Increasing global food demand is one of the greatest challenges of modern agricultural sciences. A crucial agronomic trait for plant breeding programs to increase yield production is fruit weight (FW). Although two major FW quantitative loci (FW2.2 and FW11.3) have been isolated and studied in several crop species, much still remains to be done for stone fruit trees, such as plum (Prunus domestica L.). In this study, six Italian plum varieties were evaluated for fruit size-related traits and genotypic characteristics. Data brought out that Pappacona varieties were a good model for identifying molecular markers associated with fruit size. Using the recently released plum genome assembly, 73 cell number regulator (CNR) and 42 cell size regulator (CSR) genes were finely annotated. Two FW2.2 (PdCNR-1 and PdCNR-2) and one FW11.3 (PdCSR-1) homologs were identified. To provide a first transcriptional characterization, PdCNR-1, PdCNR-2, and PdCSR-1 were analyzed by real-time PCR. PdCNR-1 and PdCSR-1 expression patterns suggested a potential novel regulatory pathway in plum, which might contribute to variations in fruit size and weight. A better understanding of plum FW quantitative loci will promote progress in both basic research and practical breeding activities aiming to select large-fruited varieties.

BACKGROUND:Fungus-resistant PIWI (Pilzwiderstandsfähig) grape cultivars are promising for reducing pesticide inputs in viticulture, but their enological potential is still poorly characterized. We performed a pilot, single-vintage study integrating berry gene expression and phenolic composition in five Italian red PIWI cultivars (Cabernet Eidos, Cabernet Volos, Julius, Merlot Kanthus and Merlot Khorus), using Pinot Noir as a non-PIWI Vitis vinifera benchmark. RESULTS:At harvest, transcript levels of 15 genes involved in sugar/energy signalling (TOR3, SnRK1.1, SnRK1.2), flavonoid biosynthesis (LAR1, LAR2, ANR, DFR, LDOX, FLS4, FLS5) and flavonoid glycosylation (GAT1, UFGT, Va5GT, Vl3GT, UGT72), were quantified, together with technological maturity traits, skin and seed phenolic fractions, and skin flavonol profiles. The PIWI panel showed marked variety-specific transcriptional and metabolic differences. SnRK1 isoforms varied more strongly among cultivars than TOR3. Hierarchical clustering of scaled transcript profiles separated samples into two major branches, indicating coordinated genotype-dependent modulation of sugar-signalling and flavonoid/glycosylation genes. Higher expression of flavonoid biosynthetic and glycosyltransferase genes (including LAR2, FLS5, Va5GT and UGT72) was associated with higher anthocyanins, quercetin- and myricetin-type flavonol glycosides, and colour intensity. Several, but not all, PIWI cultivars combined moderate-to-high sugars with comparatively high acidity, frequent enrichment in skin anthocyanins and flavonol glycosides, and lower extractable skin tannins than Pinot Noir. CONCLUSION:These results support a cultivar-resolved molecular and compositional framework for interpreting enological variability in Italian red PIWI grapes. The data may guide breeding and cultivar-tailored winemaking strategies, while broader generalization requires validation across additional genotypes, vintages and ripening stages. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Events of duplication and neo/subfunctionalization have significantly expanded the functional roles of R2R3 myeloblastosis (MYB) transcription factors in plants. In a previous study, we demonstrated that two paralogous R2R3 MYBs from Solanum tuberosum and S. commersonii, AN1 and AN2, respectively, induce anthocyanin pigmentation to varying extents when transiently overexpressed. However, questions related to the distinct functions of these genes remained unanswered. In this study, we further investigated these genes by comparing transgenic tobacco plants that constitutively overexpress AN1 and AN2. We observed differences between AN1 and AN2 that not only influenced plant pigmentation but also impacted the structural features of vascular tissues. Both genes promoted the accumulation of phenolamides; however, AN1 showed a stronger capacity to regulate the phenylpropanoid pathway. In addition, our results suggest a potential role for AN2 in regulating additional biological processes potentially involved in vascular development, as indicated by the GUS promoter localization study. Collectively, these results shed new light on the potentially ancestral functions of these R2R3 MYB genes, extending their known impact beyond anthocyanin biosynthesis.

Plants are subjected to various stresses during the growth process, including biotic stresses, as well as abiotic stresses such as temperature, drought, salt, and heavy metals. To cope with these biotic and abiotic adversities, plants have evolved complex regulatory mechanisms during their long-term environmental adaptations. In a suddenly changing environment, protein modifiers target other proteins to induce post-translational modification (PTM) in order to maintain cell homeostasis and protein biological activity in plants. PTMs modulate the activity of enzymes and transcription factors in their respective metabolic pathways, enabling plants to produce essential compounds for their survival under stress conditions. Examples of post-translational mechanisms include phosphorylation, ubiquitination, glycosylation, acetylation, protein–protein interactions, and targeted protein degradation. Furthermore, the role of histone modifications in regulating secondary metabolism deserves attention due to its potential impact on heritability and its contribution to stress tolerance. Understanding the epigenetic aspect of these modifications can provide valuable insights into the mechanisms underlying stress response. In this context, also examining PTMs that impact the biosynthesis of secondary metabolites is meaningful. Secondary metabolites encompass a wide range of compounds such as flavonoids, alkaloids, and terpenoids. These secondary metabolites play a crucial role in plant defense against herbivores, pathogens, and oxidative stress. In this context, it is imperative to understand the contribution of secondary metabolism to plant tolerance to abiotic stresses and how this understanding can be leveraged to improve long-term survival. While many studies have focused on the transcriptional regulation of these metabolites, there is a growing interest in understanding various changes in PTMs, such as acetylation, glycosylation, and phosphorylation, that are able to modulate plants’ response to environmental conditions. In conclusion, a comprehensive exploration of post-translational mechanisms in secondary metabolism can enhance our understanding of plant responses to abiotic stress. This knowledge holds promise for future applications in genetic improvement and breeding strategies aimed at increasing plant resilience to environmental challenges.

In Italy, lemon is a crucial economic cultivation, primarily grown in southern regions like Sicily, Calabria, Apulia and Campania. Despite its importance, the number of cultivars is limited and efforts are being made to both exploit and preserve local cultivars. Bio-agronomic and genetic characterization are essential steps towards achieving these goals. Our study explores the phenotypic and genetic diversity of four local cultivars from Campania region, ‘Ovale di Sorrento’, ‘Sfusato Amalfitano’, ‘Procida’ and ‘San Francesco’, over two years (2021 and 2022). We evaluated agronomic parameters of the entire plant, fruits and seeds, and conducted biochemical analyses of lemon juice. Furthermore, we addressed the challenges posed by low interspecific genetic variation through simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker analysis. Field data revealed significant differences in production between the two years and among the cultivars, with ‘Ovale di Sorrento’ and ‘Sfusato Amalfitano’ being the most productive, and ‘Procida’ recording the lowest values of soluble solids and acidity. Genotyping data from 19 SSR markers confirmed low variability, while ddRADSeq-based SNP analysis revealed clear structuration into three distinct groups: the first group comprised ‘Ovale di Sorrento’ and ‘San Francesco,’ differentiated from ‘Procida’ and ‘Sfusato Amalfitano’. Additionally, 29 high-effect variants provided valuable insights into the genetic distinctions and functional variations among the four lemon cultivars. In particular, the presence of variants in genes associated with mobile elements confirmed their significant contribution to the genetic diversity of plants. This study underscores the importance of combining phenotypic and genotypic analyses for better varietal characterization and valorization.

Solanum commersonii shows tolerance to low temperatures, a key target trait for potato breeding. Calciumdependent protein kinases (CIPKs) play a significant role in plant defence response to several stresses, including cold. In this study, we observed the expression of ScCIPK1, ScCIPK3, ScCIPK23 and ScCIPK24 in S. commersonii exposed to 4 degrees C at multiple time intervals. Initial findings revealed that these genes were under-expressed after 10 and 30 minutes of cold stress, except ScCIPK3. Notably, after 24 hours, all genes displayed higher expression levels compared to the non-stressed controls. These findings highlight the role of ScCIPK3 in the early stages of cold response and indicate a coordinated regulatory mechanism across CIPKs that likely contributes to the cold stress tolerance observed in S. commersonii. In this work, we introduce a model to elucidate the signalling crosstalk under cold stress in S. commersonii, providing insights that could facilitate the development of cold-resistant potato cultivars.

O-methyltransferases (OMTs) are group of enzymes involved in the methylation of various secondary metabolites, including anthocyanins. This secondary modification, together with hydroxylation and glycosylation, affects the chromatic properties, stability and reactivity of these pigments. Meanwhile, no detailed identification or genome-wide analysis of the OMT gene family members in potato (Solanum tuberosum) has been reported. We conducted a genome-wide identification and characterization of potato OMTs, identifying 65 OMT family members. These were characterized based on gene structure, evolutionary relationships, and promoter motifs. Analysis of available gene expression profiles from public databases revealed expression patterns indicative of tissue- and temporal-specificity Finally, we further elucidated expression differences among four selected OMT-encoding genes using potato cell cultures, which represent a smart and gainful alternative for anthocyanin production and deep knowledge about these post-biosynthetic modifications.

The DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors involved in diverse biological processes, including response to biotic and abiotic stresses. Members of this family have been reported in the cultivated potato Solanum tuberosum, but clues to the roles of several Dof genes are still lacking. Potato wild relatives represent a genetic reservoir for breeding as they could provide useful alleles for adaptation to the environment and tolerance to biotic and abiotic stresses. We performed an in silico analysis to identify genes belonging to the Dof family in the wild potato S. commersonii, confirming that the identified Dof genes can be grouped in four classes (A, B, C, D), as reported for cultivated potato. A special focus was dedicated to Cycling Dof Factors (CDFs), which play a crucial role in plant responses to abiotic stresses. Analysis of available RNA-seq data confirmed CDF genes as regulated by stresses and often in a tissue specific manner. To ascertain their involvement in the stress response, S. tuberosum and S. commersonii plantlets growing in vitro were subjected to salt stress (80mM NaCl) for short (2 days) and prolonged (7 days) times. Analysis of phenotypic traits and qRT-PCR expression profiles of target CDF genes in aerial and root tissues showed differences between the two species. In addition, after saline treatment, changes in total phenols, proline, and malondialdehyde suggested a diverse perception of saline stress in S. commersonii vs. S. tuberosum. Overall, this study provided useful clues to the involvement of CDF genes in salt response and promoted the identification of potential candidate genes for further functional studies.

Transmembrane proteins (TMPs) are pivotal components of plant defence mechanisms, serving as essential mediators in the response to biotic stresses. These proteins are among the most complex and diverse within plant cells, making their study challenging. In spite of this, relatively few studies have focused on the investigation and characterization of TMPs in plants. This is particularly true for grapevine. This review aims to provide a comprehensive overview of TMP-encoding genes involved in grapevine immunity. These genes include Lysin Motif Receptor-Like Kinases (LysM-RLKs), which are involved in the recognition of pathogens at the apoplastic level, Plant Respiratory Burst Oxidase Homologs (Rbohs), which generate reactive oxygen species (ROS) for host defense, and Sugars Will Eventually be Exported Transporters (SWEETs), which play a role in nutrient allocation and stress responses. Furthermore, the review discusses the methodologies employed to study TMPs, including in vivo, in vitro and in silico approaches, highlighting their strengths and limitations. In vivo studies include the assessment of TMP function in whole plants or plant tissues, while in vitro experiments focus on isolating and characterizing either specific TMPs or their components. In silico analyses utilize computational tools to predict protein structure, function, and interactions. By identifying and characterizing genes encoding TMPs involved in grapevine immunity, researchers can develop strategies to enhance grapevine resilience and lead to more sustainable viticulture.

Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

Potato is a perfect target for bio-fortification strategies. This crop has contributed for thousand years to human diet, and its tubers still represent a staple food fundamental for worldwide food security. Besides being an important source of energy, potato tubers contain compounds with nutraceutical properties including minerals, vitamins, proteins, and specialized metabolites. Therefore, we outlined this chapter devoting a significant space to both genomic and biotechnology studies addressed, respectively, to identify genomic sequence and genes influencing the amount nutraceutical molecules accumulated and to increment/introduce existing nutraceutical molecules or novel nutrients in the tuber. Before entering in the core of the chapter, we made an extensive introduction to the nutraceutical molecules which have been investigated in potato tubers. Then, we focused on innovative approaches, including gene editing and organelle transformation, with great potential for the nutraceutical bio-fortification of the potato. The leitmotiv of the chapter is the biodiversity of potato germplasm (including wild tuber-bearing species), which is a key aspect in potato tuber bio-fortification. The critical review of the literature suggested us to conclude pointing out the current scientific challenges for fully exploiting potato as a "vibrant feedstock for nutraceuticals."

BackgroundThe biochemical makeup of grape berries at harvest is essential for wine quality and depends on a fine transcriptional regulation occurring during berry development. In this study, we conducted a comprehensive survey of transcriptomic and metabolomic changes occurring in different berry tissues and developmental stages of the ancient grapes Aglianico and Falanghina to establish the patterns of the secondary metabolites contributing to their wine aroma and investigate the underlying transcriptional regulation.ResultsOver two hundred genes related to aroma were found, of which 107 were differentially expressed in Aglianico and 99 in Falanghina. Similarly, 68 volatiles and 34 precursors were profiled in the same samples. Our results showed a large extent of transcriptomic and metabolomic changes at the level of isoprenoids (terpenes, norisoprenoids), green leaf volatiles (GLVs), and amino acid pathways, although the terpenoid metabolism was the most distinctive for Aglianico, and GLVs for Falanghina. Co-expression analysis that integrated metabolome and transcriptome data pinpointed 25 hub genes as points of biological interest in defining the metabolic patterns observed. Among them, three hub genes encoding for terpenes synthases (VvTPS26, VvTPS54, VvTPS68) in Aglianico and one for a GDP-L-galactose phosphorylase (VvGFP) in Falanghina were selected as potential active player underlying the aroma typicity of the two grapes.ConclusionOur data improve the understanding of the regulation of aroma-related biosynthetic pathways of Aglianico and Falanghina and provide valuable metabolomic and transcriptomic resources for future studies in these varieties.

Grapevine (Vitis vinifera L.) seeds are rich in polyphenols including proanthocyanidins, molecules with a variety of biological effects including anticancer action. We have previously reported that the grape seed semi-polar extract of Aglianico cultivar (AGS) was able to induce apoptosis and decrease cancer properties in different mesothelioma cell lines. Concomitantly, this extract resulted in enriched oligomeric proanthocyanidins which might be involved in determining the anticancer activity. Through transcriptomic and metabolomic analyses, we investigated in detail the anticancer pathway induced by AGS. Transcriptomics analysis and functional annotation allowed the identification of the relevant causative genes involved in the apoptotic induction following AGS treatment. Subsequent biological validation strengthened the hypothesis that MDM2 could be the molecular target of AGS and that it could act in both a p53-dependent and independent manner. Finally, AGS significantly inhibited tumor progression in a xenograft mouse model of mesothelioma, confirming also in vivo that MDM2 could act as molecular player responsible for the AGS antitumor effect. Our findings indicated that AGS, exerting a pro-apoptotic effect by hindering MDM2 pathway, could represent a novel source of anticancer molecules.

Proof of concept salt tolerance and plasticity. Wild germplasm may represent a precious source of genetic variability for salt tolerance. This study evaluated the morphological changes occurring under controlled and saline conditions in tuber-bearing S. bulbocastanum, S. commersonii, S. chomatophyllum, S. multidissectum, S. pinnactisectum, S. phureja, and cultivated S. tuberosum. An in vitro screening method was employed. Significant phenotypic variations were observed for all phenotypic traits analyzed at all NaCl levels (0, 40, 60, and 120 mM). In addition, a significant correlation between root plasticity and salt tolerance was found. Further, changes in proline and total phenolic content were assessed to envisage the metabolic adjustments of tolerant clones towards salinity. The most promising sources of tolerance were identified in S. commersonii and S. multidissectum and information obtained is discussed from a breeding perspective.

Main conclusionDcMYB11, an R2R3 MYB gene associated with petiole anthocyanin pigmentation in carrot, was functionally characterized. A putative enhancer sequence is able to increase DcMYB11 activity.The accumulation of anthocyanin pigments can exhibit different patterns across plant tissues and crop varieties. This variability allowed the investigation of the molecular mechanisms behind the biosynthesis of these pigments in several plant species. Among crops, carrots have a well-defined anthocyanin pigmentation pattern depending on the genic background. In this work, we report on the discovery of DNA structural differences affecting the activity of an R2R3 MYB (encoded by DcMYB11) involved in anthocyanin regulation in carrot petiole. To this end, we first verified the function of DcMYB11 using heterologous systems and identified three different alleles which may explain differences in petiole pigmentation. Characterization of the DcMYB11 alleles at the 5' upstream sequence unveiled a sequence that functions as a putative enhancer. In conclusion, this study provides novel insight into the molecular mechanisms controlling anthocyanin accumulation in carrot. By these outcomes, we expanded our knowledge on the cis-regulatory sequences in plants.

The cultivated grapevine, Vitis vinifera subsp. vinifera L., is represented by an enormous population of varieties and clones. They arise from the accumulation of gametic and somatic mutations during centuries of sexual and asexual propagation. These varieties represent a vast reservoir of traits/alleles that could be useful in improving the berry quality as well as against environmental stresses. However, most of them are still unexploited. For this reason, an efficient characterization system is essential to define the varietal identity, avoid cases of synonymy (identical genotypes but different names) and homonymy (same names but different genotypes) and deepen our understanding of the existing diversity within the grape germplasm. The plethora of DNA-based high-throughput technologies currently available provides promising tools for the analysis of diversity, overcoming many of the limitations of phenotypic-based diversity analyses. However, the analysis of intra-varietal diversity remains challenging. In this scenario, after summarizing the causes and consequences of grapevine genetic inter- and intra-varietal diversity, we review the DNA-based technologies used for varietal genotyping, emphasizing those able to distinguish clones within a variety. This review provides an update on the technologies used to explore grapevine diversity, the knowledge of which is necessary for an efficient exploitation and conservation of the grapevine germplasm.