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Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

'Regent' is the fungal resistant grapevine cultivar with the highest acreage in Germany and an important resistance donor in international breeding programs. It carries the resistance loci Rpv3.1 as well as Ren3 and Ren9 against downy and powdery mildew, respectively. As the parents of 'Chambourcin', the resistant paternal ancestor of 'Regent', did not coincide with the breeder's information, the germplasm repository of JKI Geilweilerhof was screened to find the missing ancestors. SSR marker analysis revealed that 'Joannes Seyve 11369' and 'Plantet' are the true parents of 'Chambourcin' and not 'Seyve Villard 12-417' and 'Chancellor'. Furthermore, the origin of the resistance loci Ren3 and Ren9 could be traced back to the genotypes 'Seibel 4614' and 'Munson'. Since the breeder Hermann Jaeger mentioned 'Munson' as a direct descendant of Vitis aestivalis Michx. var. linsecomii (Buckley) L. H. Bailey and Vitis rupestris Scheele, one of these wild species might have been the donor of the loci. [ABSTRACT FROM AUTHOR]

Plant roots are essential for water and nutrient uptake and contribute to the plants' response to environmental stress factors. As the hidden half of a plant, investigation of root systems is highly challenging, most of available methods are destructive and very labour-intensive. In this proof-of-concept study, a non-invasive X-ray micro computed tomography (X-ray µCT) method was applied to investigate the phenotypic variation of the complex three-dimensional (3D) architecture of grapevine roots as a function of genotype and soil. Woody cuttings of 'Calardis Musqué', 'Villard Blanc' and V3125 ('Schiava Grossa' x 'Riesling') were cultivated in polypropylene columns filled with two different soil types, clay loam and sandy loam, for 6 weeks. Afterwards, the columns were scanned once using the technique of X-ray µCT. The received raw data were analysed for the reconstruction of 3D root system models (3D model), which display a non-destructive visualization of whole, intact root systems with a spatial resolution of 42 µm. The 3D models of all investigated plants (in total 18) were applied to quantify root system characteristics precisely by measuring adventitious root length, lateral root length, total root length, root system surface area, root system volume and root growth angles from the woody cutting relative to a horizontal axis. The results showed that: (i) early root formation and root growth differed between genotypes, especially between 'Calardis Musqué' and 'Villard Blanc'; and (ii) the soil type does influence adventitious root formation of V3125, but had minor effects on 'Calardis Musqué' and 'Villard Blanc'. In conclusion, this innovative, high-resolution method of X-ray µCT is suitable for high resolution phenotyping of root formation, architecture, and rooting characteristics of grapevine woody cuttings in a non-destructive manner, e.g. to investigate root response to drought stress and would provide new insights into phylloxera root infection. [ABSTRACT FROM AUTHOR]

Grape resilience towards Botrytis cinerea (B. cinerea) infections (Botrytis bunch rot) is an important concern of breeders and growers. Beside grape bunch architecture, berry surface characteristics like berry bloom (epicuticular wax) as well as thickness and permeability of the berry cuticle represent further promising physical barriers to increase resilience towards Botrytis bunch rot. In previous studies, two efficient sensor-based phenotyping methods were developed to evaluate both berry surface traits fast and objectively: (1) light-separated RGB (red-green-blue) image analysis to determine the distribution of epicuticular wax on the berry surface; and (2) electrical impedance characteristics of the grape berry cuticle based on point measurements. The present proof-of-concept study aiming at the evaluation of light-separated RGB images for both phenotyping applications, phenotyping wax distribution pattern and berry cuticle impedance values. Within the selected grapevine varieties like 'Riesling', 'Sauvignon Blanc' or 'Calardis Blanc' five contributions were achieved: (1) Both phenotyping approaches were fused into one prototypic unified phenotyping method achieving a wax detection accuracy of 98.6 % and a prediction of electrical impedance with an accuracy of 95 %. (2) Both traits are derived using only light-separated images of the grapevine berries. (3) The improved method allows the detection and quantification of additional surface traits of the grape berry surface such as lenticels (punctual lignification) and the berry stem that are also known as being able to affect the grape susceptibility towards Botrytis. (4) The improved image analysis tools are further integrated into a comprehensive workbench allowing end-users, like breeders to combine phenotyping experiments with transparent data management offering valuable services like visualizations, indexing, etc. (5) Annotation work is supported by a sophisticated annotation tool of the image analysis workbench. The usage of light-separated images enables fast and non-invasive phenotyping of different optical berry surface characteristics, which saves time-consuming labor and additionally allows the reuse of the berry samples for subsequent investigations, e.g. Botrytis infection studies. [ABSTRACT FROM AUTHOR]

Yield and its prediction is one of the most important tasks in grapevine breeding purposes and vineyard management. Commonly, this trait is estimated manually right before harvest by extrapolation, which mostly is labor- intensive, destructive and inaccurate. In the present study an automated image-based workflow was developed for quantifying inflorescences and single flowers in unprepared field images of grapevines, i.e. no artificial background or light was applied. It is a novel approach for non-invasive, inexpensive and objective phenotyping with high-throughput. First, image regions depicting inflorescences were identified and localized. This was done by segmenting the images into the classes "inflorescence" and "non-inflorescence" using a Fully Convolutional Network (FCN). Efficient image segmentation hereby is the most challenging step regarding the small geometry and dense distribution of single flowers (several hundred single flowers per inflorescence), similar color of all plant organs in the fore- and background as well as the circumstance that only approximately 5% of an image show inflorescences. The trained FCN achieved a mean Intersection Over Union (IOU) of 87.6% on the test data set. Finally, single flowers were extracted from the "inflorescence"-areas using Circular Hough Transform. The flower extraction achieved a recall of 80.3% and a precision of 70.7% using the segmentation derived by the trained FCN model. Summarized, the presented approach is a promising strategy in order to predict yield potential automatically in the earliest stage of grapevine development which is applicable for objective monitoring and evaluations of breeding material, genetic repositories or commercial vineyards. [ABSTRACT FROM AUTHOR]

Viticulture is of high economic value. Traditional grapevine cultivars (Vitis vinifera L.) are used in adaptation to the climatic conditions from Northern to Southern European growing areas. However, the recent trend of global warming causes quality deficits due to a shift of the plant's development to earlier times in the year. As a consequence, premature ripening happens under warm temperatures and interferes with the balanced accumulation of sugars, acids, aroma profiles and berry coloration. Modern grapevine breeding is challenged to include the ripening behavior as an important trait (besides pathogen resistance and other characteristics) into the development of novel cultivars well suited for sustainable viticulture. Breeders nowadays apply molecular markers to follow the introgression of desired traits on the genetic level. Previous work has identified a molecular tag on grapevine chromosome 16 strongly linked to the time of véraison, the start of the second phase of berry ripening, in a segregating cross population. In this study we analyzed the transferability of this marker to a set of 36 grapevine cultivars commonly used in German viticulture. Association analysis verified the predictive character of the time point of véraison for maturation time and confirmed the diagnostic potential of the véraison-linked marker in this extended set of cultivars. [ABSTRACT FROM AUTHOR]

The ascomycete Erysiphe necator causes powdery mildew disease of grapevine, a disastrous infection which is commonly defeated with multiple fungicide applications in viticulture. Breeding for natural resistance of quality grapes (Vitis vinifera) is thus a major aim of current efforts. The cultivar 'Regent' is resistant to powdery mildew due to an introgression from an American Vitis sp. resistance donor. To identify key regulatory elements in defense responses of 'Regent' we performed transcript analyses after challenging with E. necator inoculation in comparison with a susceptible grapevine. A set of genes selected from preliminary microarray hybridization results were investigated by RT-qPCR. The data indicate an important role of transcription factors MYB15, WRKY75, WRKY33, WRKY7, ethylene responsive transcription factors ERF2 and ERF5 as well as a CZF1/ZFAR transcripton factor in regulating the early defense when the fungus starts the interaction with its host by the formation of haustoria. [ABSTRACT FROM AUTHOR]

Parent offspring analysis already revealed genetic relationships for 'Blauer Portugieser' and 'Blaufränkisch', sharing at each locus one allele with 'Grüner Silvaner' and 'Weisser Heunisch', respectively. The missing second progenitor of 'Blauer Portugieser' and 'Blaufränkisch' is a recently rediscovered black grapevine, called 'Blaue Zimmettraube'. It was found in the largest German wine growing area Rheinhessen. The same cultivar was detected as a single vine in Friuli, Italy and named Sbulzìna. The 'Blaue Zimmettraube', bearing female flowers, and thus the female parent in the crosses, was cultivated in the 19th century in Lower Styria together with 'Grüner Silvaner' and 'Weisser Heunisch'. Because the 'Blaue Zimmettraube' did not exist in Austria and red wine production was fairly rare in that country before 1800, it is suspected that the cradle of 'Blauer Portugieser' and 'Blaufränkisch' is in Lower Styria. Furthermore, according to chlorotype analysis, it turned out that 'Blauer Gänsfüsser' is the male parent of 'Blaue Zimmettraube' and thus the 'Blaue Zimmettraube' represents a veritable "missing link". To prove the genetic relationships the nine GrapeGen06-markers and additional forty microsatellite markers were applied. Likelihood analysis with allele frequencies of 22 SSR-markers from 772 cultivars revealed a very high degree of probability that the proposed parents are consistent, due to rare alleles inherited from 'Blaue Zimmettraube'. To investigate on the geographical origin of 'Blauer Portugieser' and 'Blaufränkisch' historical Austrian and Styrian references were consulted. [ABSTRACT FROM AUTHOR]

The Vitis vinifera background of 'Catawba' and 'Concord' was investigated by using SSR analysis: 'Sémillon' was shown to be an ancestor of 'Catawba', while the wild parent remains unknown. 'Concord' was confirmed to be an offspring of 'Catawba' and another unknown wild parent. Since these two important American varieties most likely resulted from random natural crosses and successful selection, the original, wild growing wild donors remain unknown. [ABSTRACT FROM AUTHOR]

A biparental population segregating for downy mildew resistance was studied to identify resistance linked molecular markers. The progeny of 202 individuals from a cross of V3125 (susceptible breeding line) with 'Börner' (resistant rootstock) was phenotyped in the field in four seasons and by evaluating artificially infected leaf discs. QTL mapping revealed a major resistance locus on chromosome 5 that explained up to 17.4 % of the phenotypic variance. This new resistance locus was named Rpv14. It was transmitted from the male grandparent V. cinerea Arnold to 'Börner' and is associated with the marker GF05-13. [ABSTRACT FROM AUTHOR]

Delivery of DNA into dry and viable embryos of wheat by imbibition in DNA solution was detected by monitoring the transient expression of chimeric genes. The gene expression vectors used comprise of a neomycin phosphotransferase II (NPT II) reporter gene, under the control of various promoters or as part of a cloned plant virus genome. The genome of wheat dwarf virus (WDV), a monopartite Gemini virus of gramineae, has been used to amplify the NPT II gene in embryos of wheat, thereby leading to high levels of transient expression. Constructions were designed which permitted NPT II expression only if inter- or intramolecular recombination had occurred. [ABSTRACT FROM AUTHOR]

In viticulture, pathogens like the oomycete Plasmopara viticola , the causal agent of downy mildew, can cause severe yield loss and require extensive application of plant protection chemicals. Breeders are generating pathogen-resistant varieties exploiting American and Asian wild Vitis germplasm as sources of resistance. Several loci mediating resistance to P. viticola have been identified in the past but may be overcome by specifically adapted strains of the pathogen. Aiming to find and characterize novel loci, a cross population with Vitis amurensis ancestry was investigated searching for resistance-correlated quantitative trait loci (QTL). As a prerequisite, a genetic map was generated by analyzing the 244 F 1 individuals derived from a cross of the downy mildew susceptible Vitis vinifera cultivar 'Tigvoasa' and the resistant V. amurensis pBC1 breeding line We 90-06-12. This genetic map is based on the information from 627 molecular markers including 56 simple sequence repeats and 571 rhAmpSeq markers. A phenotypic characterization of the progeny showed a clear segregation of the resistance traits in the F 1 population after an experimental inoculation of leaf discs with downy mildew. Combining genetic and phenotypic data, an analysis for QTL revealed a major locus on linkage Group 9 that correlates strongly with the resistance to downy mildew. The locus was mapped to a region of about 80 kb on the PN40024 (12x.V2) grapevine reference genome. This genomic region co-localizes with the formerly identified locus Rpv10 from the grapevine cultivar 'Solaris'. As we found different allele sizes of the locus-linked SSR markers than those characterizing the known Rpv10 locus and differences in the sequence of a candidate gene, it was regarded as a haplotype variant and named Rpv10.2 .

Veraison marks the transition from berry growth to berry ripening and is a crucial phenological stage in grapevine (Vitis vinifera): the berries become soft and begin to accumulate sugars, aromatic substances, and, in red cultivars, anthocyanins for pigmentation, while the organic acid levels begin to decrease. These changes determine the potential quality of wine. However, rising global temperatures lead to earlier flowering and ripening, which strongly influence wine quality. Here, we combined genotyping-by-sequencing with a bioinformatics pipeline on ∼150 F1 genotypes derived from a cross between the early ripening variety "Calardis Musqué" and the late-ripening variety "Villard Blanc". Starting from 20,410 haplotype-based markers, we generated a high-density genetic map and performed a quantitative trait locus analysis based on phenotypic datasets evaluated over 20 yrs. Through locus-specific marker enrichment and recombinant screening of ∼1,000 additional genotypes, we refined the originally postulated 5-mb veraison locus, Ver1, on chromosome 16 to only 112 kb, allowing us to pinpoint the ethylene response factor VviERF027 (VCost.v3 gene ID: Vitvi16g00942, CRIBIv1 gene ID: VIT_16s0100g00400) as veraison candidate gene. Furthermore, the early veraison allele could be traced back to a clonal "Pinot" variant first mentioned in the seventeenth century. "Pinot Precoce Noir" passed this allele over "Madeleine Royale" to the maternal grandparent "Bacchus Weiss" and, ultimately, to the maternal parent "Calardis Musqué". Our findings are crucial for ripening time control, thereby improving wine quality, and for breeding grapevines adjusted to climate change scenarios that have a major impact on agro-ecosystems in altering crop plant phenology., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

It is crucial for winegrowers to make informed decisions about the optimum time to harvest the grapes to ensure the production of premium wines. Global warming contributes to decreasing acidity and increasing sugar levels in grapes, resulting in bland wines with high contents of alcohol. Predicting quality in viticulture is thus pivotal. To assess the average ripeness, typically a sample of one hundred berries representative for the entire vineyard is collected. However, this process, along with the subsequent detailed must analysis, is time consuming and expensive. This study focusses on predicting essential quality parameters like sugar and acid content in Vitis vinifera (L.) varieties 'Chardonnay', 'Riesling', 'Dornfelder', and 'Pinot Noir'. A small near-infrared spectrometer was used measuring non-destructively in the wavelength range from 1 100 nm to 1 350 nm while the reference contents were measured using high-performance liquid chromatography. Chemometric models were developed employing partial least squares regression and using spectra of all four grapevine varieties, spectra gained from berries of the same colour, or from the individual varieties. The models exhibited high accuracy in predicting main quality-determining parameters in independent test sets. On average, the model regression coefficients exceeded 93% for the sugars fructose and glucose, 86% for malic acid, and 73% for tartaric acid. Using these models, prediction accuracies revealed the ability to forecast individual sugar contents within an range of ± 6.97 g/L to ± 10.08 g/L, and malic acid within ± 2.01 g/L to ± 3.69 g/L. This approach indicates the potential to develop robust models by incorporating spectra from diverse grape varieties and berries of different colours. Such insight is crucial for the potential widespread adoption of a handheld near-infrared sensor, possibly integrated into devices used in everyday life, like smartphones. A server-side and cloud-based solution for pre-processing and modelling could thus avoid pitfalls of using near-infrared sensors on unknown varieties and in diverse wine-producing regions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Cornehl, Gauweiler, Zheng, Krause, Schwander, Töpfer, Gruna and Kicherer.)

The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed. A total of 24 nSSR markers were utilized to establish a fingerprint database to infer information on the population genetic diversity and structure. Three nSSR markers linked to the Ren1 locus were analyzed to identify potential resistance against powdery mildew. According to molecular fingerprinting data, the Armenian V. sylvestris gene pool conserves a high genetic diversity, displaying 292 different alleles with 12.167 allele per loci. The clustering analyses and diversity parameters supported eight genetic groups with 5.6% admixed proportion. The study of genetic polymorphism at the Ren1 locus revealed that 28 wild genotypes carried three R-alleles and 34 wild genotypes carried two R-alleles associated with PM resistance among analyzed 107 wild individuals. This gene pool richness represents an immense reservoir of under-explored genetic diversity and breeding potential. Therefore, continued survey and research efforts are crucial for the conservation, sustainable management, and utilization of Armenian wild grape resources in the face of emerging challenges in viticulture., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Margaryan, Töpfer, Gasparyan, Arakelyan, Trapp, Röckel and Maul.)

Background: Traditional wine growing regions are increasingly endangered by climatic alterations. One promising approach to mitigate advancing climate change could be an increase of soil organic matter. Here, especially subsoils are of interest as they provide higher carbon storage potential than topsoils. In this context, vineyard subsoils could be particularly suitable since they are deeply cultivated once before planting and afterwards, left at rest for several decades due to the perennial nature of grapevines., Methods: For this purpose, a biochar compost substrate and greenwaste compost were incorporated in up to 0.6 m depth before planting a new experimental vineyard with the fungus-resistant grapevine cultivar 'Calardis Musqué'. The influence of this deep incorporation on greenhouse gas emissions and grapevine performance was evaluated and compared to a non-amended control using sensor-based analyses., Results: Increased CO 2 emissions and lower N 2 O emissions were found for the incorporation treatments compared to the control, but these differences were not statistically significant due to high spatial variability. Only few plant traits like chlorophyll content or berry cuticle characteristics were significantly affected in some of the experimental years. Over the course of the study, annual climatic conditions had a much stronger influence on plant vigor and grape quality than the incorporated organic amendments., Discussion: In summary, organic soil amendments and their deep incorporation did not have any significant effect on greenhouse gas emissions and no measurable or only negligible effect on grapevine vigor, and grape quality parameters. Thus, according to our study the deposition of organic amendments in vineyard subsoils seems to be an option for viticulture to contribute to carbon storage in soils in order to mitigate climate change., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Schneider, Islam, Wehrle, Pätzold, Brüggemann, Töpfer and Herzog.)

An automatic determination of grape must ingredients during the harvesting process would support cellar logistics and enables an early termination of the harvest if quality parameters are not met. One of the most important quality-determining characteristics of grape must is its sugar and acid content. Among others, the sugars in particular determine the quality of the must and wine. Chiefly in wine cooperatives, in which a third of all German winegrowers are organized, these quality characteristics serve as the basis for payment. They are acquired upon delivery at the cellar of the cooperative or the winery and result in the acceptance or rejection of grapes and must. The whole process is very time-consuming and expensive, and sometimes grapes that do not meet the quality requirements for sweetness, acidity, or healthiness are destroyed or not used at all, which leads to economic loss. Near-infrared spectroscopy is now a widely used technique to detect a wide variety of ingredients in biological samples. In this study, a miniaturized semi-automated prototype apparatus with a near-infrared sensor and a flow cell was used to acquire spectra (1100 nm to 1350 nm) of grape must at defined temperatures. Data of must samples from four different red and white Vitis vinifera (L.) varieties were recorded throughout the whole growing season of 2021 in Rhineland Palatinate, Germany. Each sample consisted of 100 randomly sampled berries from the entire vineyard. The contents of the main sugars (glucose and fructose) and acids (malic acid and tartaric acid) were determined with high-performance liquid chromatography. Chemometric methods, using partial least-square regression and leave-one-out cross-validation, provided good estimates of both sugars (RMSEP = 6.06 g/L, R 2 = 89.26%), as well as malic acid (RMSEP = 1.22 g/L, R 2 = 91.10%). The coefficient of determination ( R 2 ) was comparable for glucose and fructose with 89.45% compared to 89.08%, respectively. Although tartaric acid was predictable for only two of the four varieties using near-infrared spectroscopy, calibration and validation for malic acid were accurate for all varieties in an equal extent like the sugars. These high prediction accuracies for the main quality determining grape must ingredients using this miniaturized prototype apparatus might enable an installation on a grape harvester in the future.

The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12 , mediating resistance against P. viticola , was originally found in Asian Vitis amurensis . This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12 -carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-seq experiment, revealing approximately 600 upregulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance and the sensitivity encoding Gf.99-03 haplotype were structurally and functionally compared with each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogs related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R -genes enable its improved applicability in marker-assisted grapevine breeding., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Frommer, Müllner, Holtgräwe, Viehöver, Huettel, Töpfer, Weisshaar and Zyprian.)

The red-fleshed grape cultivars, called teinturier or dyer grapes, contain anthocyanins in both the skin and flesh. These phenolic compounds exhibit excellent coloring ability, and as antioxidants, they are important bioactive compounds in food crops. In this work, anthocyanin patterns of grape berries of fifteen teinturier varieties collected from the gene bank located at Pécs in the southwest of Hungary were compared. Anthocyanin profiles of numerous varieties originating from Hungary such as 'Bíborkadarka', 'Kármin', 'Kurucvér', and 'Turán' are reported for the first time. Anthocyanins extracted separately from the skin and juice were analyzed using high-performance liquid chromatography coupled with a photodiode array detector. For the identification of compounds, high-resolution orbitrap mass spectrometry was used. All in all, twenty-one anthocyanins were identified and quantified. We found that anthocyanin patterns differed significantly in the skin and juice for all investigated cultivars. For Vitis vinifera varieties, the predominant anthocyanin in the skin was malvidin-3- O -glucoside, while the main pigment in the juice was peonidin-3- O -glucoside. For the first time, a significant amount of diglucosides was detected in two Vitis Vinifera cultivars with a direct relationship. In general, the pigment composition of the skin was much more complex than that of the juice. The comparative study with presented patterns gives valuable and beneficial information from a chemotaxonomical point of view. Our results also help to choose the appropriate teinturier varieties with the desired anthocyanins for food coloring or winemaking purposes.

A multitude of diverse breeding goals need to be combined in a new cultivar, which always forces to compromise. The biggest challenge grapevine breeders face is the extraordinarily complex trait of wine quality, which is the all-pervasive and most debated characteristic. Since the 1920s, Germany runs continuous grapevine breeding programmes. This continuity was the key to success and lead to various new cultivars on the market, so called PIWIs. Initially, introduced pests and diseases such as phylloxera, powdery and downy mildew were the driving forces for breeding. However, preconceptions about the wine quality of new resistant selections impeded the market introduction. These preconceptions are still echoing today and may be the reason in large parts of the viticultural community for: (1) ignoring substantial breeding progress, and (2) sticking to successful markets of well-known varietal wines or blends (e.g. Chardonnay, Cabernet Sauvignon, Riesling). New is the need to improve viticulture´s sustainability and to adapt to changing environmental conditions. Climate change with its extreme weather will impose the need for a change in cultivars in many wine growing regions. Therefore, a paradigm shift is knocking on the door: new varieties (PIWIs) versus traditional varieties for climate adapted and sustainable viticulture. However, it will be slow process and viticulture is politically well advised to pave the way to variety innovation. In contrast to the widely available PIWIs, competitive cultivars created by means of new breeding technologies (NBT, e.g. through CRISPR/Cas) are still decades from introduction to the market., (© 2022. The Author(s).)

'Riesling Weiss' is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is 'Riesling Rot', a red-berried variant of 'Riesling Weiss' that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of 'Riesling Rot' revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR . The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of 'Riesling Weiss', 'Riesling Rot', and the ancestor 'Heunisch Weiss' along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of 'Riesling Weiss' was inherited from the white-berried parent variety 'Heunisch Weiss'. Since no color mutants of 'Heunisch Weiss' are described that could have served as allele donors, we concluded that, in contrast to the public opinion, 'Riesling Rot' resulted from a mutational event in 'Riesling Weiss' and not vice versa.

Botrytis bunch rot is one of the economically most important fungal diseases in viticulture (aside from powdery mildew and downy mildew). So far, no active defense mechanisms and resistance loci against the necrotrophic pathogen are known. Since long, breeders are mostly selecting phenotypically for loose grape bunches, which is recently the most evident trait to decrease the infection risk of Botrytis bunch rot. This study focused on plant phenomics of multiple traits by applying fast sensor technologies to measure berry impedance (Z REL ), berry texture, and 3D bunch architecture. As references, microscopic determined cuticle thickness (MS CT ) and infestation of grapes with Botrytis bunch rot were used. Z REL hereby is correlated to grape bunch density OIV204 ( r = -0.6), cuticle thickness of berries ( r = 0.61), mean berry diameter ( r = -0.63), and Botrytis bunch rot ( r = -0.7). However, no correlation between Z REL and berry maturity or berry texture was observed. In comparison to the category of traditional varieties (mostly susceptible), elite breeding lines show an impressive increased Z REL value (+317) and a 1-μm thicker berry cuticle. Quantitative trait loci (QTLs) on LGs 2, 6, 11, 15, and 16 were identified for Z REL and berry texture explaining a phenotypic variance of between 3 and 10.9%. These QTLs providing a starting point for the development of molecular markers. Modeling of Z REL and berry texture to predict Botrytis bunch rot resilience revealed McFadden R 2 = 0.99. Taken together, this study shows that in addition to loose grape bunch architecture, berry diameter, Z REL , and berry texture values are probably additional parameters that could be used to identify and select Botrytis -resilient wine grape varieties. Furthermore, grapevine breeding will benefit from these reliable methodologies permitting high-throughput screening for additional resilience traits of mechanical and physical barriers to Botrytis bunch rot. The findings might also be applicable to table grapes and other fruit crops like tomato or blueberry., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Herzog, Schwander, Kassemeyer, Bieler, Dürrenberger, Trapp and Töpfer.)

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Röckel F et al.)

Armenia is an important country of origin of cultivated Vitis vinifera subsp. vinifera and wild Vitis vinifera subsp. sylvestris and has played a key role in the long history of grape cultivation in the Southern Caucasus. The existence of immense grapevine biodiversity in a small territory is strongly linked with unique relief and diverse climate conditions assembled with millennium-lasting cultural and historical context. In the present in-depth study using 25 nSSR markers, 492 samples collected in old vineyards, home gardens, and private collections were genotyped. For verification of cultivar identity, the symbiotic approach combining genotypic and phenotypic characterization for each genotype was carried out. The study provided 221 unique varieties, including 5 mutants, from which 66 were widely grown, neglected or minor autochthonous grapevine varieties, 49 turned out to be new bred cultivars created within the national breeding programs mainly during Soviet Era and 34 were non-Armenian varieties with different countries of origin. No references and corresponding genetic profiles existed for 67 genotypes. Parentage analysis was performed inferring 62 trios with 53 out of them having not been previously reported and 185 half-kinships. Instability of grapevine cultivars was detected, showing allelic variants, with three and in rare cases four alleles at one loci. Obtained results have great importance and revealed that Armenia conserved an extensive grape genetic diversity despite geographical isolation and low material exchange. This gene pool richness represents a huge reservoir of under-explored genetic diversity.

In the era of big and omics data, good organization, management, and description of experimental data are crucial for achieving high-quality datasets. This, in turn, is essential for the export of robust results, to publish reliable papers, make data more easily available, and unlock the huge potential of data reuse. Lately, more and more journals now require authors to share data and metadata according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This work aims to provide a step-by-step guideline for the FAIR data and metadata management specific to grapevine and wine science. In detail, the guidelines include recommendations for the organization of data and metadata regarding (i) meaningful information on experimental design and phenotyping, (ii) sample collection, (iii) sample preparation, (iv) chemotype analysis, (v) data analysis (vi) metabolite annotation, and (vii) basic ontologies. We hope that these guidelines will be helpful for the grapevine and wine metabolomics community and that it will benefit from the true potential of data usage in creating new knowledge being revealed.

Background: Grapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars 'Pinot Noir' (PN) and 'Pinot Noir Precoce' (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years., Results: The difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP., Conclusions: Many of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.

Grapevine ( Vitis vinifera ssp. vinifera ) is a major fruit crop with high economic importance. Due to its susceptibility towards fungal and oomycete pathogens such as Erysiphe necator and Plasmopara viticola, the causal agents of powdery and downy mildew (PM and DM, respectively), grapevine growers annually face a major challenge in coping with shortfalls of yield caused by these diseases. Here we report the confirmation of a genetic resource for grapevine resistance breeding against PM. During the delimitation process of Ren3 on chromosome 15 from the cultivar 'Regent', a second resistance-encoding region on chromosome 15 termed Ren9 was characterized. It mediates a trailing necrosis associated with the appressoria of E. necator and restricts pathogen growth. In this study, we confirm this QTL in a related mapping population of 'Regent' × 'Cabernet Sauvignon'. The data show that this locus is located at the upper arm of chromosome 15 between markers GF15-58 (0.15 Mb) and GF15-53 (4 Mb). The efficiency of the resistance against one of the prominent European PM isolates (EU-B) is demonstrated. Based on fine-mapping and literature knowledge we propose two possible regions of interest and supply molecular markers to follow both regions in marker-assisted selection.

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine ( Vitis vinifera ) early bud development. The expression of the developmental regulator VviAP1 served as an indicator of the progression of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The dataset also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker gene VviDRM1 .

Background: Grapevine trunk diseases (GTDs) such as Esca are among the most devastating threats to viticulture. Due to the lack of efficient preventive and curative treatments, Esca causes severe economic losses worldwide. Since symptoms do not develop consecutively, the true incidence of the disease in a vineyard is difficult to assess. Therefore, an annual monitoring is required. In this context, automatic detection of symptoms could be a great relief for winegrowers. Spectral sensors have proven to be successful in disease detection, allowing a non-destructive, objective, and fast data acquisition. The aim of this study is to evaluate the feasibility of the in-field detection of foliar Esca symptoms over three consecutive years using ground-based hyperspectral and airborne multispectral imaging., Results: Hyperspectral disease detection models have been successfully developed using either original field data or manually annotated data. In a next step, these models were applied on plant scale. While the model using annotated data performed better during development, the model using original data showed higher classification accuracies when applied in practical work. Moreover, the transferability of disease detection models to unknown data was tested. Although the visible and near-infrared (VNIR) range showed promising results, the transfer of such models is challenging. Initial results indicate that external symptoms could be detected pre-symptomatically, but this needs further evaluation. Furthermore, an application specific multispectral approach was simulated by identifying the most important wavelengths for the differentiation tasks, which was then compared to real multispectral data. Even though the ground-based multispectral disease detection was successful, airborne detection remains difficult., Conclusions: In this study, ground-based hyperspectral and airborne multispectral approaches for the detection of foliar Esca symptoms are presented. Both sensor systems seem to be suitable for the in-field detection of the disease, even though airborne data acquisition has to be further optimized. Our disease detection approaches could facilitate monitoring plant phenotypes in a vineyard., Competing Interests: Competing interestsThe authors declare that they do not have competing interests., (© The Author(s) 2020.)

Grapevine ( Vitis vinifera ) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. The unique and heritable mutation has been known for a long time but the underlying genetic mechanism still is not yet understood. Here we describe the association of the red-fleshed berry phenotype with a 408 bp repetitive DNA element in the promoter of the VvmybA1 gene (grapevine color enhancer, GCE). Three different clones of 'Teinturier' were discovered with two, three and five allelic GCE repeats ( MybA1t2 , MybA1t3 and MybA1t5 ). All three clones are periclinal chimeras; these clones share the same L1 layer, but have distinct L2 layers with different quantities of GCE repeats. Quantitative real time PCR and HPLC analysis of leaf and berry samples showed that the GCE repeat number strongly correlates with an increase of the expression of VvmybA1 itself and the VvUFGT gene regulated by it and the anthocyanin content. A model is proposed based on autoregulation of VvmybA1t to explain the red phenotype which is similar to that of red-fleshed apples. This study presents results about the generation and modes of action of three MybA1t alleles responsible for the red-fleshed berry phenotype of teinturier grapevines.

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' ( Vitis riparia GM183 × Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in 'Börner' were maternally inherited from Vitis riparia ., (Copyright © 2020 Frommer et al.)

Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera . In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14 , to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5., (Copyright © 2020 Holtgräwe, Rosleff Soerensen, Hausmann, Pucker, Viehöver, Töpfer and Weisshaar.)

Bunch rot caused by Botrytis cinerea infections is a notorious problem in grapevine cultivation. To produce high quality fruits, grapevine plants are treated with fungicides, which is cost intensive and harmful to the environment. Conversely, loose cluster bunches show a considerably enhanced physical resilience to bunch diseases. With the aim to identify genetic determinants that modulate the development of bunch architecture, we have compared loose and compact 'Pinot noir' clones. Loose cluster architecture was found to be correlated with increased berry size, elongated rachis and elongated pedicels. Using transcriptome analysis in combination with whole genome sequencing, we have identified a growth-regulating factor gene, VvGRF4, upregulated and harbours heterozygous mutations in the loose cluster clones. At late stages of inflorescence development, the mRNA pools of loose cluster clones contain predominantly mRNAs derived from the mutated alleles, which are resistant to miR396 degradation. Expression of the VvGRF4 gene and its mutated variants in Arabidopsis demonstrates that it promotes pedicel elongation. Taken together, VvGRF4 modulates bunch architecture in grapevine 'Pinot noir' clones. This trait can be introduced into other cultivars using marker-assisted breeding or CRISPR-Cas9 technology. Related growth-regulating factors or other genes of the same pathway may have similar functions., (© 2019 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms like A. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late flowering 'Villard Blanc' was analyzed for flowering time QTLs. In a second step we have now established a workflow combining amplicon sequencing and bioinformatics to follow alleles of selected candidate genes in the F1 individuals and the parental genotypes. Allele combinations of these genes in individuals of the mapping population were correlated with early or late flowering phenotypes. Specific allele combinations of flowering time candidate genes within and outside of the QTL regions for flowering time on chromosome 1, 4, 14, 17, and 18 were found to be associated with an early flowering phenotype. In addition, expression of many of the flowering candidate genes was analyzed over consecutive stages of bud and inflorescence development indicating functional roles of these genes in the flowering control network., Competing Interests: The authors have declared that no competing interests exist.

The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent-offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to 'Savagnin Blanc', providing evidence for 900 years of uninterrupted vegetative propagation.

Loose cluster architecture is an important aim in grapevine breeding since it has high impact on the phytosanitary status of grapes. This investigation analyzed the contributions of individual cluster sub-traits to the overall trait of cluster architecture. Six sub-traits showed large impact on cluster architecture as major determinants. They explained 57% of the OIV204 descriptor for cluster compactness rating in a highly diverse cross-population of 149 genotypes. Genetic analysis revealed several genomic regions involved in the expression of this trait. Based on the linkage of phenotypic features to molecular markers, QTL calculations shed new light on the genetic determinants of cluster architecture. Eight QTL clusters harbor overlapping confidence intervals of up to four co-located QTLs. A physical projection of the QTL clusters by confidence interval-flanking markers onto the PN40024 reference genome sequence revealed genes enriched in these regions.

Wine growers prefer cultivars with looser bunch architecture because of the decreased risk for bunch rot. As a consequence, grapevine breeders have to select seedlings and new cultivars with regard to appropriate bunch traits. Bunch architecture is a mosaic of different single traits which makes phenotyping labor-intensive and time-consuming. In the present study, a fast and high-precision phenotyping pipeline was developed. The optical sensor Artec Spider 3D scanner (Artec 3D, L-1466, Luxembourg) was used to generate dense 3D point clouds of grapevine bunches under lab conditions and an automated analysis software called 3D-Bunch-Tool was developed to extract different single 3D bunch traits, i.e., the number of berries, berry diameter, single berry volume, total volume of berries, convex hull volume of grapes, bunch width and bunch length. The method was validated on whole bunches of different grapevine cultivars and phenotypic variable breeding material. Reliable phenotypic data were obtained which show high significant correlations (up to r² = 0.95 for berry number) compared to ground truth data. Moreover, it was shown that the Artec Spider can be used directly in the field where achieved data show comparable precision with regard to the lab application. This non-invasive and non-contact field application facilitates the first high-precision phenotyping pipeline based on 3D bunch traits in large plant sets., Competing Interests: The authors declare no conflict of interests.

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.

In grapevine research the acquisition of phenotypic data is largely restricted to the field due to its perennial nature and size. The methodologies used to assess morphological traits and phenology are mainly limited to visual scoring. Some measurements for biotic and abiotic stress, as well as for quality assessments, are done by invasive measures. The new evolving sensor technologies provide the opportunity to perform non-destructive evaluations of phenotypic traits using different field phenotyping platforms. One of the biggest technical challenges for field phenotyping of grapevines are the varying light conditions and the background. In the present study the Phenoliner is presented, which represents a novel type of a robust field phenotyping platform. The vehicle is based on a grape harvester following the concept of a moveable tunnel. The tunnel it is equipped with different sensor systems (RGB and NIR camera system, hyperspectral camera, RTK-GPS, orientation sensor) and an artificial broadband light source. It is independent from external light conditions and in combination with artificial background, the Phenoliner enables standardised acquisition of high-quality, geo-referenced sensor data., Competing Interests: The authors declare no conflict of interest.

In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter., Competing Interests: The authors declare no conflict of interests.

Grapevines (Vitis vinifera L.) form the basis of viticulture, and are susceptible to diseases such as downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator). Therefore, successful viticulture programs require the use of pesticides. Breeding for resistance is the only eco-friendly solution. Marker-assisted selection is currently widely used for grapevine breeding. Consequently, traits of interest must be tagged with molecular markers linked to quantitative trait loci (QTL). We herein present our findings regarding genetic mapping and QTL analysis of resistance to downy and powdery mildew diseases in the progenies of the GF.GA-47-42 ('Bacchus' × 'Seyval') × 'Villard blanc' cross. Simple sequence repeats and single nucleotide polymorphisms of 151 individuals were analyzed. A map consisting of 543 loci was screened for QTL analyses based on phenotypic variations observed in plants grown in the field or under controlled conditions. A major QTL for downy mildew resistance was detected on chromosome 18. For powdery mildew resistance, a QTL was identified on chromosome 15. This QTL was replaced by a novel QTL on chromosome 18 in 2003 (abnormally high temperatures) and 2004. Subsequently, both QTLs functioned together. Additionally, variations in the timing of the onset of veraison, which is a crucial step during grape ripening, were studied to identify genomic regions affecting this trait. A major QTL was detected on linkage group 16, which was supplemented by a minor QTL on linkage group 18. This study provides useful information regarding novel QTL-linked markers relevant for the breeding of disease-resistant grapevines adapted to current climatic conditions.

Warm and moist weather conditions during berry ripening provoke Botrytis cinerea (B. cinerea) causing notable bunch rot on susceptible grapevines with the effect of reduced yield and wine quality. Resistance donors of genetic loci to increase B. cinerea resistance are widely unknown. Promising traits of resistance are represented by physical features like the thickness and permeability of the grape berry cuticle. Sensor-based phenotyping methods or genetic markers are rare for such traits. In the present study, the simple-to-handle I-sensor was developed. The sensor enables the fast and reliable measurement of electrical impedance of the grape berry cuticles and its epicuticular waxes (CW). Statistical experiments revealed highly significant correlations between relative impedance of CW and the resistance of grapevines to B. cinerea. Thus, the relative impedance Zrel of CW was identified as the most important phenotypic factor with regard to the prediction of grapevine resistance to B. cinerea. An ordinal logistic regression analysis revealed a R2McFadden of 0.37 and confirmed the application of Zrel of CW for the prediction of bunch infection and in this way as novel phenotyping trait. Applying the I-sensor, a preliminary QTL region was identified indicating that the novel phenotypic trait is as well a valuable tool for genetic analyses.

Background: The demand for high-throughput and objective phenotyping in plant research has been increasing during the last years due to large experimental sites. Sensor-based, non-invasive and automated processes are needed to overcome the phenotypic bottleneck, which limits data volumes on account of manual evaluations. A major challenge for sensor-based phenotyping in vineyards is the distinction between the grapevine in the foreground and the field in the background - this is especially the case for red-green-blue (RGB) images, where similar color distributions occur both in the foreground plant and in the field and background plants. However, RGB cameras are a suitable tool in the field because they provide high-resolution data at fast acquisition rates with robustness to outdoor illumination., Results: This study presents a method to segment the phenotypic classes 'leaf', 'stem', 'grape' and 'background' in RGB images that were taken with a standard consumer camera in vineyards. Background subtraction is achieved by taking two images of each plant for depth reconstruction. The color information is furthermore used to distinguish the leaves from stem and grapes in the foreground. The presented approach allows for objective computation of phenotypic traits like 3D leaf surface areas and fruit-to-leaf ratios. The method has been successfully applied to objective assessment of growth habits of new breeding lines. To this end, leaf areas of two breeding lines were monitored and compared with traditional cultivars. A statistical analysis of the method shows a significant (p <0.001) determination coefficient R (2)= 0.93 and root-mean-square error of 3.0%., Conclusions: The presented approach allows for non-invasive, fast and objective assessment of plant growth. The main contributions of this study are 1) the robust segmentation of RGB images taken from a standard consumer camera directly in the field, 2) in particular, the robust background subtraction via reconstruction of dense depth maps, and 3) phenotypic applications to monitoring of plant growth and computation of fruit-to-leaf ratios in 3D. This advance provides a promising tool for high-throughput, automated image acquisition, e.g., for field robots.

Due to its perennial nature and size, the acquisition of phenotypic data in grapevine research is almost exclusively restricted to the field and done by visual estimation. This kind of evaluation procedure is limited by time, cost and the subjectivity of records. As a consequence, objectivity, automation and more precision of phenotypic data evaluation are needed to increase the number of samples, manage grapevine repositories, enable genetic research of new phenotypic traits and, therefore, increase the efficiency in plant research. In the present study, an automated field phenotyping pipeline was setup and applied in a plot of genetic resources. The application of the PHENObot allows image acquisition from at least 250 individual grapevines per hour directly in the field without user interaction. Data management is handled by a database (IMAGEdata). The automatic image analysis tool BIVcolor (Berries in Vineyards-color) permitted the collection of precise phenotypic data of two important fruit traits, berry size and color, within a large set of plants. The application of the PHENObot represents an automated tool for high-throughput sampling of image data in the field. The automated analysis of these images facilitates the generation of objective and precise phenotypic data on a larger scale.