Design of a Custom RT-qPCR Array for Assignment of Abiotic Stress Tolerance in Traditional Portuguese Grapevine Varieties

Cytogenetic and Molecular Effects of Kaolin's Foliar Application in Grapevine (Vitis vinifera L.) under Summer's Stressful Growing Conditions

Grapevine varieties from "Douro Superior" (NE Portugal) experience high temperatures, solar radiation, and water deficit during the summer. This summer's stressful growing conditions induce nucleic acids, lipids, and protein oxidation, which cause cellular, physiological, molecular, and biochemical changes. Cell cycle anomalies, mitosis delay, or cell death may occur at the cellular level, leading to reduced plant productivity. However, the foliar application of kaolin (KL) can mitigate the impact of abiotic stress by decreasing leaf temperature and enhancing antioxidant defence. Hence, this study hypothesised that KL-treated grapevine plants growing in NE Portugal would reveal, under summer stressful growing conditions, higher progression and stability of the leaf mitotic cell cycle than the untreated (control) plants. KL was applied after veraison for two years. Leaves, sampled 3 and 5 weeks later, were cytogenetically, molecularly, and biochemically analysed. Globally, integrating these multidisciplinary data confirmed the decreased leaf temperature and enhanced antioxidant defence of the KL-treated plants, accompanied by an improved regularity and completion of the leaf cell cycle relative to the control plants. Nevertheless, the KL efficacy was significantly influenced by the sampling date and/or variety. In sum, the achieved results confirmed the hypothesis initially proposed.

Climate change impacts on temperate fruit and nut production: a systematic review

Temperate fruit and nut crops require distinctive cold and warm seasons to meet their physiological requirements and progress through their phenological stages. Consequently, they have been traditionally cultivated in warm temperate climate regions characterized by dry-summer and wet-winter seasons. However, fruit and nut production in these areas faces new challenging conditions due to increasingly severe and erratic weather patterns caused by climate change. This review represents an effort towards identifying the current state of knowledge, key challenges, and gaps that emerge from studies of climate change effects on fruit and nut crops produced in warm temperate climates. Following the PRISMA methodology for systematic reviews, we analyzed 403 articles published between 2000 and 2023 that met the defined eligibility criteria. A 44-fold increase in the number of publications during the last two decades reflects a growing interest in research related to both a better understanding of the effects of climate anomalies on temperate fruit and nut production and the need to find strategies that allow this industry to adapt to current and future weather conditions while reducing its environmental impacts. In an extended analysis beyond the scope of the systematic review methodology, we classified the literature into six main areas of research, including responses to environmental conditions, water management, sustainable agriculture, breeding and genetics, prediction models, and production systems. Given the rapid expansion of climate change-related literature, our analysis provides valuable information for researchers, as it can help them identify aspects that are well understood, topics that remain unexplored, and urgent questions that need to be addressed in the future.

Modulation of the Berry Skin Transcriptome of cv. Tempranillo Induced by Water Stress Levels

Climate change in the Mediterranean area is making summers warmer and dryer. Grapevine (Vitis vinifera L.) is mostly important for wine production in Mediterranean countries, and the variety Tempranillo is one of the most cultivated in Spain and Portugal. Drought decreases yield and quality and causes important economic losses. As full irrigation has negative effects on quality and water is scarce in this region, deficit irrigation is often applied. In this research, we studied the effects of two deficit irrigation treatments, Sustained Deficit Irrigation (SDI) and Regulated Deficit Irrigation (RDI), on the transcriptome of grape berries at full maturation, through RNAseq. The expression of differentially regulated genes (DEGs) was also monitored through RT-qPCR along berry development. Most transcripts were regulated by water stress, with a similar distribution of up- and down-regulated transcripts within functional categories (FC). Primary metabolism was the more severely affected FC under water stress, followed by signaling and transport. Almost all DEGs monitored were significantly up-regulated by severe water stress at veraison. The modulation of an auxin response repression factor, AUX22D, by water stress indicates a role of this gene in the response to drought. Further, the expression of WRKY40, a TF that regulates anthocyanin biosynthesis, may be responsible for changes in grape quality under severe water stress.

Developmental Regulation of Transcription in Touriga Nacional Berries under Deficit Irrigation

Grapevine (Vitis vinifera L.) is one of the most economically important crops worldwide, especially due to the economic relevance of wine production. Abiotic stress, such as drought, may contribute to low yield, shifts in quality, and important economic loss. The predicted climate change phenomena point to warmer and dryer Mediterranean environmental conditions; as such, it is paramount to study the effects of abiotic stress on grapevine performance. Deficit irrigation systems are applied to optimize water use efficiency without compromising berry quality. In this research, the effect of two deficit irrigation strategies, sustained deficit irrigation (SDI) and regulated deficit irrigation (RDI), in the grape berry were assessed. The effects of different levels of drought were monitored in Touriga Nacional at key stages of berry development (pea size, véraison, and full maturation) through RNA-Seq transcriptome analysis and by specific differentially expressed genes (DEGs) monitoring through RT-qPCR. Handy datasets were obtained by bioinformatics analysis of raw RNA-Seq results. The dominant proportion of transcripts was mostly regulated by development, with véraison showing more upregulated transcripts. Results showed that primary metabolism is the functional category more severely affected under water stress. Almost all DEGs selected for RT-qPCR were significantly upregulated in full maturation and showed the highest variability at véraison and the lowest gene expression values in the pea size stage.

Potential Phenotyping Methodologies to Assess Inter- and Intravarietal Variability and to Select Grapevine Genotypes Tolerant to Abiotic Stress

Plant phenotyping is an emerging science that combines multiple methodologies and protocols to measure plant traits (e.g., growth, morphology, architecture, function, and composition) at multiple scales of organization. Manual phenotyping remains as a major bottleneck to the advance of plant and crop breeding. Such constraint fostered the development of high throughput plant phenotyping (HTPP), which is largely based on imaging approaches and automatized data retrieval and processing. Field phenotyping still poses major challenges and the progress of HTPP for field conditions can be relevant to support selection and breeding of grapevine. The aim of this review is to discuss potential and current methods to improve field phenotyping of grapevine to support characterization of inter- and intravarietal diversity. Vitis vinifera has a large genetic diversity that needs characterization, and the availability of methods to support selection of plant material (polyclonal or clonal) able to withstand abiotic stress is paramount. Besides being time consuming, complex and expensive, field experiments are also affected by heterogeneous and uncontrolled climate and soil conditions, mostly due to the large areas of the trials and to the high number of traits to be observed in a number of individuals ranging from hundreds to thousands. Therefore, adequate field experimental design and data gathering methodologies are crucial to obtain reliable data. Some of the major challenges posed to grapevine selection programs for tolerance to water and heat stress are described herein. Useful traits for selection and related field phenotyping methodologies are described and their adequacy for large scale screening is discussed.

Selecting Aragonez Genotypes Able to Outplay Climate Change-Driven Abiotic Stress

High temperatures and extreme drought are increasingly more frequent in Portugal, which represents a strong threat to viticulture in certain regions of the country. These multifactorial abiotic stresses are threatening viticultural areas worldwide, and the problem can hardly be overcome only by changing cultural practices. This scenario has raised a major challenge for plant scientists to find ways to adapt existing varieties to the new conditions without loss of their characteristic flavors, yield, and associated varietal character of wines. Aragonez (syn. Tempranillo) is one such variety, widely cultivated in Portugal and Spain, with specific characteristics associated with terroir. In this context, insight into intravarietal variability to enable its exploitation for selection becomes an important tool to mitigate the effect of multifactorial stresses driven by climate changes. The present work describes an innovative selection approach: selection for abiotic stress tolerance, measured by the leaf temperature of clones under environmental conditions of drought and extreme heat. This evaluation was complemented with values of yield and quality characteristics of the must (pH, acidity, °Brix, and anthocyanins). The application of this methodology was done in an experimental population of 255 clones of Tempranillo for 3 years. The genotypes were then ranked according to their level of tolerance to abiotic stress without loss of yield/quality. To understand the differences at the transcription level that could account for such variability, several of the most tolerant and most sensitive genotypes were analyzed for key genes using reverse transcriptase-quantitative polymerase chain reaction. The results enabled the selection of a group of genotypes with increased tolerance to stress, in relation to the average of the variety, which maintained the typical must quality of Aragonez. In parallel, several transcripts previously acknowledged as markers for abiotic stress tolerance were identified in several clones and are possible targets for plant breeding and genetic modification and/or to develop screening procedures to select genotypes better adapted to the abiotic stress driven by climate change.

Heat stress tolerance assayed in four wine-producing grapevine varieties using a cytogenetic approach

The degree of tolerance to heat stress (HS) differs among grapevine varieties. HS affects the duration and the regularity of the cell cycle in plants. The cytogenetic studies in grapevine are scarce, and the consequences of HS in the mitosis are barely known. This work intends to evaluate the consequences of induced HS in the mitotic cell cycle and chromosomes of four wine-producing varieties: Touriga Franca (TF), Touriga Nacional (TN), Rabigato and Viosinho using a cytogenetic approach. HS (1h at 42 ºC) was induced in plants of the four grapevine varieties that grew in vitro for 11 months. Plants of the same varieties and with equal age were used as control (maintained in vitro at 25 ºC). Three plants per variety and treatment (control and HS) were analysed. After HS, root-tips were collected in all plants and immediately fixed to be used for the preparation of mitotic chromosome spreads. In total, 6,116 root-tip cells were scored. Among the 5,973 dividing cells, 24.33% showed different types of irregularities in all mitotic phases (prophase, metaphase, anaphase, and telophase). After HS, the mitotic index (MI) decreased in the varieties TF and Viosinho, and increased in TN and Rabigato, relatively to the control. However, the average values of MI did not show statistically significant differences (p ˃ 0.05) among varieties, treatments and for the variety x treatment interaction. The percentage of dividing cells with anomalies (%DCA) increased after HS in all varieties relatively to the control. The average values of %DCA presented statistically significant differences (p < 0.05) only between treatments. As far as we know, this work constitutes the first cytogenetic evaluation of the HS effects in the mitotic cell cycle and chromosomes of grapevine using meristematic cells of root-tips. TN has been considered tolerant to various abiotic stresses (drought and excessive heat and light) based on other methodologies. TF and Viosinho have been referred as tolerant to abiotic stress without deeper studies available, and till the development of our investigation, the sensibility of Rabigato was unknown. Among the varieties analysed in this work, Rabigato revealed to be the less tolerant to HS. This research can be useful for selection of grapevine clones more tolerant to HS for commercialization and for the improvement of the economic sustainability.

A pathway-focused RT-qPCR array study on immune relevant genes in rainbow trout (Oncorhynchus mykiss) harboring cecropin P1 transgene

Recently, our laboratory had produced five families of transgenic rainbow trout harboring cecropin P1 transgene, and via repeated challenge studies these fish exhibited a significant elevation of resistance to infection by microbial pathogens. By cDNA microarray and mRNA deep sequencing (mRNA-seq) analyses on two of the five families of cecropin P1 transgenic fish, differentially expressed genes (DEGs) relevant to the innate and adaptive immune pathways in three different immune-related tissues, (i.e. spleen, kidney and liver) were profiled. These results supported our hypothesis that in addition to its direct microbicidal activity, the transgene product of cecropin P1 induces immunomodulatory activity in the transgenic host. Here, we have adapted the technique of quantitative reverse transcription real time PCR (RT-qPCR) array to analyze the expression of genes relevant to the innate and adaptive immune pathways in the rest three families. A RT-qPCR array was constructed with oligonucleotide primers of fifty-two innate/adaptive immune relevant DEGs shown to be the most perturbed by cecropin P1 transgene product in previous studies. Messenger RNA isolated from the spleen, kidney and liver of transgenic fish and non-transgenic fish control were studied on this array. Results of RT-qPCR array revealed that statistically significant perturbations of gene expression were detected in pathways of cytokine/chemokine signaling, Toll-like receptor signaling, complement cascade, antigen processing/presentation, lysosomal phagocytosis and leukocyte trans-endothelial migration in the transgenic spleen; extracellular matrix (ECM) organization and leukocyte trans-endothelial migration pathways in the transgenic kidney; lysosomal activity pathway in the transgenic liver. Furthermore, genes related to the pathways of the peroxisome proliferator-activated receptors (PPAR) signaling, lipid metabolism process and arachidonic acid metabolism were also impacted in the transgenic liver. Findings of the current study are in good agreement with those discoveries in previous two transgenic families by cDNA microarray and mRNA-seq analyses.

Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress

Grapevine (Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait. We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 differentially expressed genes) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress. For the first time, we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and -signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought. These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.

Cutting the Gordian Knot of abiotic stress in grapevine: From the test tube to climate change adaptation

In Mediterranean climate areas, the available scenarios for climate change suggest an increase in the frequency of heat waves and severe drought in summer. Grapevine (Vitis vinifera L.) is a traditional Mediterranean species and is the most valuable fruit crop in the world. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of irrigation, with the concomitant losses in wine quality, and researchers to study tolerance to stress in existing genotypes. The viticulture and winemaking worlds are in demand to understand the physiological potential of the available genotypes to respond to climate changes. In this review, we will focus on the cross-talk between common abiotic stresses that currently affect grapevine productivity and that are prone to affect it deeper in the future. We will discuss results obtained under three experimental stress conditions and that call for specific responses: (1) acclimatization of in vitro plantlets, (2) stress combinations in controlled conditions for research purposes, (3) extreme events in the field that, driven by climate changes, are pushing Mediterranean species to the limit. The different levels of tolerance to stress put in evidence by the plasticity of phenotypic and genotypic response mechanisms, will be addressed. This information is relevant to understand varietal adaptation to impending climate changes and to assist vine growers in choosing genotypes and viticulture practices.

Grapevine adaptation to drought: New candidate genes for the genotype-dependent response

Grapevine requires irrigation supply for its cultivation, especially in the arid and semiarid geographic areas. As consequence of the severe climatic changes, water consumption is becoming more and more important as environmental and cost factor that needs to be reduced. Water deficiency can affect berry and wine quality depending on the extent of plant perceived stress, which is a cultivar specific trait. In a four-year project, we tested the physiological and molecular responses to water deficiency of two different table grape cultivars, Italia and Autumn Royal, and we highlighted that they differently adapted to drought stress conditions. Physiological analyses on field-growth plants showed cultivar-specific variations in photosynthetic carbon assimilation and, stomatal conductance under water deficiency. We further combined “omic” analyses to identify candidate genes involved in drought stress response and adaptative traits. Microarray analyses revealed a broad response of cultivar Italia to drought stress conditions characterized by the modulation of 1037 genes involved in biological processes as cell wall organization, carbohydrate metabolism, ROS response, response to hormone and osmotic stress. On the contrary, Autumn Royal response was limited to the modulation of only 29 genes mainly involved in plant stress response, nitrogen metabolism and hormone signal transduction. Our data highlighted that ABA-perception and –signalling are key factors mediating the varietal-specific behavior of the early response to drought.

Effects of heat stress in the leaf mitotic cell cycle and chromosomes of four wine-producing grapevine varieties

Grapevine varieties respond differentially to heat stress (HS). HS ultimately reduces the photosynthesis and respiratory performance. However, the HS effects in the leaf nuclei and mitotic cells of grapevine are barely known. This work intends to evaluate the HS effects in the leaf mitotic cell cycle and chromosomes of four wine-producing varieties: Touriga Franca (TF), Touriga Nacional (TN), Rabigato, and Viosinho. In vitro plants with 11 months were used in a stepwise acclimation and recovery (SAR) experimental setup comprising different phases: heat acclimation period (3 h-32 °C), extreme HS (1 h-42 °C), and two recovery periods (3 h-32 °C and 24 h-25 °C), and compared to control plants (maintained in vitro at 25 °C). At the end of each SAR phase, leaves were collected, fixed, and used for cell suspensions and chromosome preparations. Normal and abnormal interphase and mitotic cells were observed, scored, and statistically analyzed in all varieties and treatments (control and SAR phases). Different types of chromosomal anomalies in all mitotic phases, treatments, and varieties were found. In all varieties, the percentage of dividing cells with anomalies (%DCA) after extreme HS increased relative to control. TF and Viosinho were considered the most tolerant to HS. TF showed a gradual MI reduction from heat acclimation to HS and the lowest %DCA after HS and 24 h of recovery. Only Viosinho reached the control values after the long recovery period. Extrapolating these data to the field, we hypothesize that during consecutive hot summer days, the grapevine plants will not have time or capacity to recover from the mitotic anomalies caused by high temperatures.