Instituto de Ciencias de la Vid y del Vino

The lack of experimental structures for the majority of protein-protein complexes has motivated the development of a variety of strategies for the structural modeling of protein complexes, such as computational docking, in active development for the last decades, and the more recent artificial intelligence (AI)-based ground-breaking methodologies. Among the existing computational docking methods, Python docking (pyDock) has shown competitive predictive rates and high robustness over the years. However, the field has dramatically changed with the appearance of artificial intelligence (AI)-based methods, like AlphaFold. While structure prediction of individual proteins is virtually solved by this program, the focus is now on how to improve the prediction of challenging cases like antibody-antigen complexes, multiprotein complexes, weak interactions, or highly flexible interacting proteins. Successful strategies are based on the generation of more diverse sets of models and the integration with other "classical" approaches that facilitate the identification of the correct models. Here, we will show in practical terms how to combine the structural modeling capabilities of AlphaFold with the energy-based scoring function in pyDock to improve structural predictions in challenging protein-protein complexes.

Abstract Background Because grapevine (Vitis vinifera L.) cultivars are highly heterozygous, they must be clonally propagated to preserve their varietal attributes. Over extended cultivar propagation histories, somatic mutations arise and can generate new phenotypes useful for intra-varietal improvement. Somatic variants with looser bunches – associated with more uniform berry ripening and reduced bunch rot incidence – are particularly valuable in compact-bunch cultivars. To understand the basis of this trait, we combined phenotyping, genomics, and genetic analyses to study VP11, a loose-bunch somatic variant clone of the wine grape cultivar ‘Tempranillo Tinto’. Results Pollen viability and the number of seeds per berry were reduced by ~50% in VP11 compared to a control clone of ‘Tempranillo Tinto’. Long-read whole-genome sequencing identified eleven large somatic structural variants (SVs) in VP11, including three inter-chromosomal events. These consisted of one fixed reciprocal translocation (Tra1-3), with duplications spanning tens of kilobases at the translocation breakpoints, and two segmental duplications (one fixed and one likely L2 meristem cell layer-restricted). All three SVs were molecularly validated, including the phasing and exchange of distal chromosome segments in Tra1-3. In VP11 self-cross progeny, pollen viability was significantly reduced among individuals carrying Tra1-3, and the two translocation chromosomes were always inherited together, indicating that gametes with an unbalanced chromosomal content are non-viable. Conclusions This study identifies reduced gamete viability caused by a heterozygous balanced reciprocal translocation as a mechanism underlying the loose-bunch trait in grapevine. We conclude that even if a genetic defect reduces gamete viability, it can still be useful to decrease seed and fruit set in vegetatively propagated crops where these traits are desirable.

DNA methylation plays an important role in mediating the phenotypic variations observed in many traits and plants. In this study, we explored the origin of berry flesh color at the metabolic, transcriptional, and epigenetic levels. To this end, a comprehensive multiomics analysis of grape (Vitis vinifera L.) berry flesh was carried out in an F1 breeding population segregating for white- and red-fleshed siblings. The results showed that differences in DNA methylation levels at the MYBA1 promoter could effectively distinguish the white- and red-fleshed varieties. More precisely, an approximately 1-kb region in the MYBA1 promoter was hypermethylated in white-fleshed genotypes compared with the red-fleshed genotypes. This variation in methylation level was consistent among leaves, berry skin, and flesh for a given genotype, and was inherited by the F1 generation arising from crosses between parents with different phenotypes. A targeted increase in the DNA methylation levels in the MYBA1 promoter led to decreased MYBA1 expression and anthocyanin levels in transgenic grapevine hairy roots, indicating that anthocyanin biosynthesis is modulated by differential methylation at this locus. Taken together, these results suggest that the variation in methylation at the MYBA1 promoter is stable, heritable and co-segregates with grape flesh color, providing a pertinent epiallelic variation that could be used as a breeding marker to select for grape flesh color. Our findings also offer insights into the mechanisms regulating anthocyanin accumulation in grape flesh.

Winemaking involves a microbial ecosystem where yeast diversity, shaped by terroir and winemaking conditions, determines wine characteristics. Understanding the microbial diversity of vineyards and spontaneous fermentation is crucial for explaining a winery’s typical wine profile. Studying and inoculating indigenous strains make it possible to produce high quality wines, reflecting the production environment. This study analyzes the yeast species involved in 16 spontaneous fermentations (8 in 2022 and 8 in 2023) from grapes of four distinct vineyards under two sets of winemaking conditions. A total of 1100 yeast colonies were identified by MALDI-TOF and DNA sequencing techniques. Saccharomyces (S.) cerevisiae and Hanseniaspora uvarum were the most prevalent species, alongside significant populations of non-Saccharomyces yeasts such as Lachancea thermotolerans and Metchnikowia pulcherrima, which were the most abundant ones. Minor yeast species, including Aureobasidium pullulans, Starmerella bacillaris, Kazachstania servazzi, and other Hanseniaspora spp., were also detected. The results demonstrated that yeast diversity in spontaneous fermentations varied according to vineyard origin and winemaking conditions. Differences between the two vintages studied indicated that annual climatic conditions significantly influenced yeast diversity, especially among non-Saccharomyces species. This substantial diversity represents a valuable source of indigenous yeasts for preserving the typicity of a winery’s wines under controlled conditions.

Reliable early-stage yield forecasts are essential in precision viticulture, enabling timely interventions such as harvest planning, canopy management, and crop load regulation. Since grape yield is directly related to the number and size of bunches, the early detection of inflorescences and bunches, carried out even before flowering, provides a valuable foundation for estimating potential yield far in advance of veraison. Traditional yield prediction methods are labor-intensive, subjective, and often restricted to advanced phenological stages. This study presents a deep learning-based approach for detecting grapevine inflorescences and bunches during early development, assessing how phenological stage and illumination conditions influence detection performance using the YOLOv11 architecture under commercial field conditions. A total of 436 RGB images were collected across two phenological stages (pre-bloom and fruit-set), two lighting conditions (daylight and artificial night-time illumination), and six grapevine cultivars. All images were manually annotated following a consistent protocol, and models were trained using data augmentation to improve generalization. Five models were developed: four specific to each condition and one combining all scenarios. The results show that the fruit-set stage under daylight provided the best performance (F1 = 0.77, R2 = 0.97), while for inflorescences, night-time imaging yielded the most accurate results (F1 = 0.71, R2 = 0.76), confirming the benefits of artificial lighting in early stages. These findings define optimal scenarios for early-stage organ detection and support the integration of automated detection models into vineyard management systems. Future work will address scalability and robustness under diverse conditions.

Aligned with the principles of the circular bioeconomy, this study explores the use of winemaking by-products as a source of bioactive phenolic compounds. Skins and seeds from Tempranillo and Graciano grapevine varieties were conditioned to prepare a phenolic-rich beverage. To study its hypoglycemic properties, a pilot trial was conducted to evaluate postprandial glycemia after the intake of the wine by-product-based beverage (WBB). The postprandial glycemia of 10 healthy adults was measured after the intake of: (i) water + sugar solution, (ii) WBB + sugar solution, and (iii) WBB + water. In parallel to blood glucose measurement, blood samples were also collected using dried blood spot cards to determine the phenolic metabolites by UHPLC-QqQ-MS/MS. Although blood glucose levels tended to decrease after WBB intervention, these changes were not statistically significant related to the interindividual variability. The volunteers showing a reduction in blood glucose were classified as "responders", and those who showed no changes were classified as "non-responders". Wine by-products can be effectively used in functional beverages formulation to increase bioactive compound content and manage postprandial glucose in some individuals.

The importance of mouthfeel in the comprehensive evaluation of red wine quality is widely acknowledged; however, instruments that are capable of differentiating between wines based on this attribute are scarce. The objective of this study was to develop handfeel touch reference materials that can be used to describe mouthfeel characteristics of red wine. This was achieved through a transdisciplinary approach based on the hypothesis that sensory transfer occurs between handfeel and mouthfeel. An initial list of 44 mouthfeel terms was compiled by 193 technical experts, wine sellers and regular consumers, from which 25 terms were selected for further consideration. Applying an art-based methodology, 74 handfeel touch reference standards were developed to exemplify the 25 mouthfeel terms. First, the capacity of the tactile references to differentiate between red wines was validated through a check-all-that-apply (CATA) strategy, with 31 participants describing six red wines. Then a sorting task was conducted on the 74 references, and the 19 most discriminant references were selected for inclusion in a final set of handfeel touch reference materials. The findings support the initial hypothesis of the study, namely that sensory associations exist between handfeel and wine mouthfeel. The results demonstrate that differences in the mouthfeel properties of wines can be described by the proposed CATA-based approach involving handfeel touch references. This confirms the sensory correspondence of handfeel cues and mouthfeel sensations elicited by red wines. The study provides practical guidelines for the development of reference materials that can be used to describe wine perception and to explore the mouthfeel perceptual space of wines.

The epidemiological assessment of wine consumption usually has been obtained using self-reporting questionnaires. In this study, two metabolomic approaches, targeted and untargeted, were applied to 24-h urine samples from a cohort of La Rioja (Spain) (aged 52-78), comparing moderate and daily wine consumers (20 males and 13 females) without diet intervention, versus non-consumers (8 males and 35 females). Results showed that the non-targeted metabolomics approach has allowed for the annotation of sixteen compounds in 24-h urine samples from regular wine-consumers that were not detected in the urine of non-wine consumers. Additionally, the targeted metabolomics approach showed a wide range of phenol metabolites, mainly hepatic phase-II conjugates, whose concentration was significantly higher in the urine of wine consumers. As a novelty, this study focuses on discovering the main urinary biomarkers of regular wine consumption involving free-living volunteers, without dietary intervention or restrictions that might alter their regular behaviors and lifestyles.

Vineyards are significant demanders of fertilisers, pesticides, soil tillage and water. This study assessed the environmental profile of an organic grape production system with La Rioja qualified designation of origin using a cradle-to-gate life cycle assessment (LCA). The ReCiPe method was applied to assess the environmental impacts, while the Available WAter REmaining method was used to estimate the water scarcity. Additionally, the biodiversity loss, a global issue exacerbated by agricultural practices, was evaluated along with an ecosystem service indicator, pollination, to provide a more comprehensive analysis. This study employed two functional units: one kilogram of grapes and one hectare of land. The results revealed that the environmental impacts on global warming were more than ten times lower than those reported in most studies reviewed in the literature, primarily due to the effects of direct land use changes associated with pruning waste management. The total emissions in this category were 99.51 kg CO2 eq per hectare or 15.31 g CO2 eq per kilogram of grapes. Agrochemical-related emissions were identified as the environmental hotspot. The water scarcity was estimated at 48.4 litres per kilogram of grapes, mainly attributed to agrochemical dispersion. The biodiversity loss was largely driven by land transformation, with plants being the most impacted taxon. However, a high abundance of pollinators was observed in spring, contributing to improved grape quality and natural pest control. These findings could help highlight the environmental benefits of organic viticulture and the good practices implemented in this pilot.