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Summary: Drought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID‐INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP‐seq), we show that the sorghum BRI1‐EMS‐SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G‐box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1‐mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought. [ABSTRACT FROM AUTHOR]

Statistical tools are crucial for a variety of hydrological applications, whether to model processes and enhance understanding and knowledge or to design infrastructure systems. Given the rapid evolution of statistical methods and the need for a solid theoretical foundation for their correct application, a multidisciplinary community STAtistics in HYdrology Working Group (STAHY-WG) aggregated under the International Association of Hydrological Sciences (IAHS) umbrella to contribute to this research field. Now, more than 15 years since its inception, this paper summarizes the main achievements of this productive community collaboration in four (of many) branches of statistical hydrology: extreme value analysis, multivariate analysis, time series analysis, and regionalization. The aim is to provide an overview of recent developments, offer practical suggestions (e.g. software packages), and outline future challenges to support scientists and practitioners in their endeavours within the realm of statistical hydrology studies. [ABSTRACT FROM AUTHOR]

SUMMARY: Fruit ripening is an essential developmental stage in Angiosperms triggered by hormonal signals such as ethylene, a major player in climacteric ripening. Melon is a unique crop showing both climacteric and non‐climacteric cultivars, offering an ideal model for dissecting the genetic mechanisms underpinning this process. The major quantitative trait locus ETHQV8.1 was previously identified as a key regulator of melon fruit ripening. Here, we narrowed down ETHQV8.1 to a precise genomic region containing a single gene, the transcription factor CmERF024. Functional validation using CRISPR/Cas9 knock‐out plants unequivocally identified CmERF024 as the causal gene governing ETHQV8.1. The erf024 mutants exhibited suppression of ethylene production, leading to a significant delay and attenuation of fruit ripening. Integrative multi‐omic analyses encompassing RNA‐seq, DAP‐seq, and DNase‐seq revealed the association of CmERF024 with chromatin accessibility and gene expression dynamics throughout fruit ripening. Our data suggest CmERF024 as a novel regulator of climacteric fruit ripening in melon. Significance Statement: The current study describes a novel regulator of climacteric fruit ripening in melon, ERF024 (an ethylene‐responsive transcription factor), providing new insights into this complex system. This transcription factor would act in the first stages of fruit ripening, adding a new layer to the control of this key process in plant life cycle. [ABSTRACT FROM AUTHOR]

During late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes involved in berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves resulted in low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61 and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14 , the osmotic stress-related gene DHN1b , the Botrytis cinerea susceptibility gene WRKY52 , and NAC61 itself was validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulatory network that governs stilbenoid metabolism and osmotic, oxidative, and biotic stress responses that are the hallmark of late- and post-ripening grape stages. [ABSTRACT FROM AUTHOR]

Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets from three different tissues (leaf, berry, and 'all organs'). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied aggGCNs to study several transcription factor gene families, showing their capacity for detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC, and multiple specialized metabolic pathways. Specifically, transcription factor gene- and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p -coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino acid pathways. This network was validated using DNA affinity purification sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks in other crops and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships. [ABSTRACT FROM AUTHOR]

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future. [ABSTRACT FROM AUTHOR]

SUMMARY: The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP‐Seq) allows for the genome‐wide TF‐binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP‐Seq of MYB14/MYB15 was combined with aggregate gene co‐expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co‐regulator and resveratrol‐modifying gene candidates among which ROMT2‐3 were validated enzymatically. A high proportion of DAP‐Seq bound genes were induced in the activated transcriptomes of transient MYB15‐overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3‐MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP‐Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome‐wide approaches in the context of non‐model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism. [ABSTRACT FROM AUTHOR]

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications. [ABSTRACT FROM AUTHOR]

NACs (NAM/ATAF/CUC) are plant-specific transcription factors (TFs) and represent an interesting family due to their key role in plant development processes and stress responses. Among the 74 Vitis vinifera family members, VviNAC61 was selected for functional characterization as one of the key candidates of the major transcriptome reprogramming occurring during grapevine development and for its role as a molecular marker of the grape postharvest withering process. VviNAC61 is particularly expressed at veraison and post-veraison berry stages and shows a high expression also in lignified tissues such as roots, tendrils, seeds and rachis. In leaves, VviNAC61 achieves its higher level of expression in the senescence stage; in line with this observation, a NAC family multispecies phylogenetic tree revealed that VviNAC61 clusters with VviNAC33 and AtANAC046, both involved in the senescence processes. The effect of VviNAC61 over-expression was investigated through the agroinfiltration of N. benthamiana leaves, showing clear wilting symptoms and altered stomatal conductance. A transcriptomic analysis was performed on cv. 'Sultana' leaves transiently overexpressing VviNAC61 and a search of TF-bound genes by DNA Affinity Purification and sequencing (DAP-seq) was performed to narrow down the list of VviNAC61-regulated candidate genes. The "secondary metabolism", "transcription facor regulation" and "oxidative stress" functional categories were found as mainly enriched among candidate target genes. More in detail, several laccases and genes encoding for the phenylpropanoid pathway-related enzymes, senescence-related genes and several MYB and NAC genes (including VviNAC61) were bound in their promoter region by this TF. The control of the stilbene synthase regulator VviMYB14, the chlorophyll degradation regulator VviSGR1, as well as the VviNAC61 self regulation were validated through the luciferase assay. As last, the upstream regulation mechanism of VviNAC61 was further investigated demonstrating that VviNAC61 is controlled and interacts with CARPO (VviNAC60), a previously characterized master regulator of grapevine organ maturation. [ABSTRACT FROM AUTHOR]

Climate change will affect rainfall extremes and temperatures in the future. Therefore, floodsare expected to change. This study aims to identify such expected changes in flood behaviourthrough a rainfall-runoff simulation approach. Climate change precipitation and temperatureprojections are used as input data in a hydrological model. Changes in both flow peak andhydrograph volume frequency curves are identified from the output flow series of thehydrological model. Climate projections provided by EURO-CORDEX are used, as a recent study has shownthat they characterise extreme events better than Spanish AEMET projections. Fourcatchments located in northwestern Spain have been selected as case studies. Flood responsein such catchments has been simulated by using the HBV rainfall-runoff model.The model has been calibrated in each catchment by comparing the observed datawith the model outputs in the control period (1971-2004). In addition, the best biascorrection techniques have been identified in each catchment, in order to obtainthe most similar behaviour of floods compared with observations in the controlperiod. Three periods in the future have been simulated (2011-2040; 2041-2070;2071-2095) with the calibrated HBV models and bias corrected data. Expected changes infrequency curves of floods and accumulated volume in one, two, three, four and fivedays have been identified. The study finds that the simulations obtained by theHBV model show a general reduction in flood and volume quantiles, smoothingthe expected increases in precipitation quantiles. In general, the period 2071-2095presents the smallest reductions, as well as the larger increases in flow peak andvolume quantiles in some cases. Finally, expected changes in volumes and flowpeaks can differ. For instance, if flow peak quantiles decrease, volume quantiles canincrease. Therefore, both peak flow and hydrograph volume changes must be studied toobtain a complete knowledge about the expected behaviour of floods in the future. [ABSTRACT FROM AUTHOR]

The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from 9 selfings of cv. “Helfensteiner” (cross of cv. “Pinot noir” and “Schiava grossa”) instead of a single “Pinot noir”. These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing toward the eventual elaboration of the grapevine pangenome. [ABSTRACT FROM AUTHOR]