As grapevine production is converting into irrigated systems worldwide, understanding rootstock-scion interactions at different stages of moderate drought can help to better manage water resources and the choice of rootstock. This study compared the physio-morphological drought response and recovery of a drought-sensitive (Riparia Gloire (Vitis riparia)) and a drought-tolerant rootstock (Ramsey (Vitis champinii)) grafted with Cabernet Sauvignon (Vitis vinifera), and the self-grafted control in a pot study. Ramsey had lower root-to-shoot ratio but higher performance of the root system under drought, explained by the lower root tissue density and tip suberization and higher VviPIP2;1 aquaporin expression, and faster recovery of root hydraulic conductivity and stomatal conductance after re-watering than Riparia. Riparia maintained better water status under moderate drought by early root suberization, but it was less able to restore water uptake capacity and support scion growth and leaf gas exchange after re-watering. This study shows a suite of rootstock traits that improve scion growth in response to moderate drought. Thus, these results identify traits for breeding programs and the selection of rootstocks for sustainable management of water resources under irrigated production.

Abscisic acid (ABA) metabolism is complex involving biosynthesis, conjugation, and catabolism. Differences in ABA metabolism (ABA, ABA-related metabolites, and transcripts) in response to water deficit (WD) were detected in leaves and roots of four Vitis species differing in drought tolerance: Vitis vinifera (Cabernet Sauvignon), Vitis champinii (Ramsey), Vitis riparia (Riparia Gloire), and Vitis vinifera x girdiana (SC2). Concentrations of ABA and ABA-related metabolites increased after moderate or severe WD depending on species, organ, and time. Differences in ABA, glycosylated-ABA, and ABA catabolite concentrations, as well as previously investigated related transcript abundances, revealed differences in ABA metabolism pathways among the species and organs. NCED3 was a key gene in the WD response of leaves and roots of all species. NCED3 transcript abundance and ABA concentration in drought-tolerant Ramsey increased earlier and to a greater extent than other species. These species provide informative genetic resources to study ABA metabolism and drought tolerance further.

Moderate levels of Cl- have been associated with grapevine salt tolerance. The hypothesis to be tested in this work is: photosynthesis in grapevine is negatively correlated with foliar Cl- concentration. To further test this hypothesis, multiple mild salinity experiments on four different Vitis genotypes (Cabernet-Sauvignon, Riparia Gloire, Ramsey and SC2) were conducted and photosynthesis, ion concentrations and gene expression responses were quantified. The salt-tolerant rootstock Ramsey had greater Cl- exclusion capabilities than V. vinifera cultivars both during rooted cutting greenhouse experiments and three years of field-grafted experiments; SC2 also excluded Cl-. Differential gene expression indicated that salinity affected transcript abundance more in salt-sensitive genotypes (97.7 % of DEGs in the dataset), especially chloroplast-related transcripts. The transcript abundances of known anion transporters were determined and a family of putative B transporters was associated with the Cl- exclusion phenotype. Photosynthesis and growth were maintained in Ramsey and SC2 under mild salinity. However, photosynthesis declined in Cabernet-Sauvignon with isosmotic 20 mM salt concentrations of NaCl, KCl or NaNO3, independent of the salt type. While foliar Cl- concentrations did correlate with salt tolerance during control and NaCl conditions, it was not found to be the cause of photosynthetic decline in Vitis during mild salinity.

Background: Abscisic acid is a phytohormone involved in water deficit response. Abscisic acid metabolism is regulated by biosynthesis, conjugation, and catabolism. NCED3 is the rate limiting step of abscisic acid biosynthesis and is a key contributor to plant water deficit responses. In this study NCED3 transcript accumulation and abscisic acid metabolism were further characterized as key water deficit responses in four Vitis species ( Vitis vinifera (Cabernet Sauvignon), Vitis champinii (Ramsey), Vitis riparia (Riparia Gloire), and Vitis vinifera x Vitis girdiana (SC2)) under three levels of water deficit in leaves and roots. Results: The concentrations of abscisic acid and derivative metabolites increased with water deficit and was dependent upon the species. RNA-Seq and RT-qPCR data were consistent with the changes in abscisic acid metabolite concentrations; the corresponding transcript abundances substantiate NCED3 as a key gene in the water deficit response; however, NCED3 protein concentrations assayed in Western Blots were not affected. Major differences in abscisic acid metabolism at the gene, protein, and metabolite levels were detected between leaves and roots in these four species. NCED3 transcript abundance and abscisic acid concentration in drought-tolerant Ramsey increased earlier and more significantly than the other species during long-term, moderate to severe water deficits but were not stimulated as much by short-term, rapid dehydration. In drought-sensitive Riparia, NCED3 transcript abundance and abscisic acid metabolite concentrations increased to a lower extent than in Ramsey during moderate to severe water deficits, but short-term rapid dehydration induced a significantly higher abscisic acid concentration in Riparia than Ramsey. Conclusions: Grapevine species have distinct abscisic acid metabolism that depends highly on the severity and duration of stress and organ (leaves or roots). This study confirms that abscisic acid metabolism and NCED3 are part of a core water deficit response in Vitis species. Relative quantities of transcripts, proteins, abscisic acid and derivative metabolites were determined, but many aspects of abscisic acid metabolism and water deficit responses warrant additional investigation. This study provides a better understanding of how Vitis is adapted to dry environments, which may be exploited for future breeding programs.

DEA and TPM values for the MIP family genes from comparison results between drought treated and control vines for each organ x week x genotype combinations. (XLSX 62 kb)

Additional file 10. Percent identity of PN40024 and Cabernet Sauvignon (CS) VviERF6L protein motifs.

Summary of the WGCNA modules in the leaves. (XLSX 29 kb)

Climate change threatens food security, and plant science researchers have investigated methods of sustaining crop yield under drought. One approach has been to overproduce abscisic acid (ABA) to enhance water use efficiency. However, the concomitant effects of ABA overproduction on plant vascular system functioning are critical as it influences vulnerability to xylem hydraulic failure. We investigated these effects by comparing physiological and hydraulic responses to water deficit between a tomato (Solanum lycopersicum) wild type control (WT) and a transgenic line overproducing ABA (sp12). Under well-watered conditions, the sp12 line displayed similar growth rate and greater water use efficiency by operating at lower maximum stomatal conductance. X-ray microtomography revealed that sp12 was significantly more vulnerable to xylem embolism, resulting in a reduced hydraulic safety margin. We also observed a significant ontogenic effect on vulnerability to xylem embolism for both WT and sp12. This study demonstrates that the greater water use efficiency in the tomato ABA overproducing line is associated with higher vulnerability of the vascular system to embolism and a higher risk of hydraulic failure. Integrating hydraulic traits into breeding programmes represents a critical step for effectively managing a crop's ability to maintain hydraulic conductivity and productivity under water deficit.

Background: VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq. Results: A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions: VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

Background: Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results: To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions: Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

Background Grapevine is an economically important crop for which yield and berry quality is strongly affected by climate change. Large variations in drought tolerance exist across Vitis species. Some of these species are used as rootstock to enhance abiotic and biotic stress tolerance. In this study, we investigated the physiological and transcriptomic responses to water deficit of four different genotypes that differ in drought tolerance: Ramsey (Vitis champinii), Riparia Gloire (Vitis riparia), Cabernet Sauvignon (Vitis vinifera), and SC2 (Vitis vinifera x Vitis girdiana). Results Ramsey was particularly more drought tolerant than the other three genotypes. Ramsey maintained a higher stomatal conductance and photosynthesis at equivalent levels of moderate water deficit. We identified specific and common transcriptomic responses shared among the four different Vitis species using RNA sequencing analysis. A weighted gene co-expression analysis identified a water deficit core gene set with the ABA biosynthesis and signaling genes, NCED3, RD29B and ABI1 as potential hub genes. The transcript abundance of many abscisic acid metabolism and signaling genes was strongly increased by water deficit along with genes associated with lipid metabolism, galactinol synthases and MIP family proteins. This response occurred at smaller water deficits in Ramsey and with higher transcript abundance than the other genotypes. A number of aquaporin genes displayed differential and unique responses to water deficit in Ramsey leaves. Genes involved in cysteine biosynthesis and metabolism were constitutively higher in the roots of Ramsey; thus, linking the gene expression of a known factor that influences ABA biosynthesis to this genotype's increased NCED3 transcript abundance. Conclusion The drought tolerant Ramsey maintained higher photosynthesis at equivalent water deficit than the three other grapevine genotypes. Ramsey was more responsive to water deficit; its transcriptome responded at smaller water deficits, whereas the other genotypes did not respond until more severe water deficits were reached. There was a common core gene network responding to water deficit for all genotypes that included ABA metabolism and signaling. The gene clusters and sub-networks identified in this work represent interesting gene lists to explore and to better understand drought tolerance molecular mechanisms.

Transcript abundances in the skins of 'Cabernet Sauvignon' grapes grown in Bordeaux (BOD), France, were compared with those grown in Reno (RNO), Nevada, USA, during the late stages of berry development at similar berry sugar levels (19-26 degrees Brix). Day lengths were similar in the two locations, but day temperatures were higher and night temperatures lower in RNO. Sugar levels were estimated by measuring total soluble solids (TSS). TSS was lower in berries harvested in BOD compared with RNO at maturity levels considered optimum for harvest in their local locations. RNA-seq analysis revealed that there were 4455 differentially expressed genes (DEGs) between BOD and RNO grape skins at approximately 22 degrees Brix. The top gene ontology ( GO) categories of the DEGs were involved in response to stimulus, response to stress, and transport. DEGs included autophagy, terpene synthase and pathogen-response genes. Transcript abundance profiles in the berry skins at maturity were highly dynamic and sensitive to the environment in both BOD and RNO. Many DEGs could be associated with different environmental conditions that affected the berries in the two locations.

Background: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. Results: Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value <0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. Conclusions: This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot.

Table S3. Differentially expressed genes in water defict root (WD root) and well-watered root (C root). Values are normalized RPKM for each treatment, fold change (FC) and test statistic and q-value. Genes highlighted in gray were up-regulated in WD root relative to C root. Genes in bold were differentially express in common in WD root and WD shoot relative to their respective C tissue. (XLSX 176 kb)

The release of the grapevine genome sequence has allowed the generation of invaluable data on gene function, providing tools for a better understanding of the plant biology. To capitalize on this information, the annotation of the genome has been an ongoing effort performed by the research community on that species. Annotation initiatives can take the form of automatic annotation with gene prediction performed in silico based on the knowledge of other species and transcriptomic data as well as manual curation and integration of results from the literature. The International Grape Genome Program created recently a committee to harmonize the annotation process. The primary aims of the committee are to provide a unified high quality and highly accessible annotation of grapevine genes. To reach that objective, standard nomenclature for locus identifiers and conventions for a gene naming system were set up. Genome annotation is a work in progress because of new improved annotation technologies and new discoveries of structural components and functions within the genome. As technology and knowledge on genome functioning improves, it is expected that new challenges and perspectives will arise in the field of genome annotation such as the integration of the role of non-coding areas of the genome or the integration of polymorphic diversity within cultivars.

The inclusive threshold policy for publication in BMC journals including BMC Plant Biology means that editorial decisions are largely based on the soundness of the research presented rather than the novelty or potential impact of the work. Here we discuss what is required to ensure that research meets the requirement of scientific soundness. BMC Plant Biology and the other BCM-series journals ( https://www.biomedcentral.com/p/the-bmc-series-journals ) differ in policy from many other journals as they aim to provide a home for all publishable research. The inclusive threshold policy for publication means that editorial decisions are largely based on the soundness of the research presented rather than the novelty or potential impact of the work. The emphasis on scientific soundness ( http://blogs.biomedcentral.com/bmcseriesblog/2016/12/05/vital-importance-inclusive/ ) rather than novelty or impact is important because it means that manuscripts that may be judged to be of low impact due to the nature of the study as well as those reporting negative results or that largely replicate earlier studies, all of which can be difficult to publish elsewhere, are available to the research community. Here we discuss the importance of the soundness of research and provide some basic guidelines to assist authors to determine whether their research is appropriate for submission to BMC Plant Biology.Prior to a research article being sent out for review, the handling editor will first determine whether the research presented is scientifically valid. To be valid the research must address a question of biological significance using suitable methods and analyses, and must follow community-agreed standards relevant to the research field.

Two different osmotic stress experiments using different proteomic methods were compared. In Experiment 1, two osmotic stress treatments of growing shoot tips of 'Cabernet Sauvignon' grapevines were compared over 16 days; one was a gradually-applied, long-term water deficit and the second was an equivalent salinity stress. Proteins were analyzed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In Experiment 2, a water deficit treatment was applied; protein extracts were analyzed using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS). In both experiments, osmotic stress progressively reduced growth with time. In Experiment 1, 82 out of 645 (13%) proteins had significant changes in abundance in response to stress over time. and were identified by matrix-assisted laser desorption ionization time of flight tandem (MALDI TOF/TOF) mass spectrometry. The average coefficient of variation (CV) of the protein abundance for all 645 proteins was approximately 50%. In Experiment 2, 2,277 proteins were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins clustered into four groups: increased and decreased abundance of early-and late-responding protein profiles. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, and growth-related categories (steroid metabolism and water transport), whereas those for late-responding proteins were involved with transport, antioxidants, amino acid and carbohydrate metabolism. More proteins with less error were identified with gel-free shotgun proteomics than with 2D PAGE. Most proteins could be matched with a probe set on the Affymetrix Vitis vinifera Genome Array. Only 25 and 28% of the protein profiles in Experiment 1 and 2, respectively, had a significant Pearson correlation with their transcript profiles; less than 20% for early responding proteins and more than 60% for late responding proteins.

Annotation of the differentially expressed genes (DEGs) and count data associated with each gene. V1 ID is the same as in Additional file 3. AtID refers to Arabidopsis thaliana gene loci. Headings on the column refer to the cultivar abbreviation followed by the number of the replicate and the number of the °Brix level. The final columns compute the differences between °Brix levels for each cultivar and average them for all cultivars. Color highlights represent decreasing (green) or increasing (red) differences for the gene for the 26 to 20 °Brix comparison (26–20) (XLSX 3136 kb).

BinGO analysis of the top 500 DEGs with a positive difference between 26 and 20° Brix (26–20) (XLSX 73 kb).