

bioRxiv2018

Functional Analysis of TM6 MADS box gene in the Octoploid Strawberry by CRISPR/Cas9 directed mutagenesis

The B-class of MADS-box transcription factors has been studied in many plant species, but remain functionally uncharacterized in the Rosaceae family. APETALA3 (AP3), a member of this class, controls the identity of petals and stamens in Arabidopsis thaliana. In this work, we identified two members of the AP3 lineage in the cultivated strawberry (Fragaria x ananassa): FaAP3 and FaTM6. Interestingly, FaTM6, and not FaAP3, shows an expression pattern equivalent to that of AP3 in Arabidopsis. Genome editing using Cluster Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system is becoming a robust tool for targeted and stable mutagenesis of DNA. However, whether it can be efficiently used in an octoploid species such as F. x ananassa is not known. Here we report for the first time the application of CRISPR/Cas9 in F. x ananassa to characterize the function of FaTM6 in flower development. An exhaustive analysis by high-throughput sequencing of the FaTM6 locus spanning the target sites showed a high efficiency genome editing already in the T0 generation. The phenotypic characterization of the mutant lines indicates that FaTM6 plays a key role in petal and especially in anther development in strawberry. in an octoploid species such as F. x ananassa, and offer new opportunities for engineering strawberry to improve traits of interest in breeding programs.

molecular biology↗