Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, various phenotypes are often present within the same vineyard due to the accumulation of somatic mutations. These mutations are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as a pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of domestication on methylation patterns in cultivated grapevines. Reduced-representation bisulfite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% were hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (consistently methylated in both wild and cultivated accessions) are associated with stress response and terpenoid/isoprenoid metabolic processes. Meanwhile, genes with differential methylation are linked to protein targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Collectively, our results highlight the significant roles that epialleles may have played throughout the domestication history of grapevines.

Three-year study of DNA cytosine methylation dynamics in transplanted Malbec grapevines

DNA cytosine methylation, an epigenetic mechanism involved in gene regulation and genome stability, remains poorly understood in terms of its role under changing environmental conditions. Previous research using methylation-sensitive amplified polymorphism (MSAP) markers in a Vitis vinifera L. cv. Malbec clone showed vineyard-specific DNA methylation polymorphism, but no change in overall methylation levels. To complement these findings, the present study investigates the intra-seasonal epigenetic dynamics between genetically identical plants grown in different vineyards through a transplanting experiment. Cuttings of the same clone, showing differential methylation patterns imposed by the vineyard of origin (Agrelo and Gualtallary), were cultivated in a common vineyard (Lunlunta). Using high-performance liquid chromatography-ultraviolet detection, the quantification of global DNA 5-methylcytosine (5-mC) levels revealed relatively low overall 5-mC percentages in grapevines, with higher levels in Agrelo (5.8%) compared to Gualtallary plants (3.7%). The transplanted plants maintained the 5-mC levels differences between vineyards (9.8% vs 6.2%), which equalized in subsequent seasons (7.5% vs 7%). Additionally, the study examined 5-mC polymorphism using MSAP markers in Lunlunta transplanted plants over three seasons. The observed differences between vineyards in MSAP patterns during the initial growing season gradually diminished, suggesting a reprogramming of the hemimethylated pattern following implantation in the common vineyard. In contrast, the non-methylated pattern exhibited greater stability, indicating a potential memory effect. Overall, this study provides valuable insights into the dynamic nature of DNA methylation in grapevines under changing environmental conditions, with potential implications for crop management and breeding strategies.

Emerging Roles of Epigenetics in Grapevine and Winegrowing

Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.

Inter- and intra-varietal genetic variations co-shape the polyphenol profiles of Vitis vinifera L. grapes and wines

Inheritance and mutations are important factors affecting grape phenolic composition. To investigate the inter- and intra-varietal differences in polyphenolic compounds among grapes and wines, 27 clones belonging to eight varieties of Vitis vinifera L. were studied over two consecutive years. A total of 24 polyphenols (nine anthocyanins, three flavanols, five flavonols, and seven phenolic acids) were analyzed, and the physicochemical parameters of the grapes and wines were determined. Polyphenol profiles showed significant varietal and clonal polymorphisms, and malvidin-3-O-glucoside, peonidin-3-O- glucoside, and epicatechin were identified as key biomarkers distinguishing different grapes and wines when using an orthogonal partial least squares discriminant analysis. Further multivariate analysis classified these genotypes into three subclasses, and a somatic variant of 'Malbec', MBVCR6, had the most abundant polyphenolic compounds that were related to the titratable acid content. The current results reveal that varietal and clonal variations are important for obtaining wines with high polyphenol content.

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress

Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.

Machine learning extracts marks of thiamine's role in cold acclimation in the transcriptome of Vitis vinifera

Introduction

The escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.

Methods

We used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific "portraits" of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.

Results

Our analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.

Discussion

Application of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.

Investigating the impact of pedoclimatic conditions on the oenological performance of two red cultivars grown throughout southern Italy

The cultivated grapevine, Vitis vinifera subsp. vinifera, possesses a rich biodiversity with numerous varieties. Each variety adapts differently to varying pedoclimatic conditions, which greatly influence the terroir expression of wine regions. These conditions impact vine growth, physiology, and berry composition, ultimately shaping the unique characteristics and typicity of the wines produced. Nowadays, the potential of the different adaptation capacities of grape varieties has not yet been thoroughly investigated. We addressed this issue by studying two grape varieties, Aglianico and Cabernet Sauvignon, in two different pedoclimatic conditions of Southern Italy. We evaluated and compared the effect of different pedoclimatic conditions on plant physiology, the microbial quality of grapes using Next-Generation Sequencing (NGS) technology, the expression trends of key genes in ripe berries and the concentration of phenolic compounds in grapes and wines by HPLC-MS, HPLC-DAD, NMR and spectrophotometric analyses. Metabolomic and microbiome data were integrated with quantitative gene expression analyses to examine varietal differences and plasticity of genes involved in important oenological pathways. The data collected showed that the phenotypic response of studied grapes in terms of vigor, production, and fruit quality is strongly influenced by the pedoclimatic conditions and, in particular, by soil physical properties. Furthermore, Aglianico grape variety was more influenced than the Cabernet Sauvignon by environmental conditions. In conclusion, the obtained findings not only reinforce the terroir concept and our comprehension of grape's ability to adapt to climate variations but can also have implications for the future usage of grape genetic resources.

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

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.

Endoreplication-Why Are We Not Using Its Full Application Potential?

Endoreplication-a process that is common in plants and also accompanies changes in the development of animal organisms-has been seen from a new perspective in recent years. In the paper, we not only shed light on this view, but we would also like to promote an understanding of the application potential of this phenomenon in plant cultivation. Endoreplication is a pathway for cell development, slightly different from the classical somatic cell cycle, which ends with mitosis. Since many rounds of DNA synthesis take place within its course, endoreplication is a kind of evolutionary compensation for the relatively small amount of genetic material that plants possess. It allows for its multiplication and active use through transcription and translation. The presence of endoreplication in plants has many positive consequences. In this case, repeatedly produced copies of genes, through the corresponding transcripts, help the plant acquire the favorable properties for which proteins are responsible directly or indirectly. These include features that are desirable in terms of cultivation and marketing: a greater saturation of fruit and flower colors, a stronger aroma, a sweeter fruit taste, an accumulation of nutrients, an increased resistance to biotic and abiotic stress, superior tolerance to adverse environmental conditions, and faster organ growth (and consequently the faster growth of the whole plant and its biomass). The two last features are related to the nuclear-cytoplasmic ratio-the greater the content of DNA in the nucleus, the higher the volume of cytoplasm, and thus the larger the cell size. Endoreplication not only allows cells to reach larger sizes but also to save the materials used to build organelles, which are then passed on to daughter cells after division, thus ending the classic cell cycle. However, the content of genetic material in the cell nucleus determines the number of corresponding organelles. The article also draws attention to the potential practical applications of the phenomenon and the factors currently limiting its use.

Secondary metabolites in grapevine: crosstalk of transcriptional, metabolic and hormonal signals controlling stress defence responses in berries and vegetative organs

Abiotic stresses, such as temperature, heat waves, water limitation, solar radiation and the increase in atmospheric CO₂ concentration, significantly influence the accumulation of secondary metabolites in grapevine berries at different developmental stages, and in vegetative organs. Transcriptional reprogramming, miRNAs, epigenetic marks and hormonal crosstalk regulate the secondary metabolism of berries, mainly the accumulation of phenylpropanoids and of volatile organic compounds (VOCs). Currently, the biological mechanisms that control the plastic response of grapevine cultivars to environmental stress or that occur during berry ripening have been extensively studied in many worlds viticultural areas, in different cultivars and in vines grown under various agronomic managements. A novel frontier in the study of these mechanisms is the involvement of miRNAs whose target transcripts encode enzymes of the flavonoid biosynthetic pathway. Some miRNA-mediated regulatory cascades, post-transcriptionally control key MYB transcription factors, showing, for example, a role in influencing the anthocyanin accumulation in response to UV-B light during berry ripening. DNA methylation profiles partially affect the berry transcriptome plasticity of different grapevine cultivars, contributing to the modulation of berry qualitative traits. Numerous hormones (such as abscisic and jasmomic acids, strigolactones, gibberellins, auxins, cytokynins and ethylene) are involved in triggering the vine response to abiotic and biotic stress factors. Through specific signaling cascades, hormones mediate the accumulation of antioxidants that contribute to the quality of the berry and that intervene in the grapevine defense processes, highlighting that the grapevine response to stressors can be similar in different grapevine organs. The expression of genes responsible for hormone biosynthesis is largely modulated by stress conditions, thus resulting in the numeourous interactions between grapevine and the surrounding environment.

Terroir Influence on Polyphenol Metabolism from Grape Canes: A Spatial Metabolomic Study at Parcel Scale

The composition of bioactive polyphenols from grape canes, an important viticultural byproduct, was shown to be varietal-dependent; however, the influence of soil-related terroir factors remains unexplored. Using spatial metabolomics and correlation-based networks, we investigated how continuous changes in soil features and topography may impact the polyphenol composition in grape canes. Soil properties, topography, and grape cane extracts were analyzed at georeferenced points over 3 consecutive years, followed by UPLC-DAD-MS-based metabolomic analysis targeting 42 metabolites. Principal component analyses on intra-vintage metabolomic data presented a good reproducibility in relation to geographic coordinates. A correlation-driven approach was used to explore the combined influence of soil and topographic variables on metabolomic responses. As a result, a metabolic cluster including flavonoids was correlated with elevation and curvature. Spatial metabolomics driven by correlation-based networks represents a powerful approach to spatialize field-omics data and may serve as new field-phenotyping tool in precision agriculture.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

Transcriptomic and methylation analysis of susceptible and tolerant grapevine genotypes following Plasmopara viticola infection

Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of chemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for sustainable strategies of disease control. Improved knowledge of plant mechanisms to counteract pathogen infection may allow the development of alternative strategies for plant protection. Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions associated with the expression modulation of defence genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 h post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to the pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and the gene expression profile. The results indicate a genotype-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/020), and it shows an early modulation (at 6 hpi) of defence and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.

Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal

Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.

Changes in global DNA methylation under climatic stress in two related grasses suggest a possible role of epigenetics in the ecological success of polyploids

Polyploidization drives the evolution of grasses and can result in epigenetic changes, which may have a role in the creation of new evolutionary lineages and ecological speciation. As such changes may be inherited, they can also influence adaptation to the environment. Populations from different regions and climates may also differ epigenetically; however, this phenomenon is poorly understood. The present study analyzes the effect of climatic stress on global DNA methylation based on a garden collection of two related mountain grasses (the narrow endemic diploid Festuca tatrae and the more widely distributed mixed-ploidy F. amethystina) with different geographic ranges and ecological niches. A lower level of DNA methylation was observed for F. tatrae, while a higher mean level was obtained for the diploid and tetraploid of F. amethystina; with the tetraploids having a higher level of global methylated DNA than the diploids. The weather conditions (especially insolation) measured 24 h prior to sampling appeared to have a closer relationship with global DNA methylation level than those observed seven days before sampling. Our findings suggest that the level of methylation during stress conditions (drought, high temperature and high insolation) may be significantly influenced by the ploidy level and bioclimatic provenance of specimens; however an important role may also be played by the intensity of stress conditions in a given year.

Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province

As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples from five regions in Heilongjiang Province, China. In addition, the phenotypic indicators of japonica rice samples and the environmental conditions of the sampling sites were investigated and analysed. Based on the MSAP analysis technique, using eight pairs of selective primers, we identified a total of 551 amplified loci, of which 267 (48.5%) were classified as methylation loci. The methylation status and levels of the japonica rice genome in different regions differed significantly (p < 0.05). The results of the analysis of molecular variance (AMOVA) revealed that most of the molecular variation (91%) came from within the groups (regions) and was caused by individual variation within the region. Furthermore, the results of principal coordinates analysis (PCoA), cluster analysis, and population structure analysis indicated that there was no obvious correlation between the epigenetic differences and geographical locations, which may have been due to the limited range of sampling sites. When environmental factors, phenotypic indicators, and epigenetic data analysis are combined, it is easy to conclude that japonica rice grown in the same latitudinal region has increased epigenetic and phenotypic similarities due to similar climatic conditions and production practices.

Study of Inter- and Intra-varietal Genetic Variability in Grapevine Cultivars

Vitis vinifera includes a large number of cultivars that are further distinguished in biotypes and clones, and it is actually hard to differentiate them, even through complex molecular techniques. In this work, the plant materials of 56 putative Sangiovese and 14 putative Montepulciano biotypes, two of the most widespread black-berried Italian cultivars, were collected in different wine-growing areas of Italy distributed in 13 regions, from north to south. Firstly, the samples were analyzed using SSR markers to have proper varietal identification. According to the results, the genotypes belonged to three different cultivars: Sangiovese, Sanforte, and Montepulciano. Subsequently, the samples were investigated using AFLP, SAMPL, M-AFLP, and I-SSR molecular markers to estimate their intra-varietal genetic variability. The DNA marker-based method used turned out to be performing to bring out the geographic differences among the biotypes screened, and it can therefore be considered as a powerful tool available for all the grapevine varieties.

Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

Background

Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.

Results

We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes.

Conclusions

This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07973-9.

Epigenetics for Crop Improvement in Times of Global Change

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

Stories that can't be told by SNPs; DNA methylation variation in plant populations

Epigenetic variation has been observed in many plant populations. This variation can influence qualitative and quantitative traits. A key question is whether there is novel information in the epigenome that is not captured by SNP-based genetic markers. The answer likely varies depending on the sources and stability of epigenetic variation as well as the type of population being studied. We consider the epigenetic variation in several plant systems and how this relates to potential for hidden information that could increase our understanding of phenotypic variation.

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include non-coding RNA species, such as small nucleolar RNAs and microRNAs. It is not known, however, the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors contributing to their expression. We analysed tRNA-mRNA dicistronic transcripts in the major horticultural crop grapevine (Vitis vinifera) using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA-sequencing data. We identified dicistronic tRNA-mRNA in leaf and berry samples from 22 commercial vineyards. Of the 124 tRNA genes that were expressed in both tissues, 18 tRNA were expressed forming part of 19 dicistronic tRNA-mRNAs. The presence and abundance of dicistronic molecules was tissue and geographic sub-region specific. In leaves, the expression patterns of dicistronic tRNA-mRNAs significantly correlated with tRNA expression, suggesting that their transcriptional regulation might be linked. We also found evidence of syntenic genomic arrangements of tRNAs and protein-coding genes between grapevine and Arabidopsis thaliana, and widespread prevalence of dicistronic tRNA-mRNA transcripts among vascular land plants but no evidence of these transcripts in non-vascular lineages. This suggests that the appearance of plant vasculature and tRNA-mRNA occurred concurrently during the evolution of land plants.

Secondary Metabolism and Defense Responses Are Differently Regulated in Two Grapevine Cultivars during Ripening

Vitis vinifera ‘Nebbiolo’ is one of the most important wine grape cultivars used to produce prestigious high-quality wines known throughout the world, such as Barolo and Barbaresco. ‘Nebbiolo’ is a distinctive genotype characterized by medium/high vigor, long vegetative and ripening cycles, and limited berry skin color rich in 3′-hydroxylated anthocyanins. To investigate the molecular basis of these characteristics, ‘Nebbiolo’ berries collected at three different stages of ripening (berry pea size, véraison, and harvest) were compared with V. vinifera ‘Barbera’ berries, which are rich in 3′,5′-hydroxylated anthocyanins, using transcriptomic and analytical approaches. In two consecutive seasons, the two genotypes confirmed their characteristic anthocyanin profiles associated with a different modulation of their transcriptomes during ripening. Secondary metabolism and response to stress were the functional categories that most differentially changed between ‘Nebbiolo’ and ‘Barbera’. The profile rich in 3′-hydroxylated anthocyanins of ‘Nebbiolo’ was likely linked to a transcriptional downregulation of key genes of anthocyanin biosynthesis. In addition, at berry pea size, the defense metabolism was more active in ‘Nebbiolo’ than ‘Barbera’ in absence of biotic attacks. Accordingly, several pathogenesis-related proteins, WRKY transcription factors, and stilbene synthase genes were overexpressed in ‘Nebbiolo’, suggesting an interesting specific regulation of defense pathways in this genotype that deserves to be further explored.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

Current status and prospects of plant genome editing in Australia

Plant genome editing, particularly CRISPR-Cas biotechnologies, has rapidly evolved and drawn enormous attention all around the world in the last decade. The cutting-edge technologies have had substantial impact on precise genome editing for manipulating gene expression, stacking gene mutations, and improving crop agronomic traits. Following the global trends, investigations on CRISPR-Cas have been thriving in Australia, especially in agriculture sciences. Importantly, CRISPR-edited plants, classified as SDN-1 organisms (SDN: site-directed nuclease), have been given a green light in Australia, with regulatory bodies indicating they will not be classified as a genetically modified organism (GMO) if no foreign DNA is present in an edited plant. As a result, genome-edited products would not attract the onerous regulation required for the introduction of a GMO, which could mean more rapid deployment of new varieties and products that could be traded freely in Australia, and potentially to export markets. In the present review, we discuss the current status and prospects of plant genome editing in Australia by highlighting several species of interest. Using these species as case studies, we discuss the priorities and potential of plant genome editing, as well as the remaining challenges.

Vineyard environments influence Malbec grapevine phenotypic traits and DNA methylation patterns in a clone-dependent way

By studying three cv. Malbec clones cultivated in two vineyards with contrasting environmental conditions, we demonstrated that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent. Clonal selection and vegetative propagation determine low genetic variability in grapevine cultivars, although it is common to observe diverse phenotypes. Environmental signals may induce epigenetic changes altering gene expression and phenotype. The range of phenotypes that a genotype expresses in different environments is known as phenotypic plasticity. DNA methylation is the most studied epigenetic mechanism, but only few works evaluated this novel source of variability in grapevines. In the present study, we analyzed the effects on phenotypic traits and epigenome of three Vitis vinifera cv. Malbec clones cultivated in two contrasting vineyards of Mendoza, Argentina. Anonymous genome regions were analyzed using methylation-sensitive amplified polymorphism (MSAP) markers. Clone-dependent phenotypic and epigenetic variability between vineyards were found. The clone that presented the clearer MSAP differentiation between vineyards was selected and analyzed through reduced representation bisulfite sequencing. Twenty-nine differentially methylated regions between vineyards were identified and associated to genes and/or promoters. We discuss about a group of genes related to hormones homeostasis and sensing that could provide a hint of the epigenetic role in the determination of the different phenotypes observed between vineyards and conclude that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset

Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.

Greenhouse Spatial Effects Detected in the Barley (Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation

Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.

Distinct Metabolic Signals Underlie Clone by Environment Interplay in "Nebbiolo" Grapes Over Ripening

Several research studies were focused to understand how grapevine cultivars respond to environment; nevertheless, the biological mechanisms tuning this phenomenon need to be further deepened. Particularly, the molecular processes underlying the interplay between clones of the same cultivar and environment were poorly investigated. To address this issue, we analyzed the transcriptome of berries from three "Nebbiolo" clones grown in different vineyards, during two ripening seasons. RNA-sequencing data were implemented with analyses of candidate genes, secondary metabolites, and agronomical parameters. This multidisciplinary approach helped to dissect the complexity of clone × environment interactions, by identifying the molecular responses controlled by genotype, vineyard, phenological phase, or a combination of these factors. Transcripts associated to sugar signalling, anthocyanin biosynthesis, and transport were differently modulated among clones, according to changes in berry agronomical features. Conversely, genes involved in defense response, such as stilbene synthase genes, were significantly affected by vineyard, consistently with stilbenoid accumulation. Thus, besides at the cultivar level, clone-specific molecular responses also contribute to shape the agronomic features of grapes in different environments. This reveals a further level of complexity in the regulation of genotype × environment interactions that has to be considered for orienting viticultural practices aimed at enhancing the quality of grape productions.

Common garden experiment reveals altered nutritional values and DNA methylation profiles in micropropagated three elite Ghanaian sweet potato genotypes

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on the production of key nutrients by field-grown plants has not been previously studied. Here we assessed the extent of in vitro culture induced somaclonal variation, at a phenotypic, compositional and genetic/epigenetic level, by comparing field-maintained and micropropagated lines of three elite Ghanaian sweet potato genotypes grown in a common garden. Although micropropagated plants presented no observable morphological abnormalities compared to field maintained lines, they presented significantly lower levels of iron, total protein, zinc, and glucose. Methylation Sensitive Amplification Polymorphism analysis showed a high level of in vitro culture induced molecular variation in micropropagated plants. Epigenetic, rather than genetic variation, accounts for most of the observed molecular variability. Taken collectively, our results highlight the importance of ensuring the clonal fidelity of the micropropagated biofortified lines in order to reduce potential losses in the nutritional value prior to their commercial release.

Changes in grapevine DNA methylation and polyphenols content induced by solar ultraviolet-B radiation, water deficit and abscisic acid spray treatments

Environment and crop management shape plant's phenotype. Argentinean high-altitude vineyards are characterized by elevated solar ultraviolet-B radiation (UVB) and water deficit (D) that enhance enological quality for red winemaking. These signals promote phenolics accumulation in leaves and berries, being the responses mediated by abscisic acid (ABA). DNA methylation is an epigenetic mechanism that regulates gene expression and may affect grapevine growth, development and acclimation, since methylation patterns are mitotically heritable. Berry skins low molecular weight polyphenols (LMWP) were characterized in field grown Vitis vinifera L. cv. Malbec plants exposed to contrasting UV-B, D, and ABA treatments during one season. The next season early fruit shoots were epigenetically (methylation-sensitive amplification polymorphism; MSAP) and biochemically (LMWP) characterized. Unstable epigenetic patterns and/or stochastic stress-induced methylation changes were observed. UV-B and D were the treatments that induced greater number of DNA methylation changes respect to Control; and UV-B promoted global hypermethylation of MSAP epiloci. Sequenced MSAP fragments associated with UV-B and ABA showed similarities with transcriptional regulators and ubiquitin ligases proteins activated by light. UV-B was associated with flavonols accumulation in berries and with hydroxycinnamic acids in the next season fruit shoots, suggesting that DNA methylation could regulate the LMWP accumulation and participate in acclimation mechanisms.

Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Changes in the performance of genotypes in different environments are defined as genotype × environment (G×E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G×E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G×E-related. The G×E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G×E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.