In viticulture, yield estimation is a key activity, which is important throughout the wine industry value chain. The earlier that an accurate yield estimation can be made the greater its value, increasing management options for grape growers and commercial options for winemakers. For the yield estimate based on in- field measurements at scale, the number of inflorescences emerging after bud-burst offers the earliest practical signal, allowing a yield potential to be determined months before harvest. This paper presents an approach to automatically count the inflorescence number at the phenological stage E-L 12 using RGB video data and demonstrates its use for estimating yield. A dataset consisting of RGB videos was collected shortly after bud-burst from multiple vineyards, in conjunction with hand counts to produce a manual ground-truth for the inflorescence counting task. The video frames were annotated using bounding-boxes around the inflorescences to produce a digital ground-truth. A deep learning architecture was developed to learn features from the video frames during training and detect the inflorescences at the later inference stage. The detection results were fed to a tracking pipeline built using computer vision and deep learning techniques to generate numbers of inflorescences present in test videos. The visual and quantitative results are presented and evaluated for the inflorescence detection and counting tasks. The developed inflorescence detector achieves an average precision of 80.00%, a recall of 83.92%, and an F1-score of 80.48%, through a five-fold cross-validation on the annotated dataset. For the test videos, the developed automatic inflorescence counting model reports an absolute error of 11.03 inflorescences per panel, a normalized mean absolute error of 10.80%, and an R(2 )of 0.86, when the predicted per-panel counts were compared to the corresponding manual ground-truth. Based on the counting results, we estimate an early yield that is within 4% to 11% error when compared to the actual yield after harvest. Based on these results and a separate analysis of the relationship between hand counts of inflorescences and harvest yields in three vineyards over three growing seasons, we conclude that computer vision and machine learning based methods have the potential to provide early yield estimation in viticulture with a commercially viable accuracy.

This review highlights the contributions of CSIRO to the development of new scions and rootstocks for the Australian winegrape, driedgrape and tablegrape industries. Initially, CSIRO played a pivotal role in the selection of high-yielding Sultana clones which contributed over half the total Australian grape crop in the 1970s used for wine- and driedgrape production. It was also responsible for importation and evaluation of the Salt Creek (syn. Ramsey) rootstock which provided tolerance to root-knot nematodes and salinity and became the most widely adopted rootstock for the emerging Australian wine industry in the 1980–1990s. The CSIRO has also successfully bred or released several new grape cultivars. While the adoption rate for the CSIRO wine cultivars has been limited, CSIRO-selected cultivars dominate the Australian driedgrape industry, while CSIRO-released cultivars continue to play an important role in the Australian tablegrape industry. In the 1990s, CSIRO commenced the application of molecular biology techniques for grapevine germplasm improvement. Researchers from CSIRO were some of the first in the world to successfully regenerate transgenic grapevines and demonstrate the potential of this technology to produce low-browning driedgrapes and mildew-resistant premium winegrapes. More recently, the focus has shifted to the mapping of resistance loci from wild grape species and their introgression into new winegrape scions to provide resistance to mildews and new rootstocks to provide durable resistance to rootknot nematodes and phylloxera. Finally, this review considers some future challenges faced by the Australian grape industries and how these might be addressed using conventional or molecular breeding strategies.

Plant genetic sex determinants that mediate the transition to dioecy are predicted to be diverse, as this type of mating system independently evolved multiple times in angiosperms. Wild Vitis species are dioecious with individuals producing morphologically distinct female or male flowers; whereas, modern domesticated Vitis vinifera cultivars form hermaphrodite flowers capable of self-pollination. Here, we identify the VviPLATZ1 transcription factor as a key candidate female flower morphology factor that localizes to the Vitis SEX-DETERMINING REGION. The expression pattern of this gene correlates with the formation reflex stamens, a prominent morphological phenotype of female flowers. After generating CRISPR/Cas9 gene-edited alleles in a hermaphrodite genotype, phenotype analysis shows that individual homozygous lines produce flowers with reflex stamens. Taken together, our results demonstrate that loss of VviPLATZ1 function is a major factor that controls female flower morphology in Vitis.

Evaluating new grape cultivars for their performance is crucial to determine their suitability for a region, but assessing wines made from grapes from these cultivars is equally important to validate market potential. Breeding grapevine cultivars with disease resistance is a high priority, particularly resistance to the two major diseases, downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator syn. Uncinula necator). Downy mildew requires high humidity and rainfall to germinate and grow, whereas powdery mildew develops under a wide range of climatic conditions. The drivers for breeding disease-resistant winegrape cultivars include lowering the cost of production by reducing spray applications and thus the need for labour, chemicals and fuel, improving the microbial activity of the soil in the vineyard by reducing the compaction caused by tractor usage, and to provide a healthier environment around vineyards. From the first generation crosses made by CSIRO, a total of 20 white and 20 red cultivars exhibiting promising viticultural and winemaking characteristics have been selected. These selections have been planted in diverse grape growing regions around Australia and are under evaluation. NSW DPI evaluates these selections in the Orange and Riverina regions in New South Wales (south-eastern Australia) for productivity, grape composition and wine attributes. The most comprehensive results from the white selections growing in the Riverina region showed considerable differences in yield, yield parameters and must composition. Experimental wines made from these selections showed not only a considerable range in the overall scores, but also differences in aromas and attributes. In the future these cultivars will allow reduced production costs of wines exhibiting style characteristics similar to current major cultivars.

The majority of grapevine cultivars used for wine, table grape and dried-fruit production are derived from the Eurasian grape species Vitis vinifera because of its superior aroma and flavour characteristics. However, this species has little or no genetic resistance against the major pests and pathogens that attack above-ground parts of the grapevine including the trunk, canopy and bunches. As a result, grape production is highly dependent on the frequent use of fungicides and pesticides, which has significant implications for the economic and environmental sustainability of grape production. This chapter will summarize our current knowledge of the different resistance loci/genes that have been identified in wild grapevine species that could potentially be used to develop new grapevine cultivars with enhanced genetic resistance by marker-assisted selection.

Context of the review: The manipulation of the genetic basis controlling grapevine adaptation and phenotypic plasticity can be performed either by classical genetics or biotechnologies. In the last 15 years, considerable knowledge has accumulated about the grapevine genome as well as the mechanisms involved in the interaction of the vine with the environment, pests and diseases. Despite the difficulties associated with genetic mapping in this species (allele diversity, chimerism, long generation intervals...), several major controlling important vegetative or reproductive traits have been identified. Considering the huge genotypic and phenotypic diversities existing in Vitis, breeding offers a substantial range of options to improve the performances of cultivars. However, even if marker-assisted selection was largely developed to shorten breeding programs, the selection of improved cultivars, whether for agronomic traits or disease tolerances, is still long and uncertain. Moreover, breeding by crossing does not preserve cultivar genetic background, when the wine industry and market are still based on varietal wines. Significance of the review: In grapevine, pioneering biotechnologies were set up in the 1960s to propagate and/or clean the material from micro-organisms. In the 1990s, the basis of genetic engineering was primary established through biolistic or Agrobacterium with several derived technologies refined in the last 10 years. The latest advance is represented by a group of technologies based on genome editing which allows a much more precise modification of the genome. These technologies, so-called NBTs (new breeding technologies), which theoretically do not deconstruct the phenotype of existing cultivars, could be potentially better accepted by the wine industry and consumers than previous GMO (genetically modified organism) approaches. This paper reviews the current state-of-the-art of the biotechnologies available for grapevine genome manipulation and future prospects for genetic improvement.

Background Grape phylloxera ( Daktulosphaira vitifoliae Fitch) is a major insect pest that negatively impacts commercial grapevine performance worldwide. Consequently, the use of phylloxera resistant rootstocks is an essential component of vineyard management. However, the majority of commercially available rootstocks used in viticulture production provide limited levels of grape phylloxera resistance, in part due to the adaptation of phylloxera biotypes to different Vitis species. Therefore, there is pressing need to develop new rootstocks better adapted to specific grape growing regions with complete resistance to grape phylloxera biotypes. Results Grapevine rootstock breeding material, including an accession of Vitis cinerea and V. aestivalis , DRX55 ([ M. rotundifolia x V. vinifera ] x open pollinated) and MS27-31 ( M. rotundifolia specific hybrid), provided complete resistance to grape phylloxera in potted plant assays. To map the genetic factor(s) of grape phylloxera resistance, a F 1 V. cinerea x V. vinifera Riesling population was screened for resistance. Heritability analysis indicates that the V. cinerea accession contained a single allele referred as RESISTANCE TO DAKTULOSPHAIRA VITIFOLIAE 2 ( RDV2 ) that confers grape phylloxera resistance. Using genetic maps constructed with pseudo-testcross markers for V. cinerea and Riesling, a single phylloxera resistance locus was identified in V. cinerea . After validating SNPs at the RDV2 locus, interval and linkage mapping showed that grape phylloxera resistance mapped to linkage group 14 at position 16.7 cM. Conclusion The mapping of RDV2 and the validation of markers linked to grape phylloxera resistance provides the basis to breed new rootstocks via marker-assisted selection that improve vineyard performance.

Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soil pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed new root knot nematode resistant rootstocks, which have no impact on wine quality. To develop molecular markers that predict root knot nematode resistance for marker assisted breeding, a genetic approach was employed to identify a root knot nematode resistance locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis cinerea accession was crossed to a susceptible Vitis vinifera cultivar Riesling and results from screening the F1 individuals support a model that root knot nematode resistance, is conferred by a single dominant allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1 resistance appears to be mediated by a hypersensitive response that occurs in the root apical meristem. Single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing and results from association and genetic mapping identified the MJR1 locus, which is located on chromosome 18 in the Vitis cinerea accession. Validation of the SNPs linked to the MJR1 locus using a Sequenom MassARRAY platform found that only 50% could be validated. The validated SNPs that flank and co-segregate with the MJR1 locus can be used for marker-assisted selection for Meloidogyne javanica resistance in grapevine.

This paper introduces GRover (the grapevine rover), an adaptable mobile platform for the deployment and testing of proximal imaging sensors in vineyards for the non-destructive assessment of trunk and cordon volume and pruning weight. A SICK LMS-400 light detection and ranging (LiDAR) radar mounted on GRover was capable of producing precise (±3 mm) 3D point clouds of vine rows. Vineyard scans of the grapevine variety Shiraz grown under different management systems at two separate locations have demonstrated that GRover is able to successfully reproduce a variety of vine structures. Correlations of pruning weight and vine wood (trunk and cordon) volume with LiDAR scans have resulted in high coefficients of determination (R2 = 0.91 for pruning weight; 0.76 for wood volume). This is the first time that a LiDAR of this type has been extensively tested in vineyards. Its high scanning rate, eye safe laser and ability to distinguish tissue types make it an appealing option for further development to offer breeders, and potentially growers, quantified measurements of traits that otherwise would be difficult to determine.

Background and Aims Root-knot nematodes (Meloidogyne spp.) are endo-parasites of plant roots and parasitisation can lead to diminished grape yields. Worldwide viticulture production is impacted primarily by four species of root-knot nematode (Meloidogyne arenaria, Meloidogyne hapla, Meloidogyne incognita and Meloidogyne javanica). Meloidogyne javanica is the predominant root-knot nematode found in Australian vineyards. A glasshouse-based experiment was conducted to identify grapevine cultivars and accessions with complete resistance (i.e. no reproduction of nematode) to an aggressive pathotype of M. javanica isolated from an Australian vineyard. Methods and Results Single-grapevine plants were inoculated with approximately 1500 second stage juveniles of M. javanica in a replicated study. Six weeks after inoculation, roots were washed free of soil, and egg masses were stained and tallied. The final dry mass of roots was measured to determine the ratio of egg masses to root mass. Conclusions Complete resistance to M. javanica was found in 42 of 75 Vitis cultivars and accessions screened. Significance of Study The M. javanica resistant cultivars and accessions identified in this study provide valuable material for future breeding in order to develop new rootstocks for the Australian wine and grape industry with durable resistance to root-knot nematode.

Background and AimsThe chemical composition of grape berries during development exhibits large variation within a single bunch. To monitor the change in the concentration of tartaric acid and malic acid between individual berries, a high-throughput method using UHPLC-MS/MS was developed to quantify these acids in berry extracts.Methods and ResultsThe results from analysis of single-vine datasets indicated that there was a large variation in the concentration of tartaric acid and malic acid between individual berries and also between bunches of berries across a vine. From these data, an optimum sampling size of 30 berries per vine was determined, which has an estimated standard error under 10% of the expected average berry acid concentration.ConclusionsA high-throughput UHPLC-MS/MS method using the stable isotope dilution analysis has been developed to quantify tartaric acid and malic acid in individual berry extracts and extracts prepared from samples of multiple berries.Significance of the StudyThis method enabled the study of variation in acid concentration and content between individual berries. This makes it possible to quantify the variation in the acids at several levels (berries, bunches and plants) and to recommend ideal sampling sizes for data collection in vineyards.

Grapevine (Vitis) is considered to be one of the major fruit crops in the world based on hectares cultivated and economic value. Grapes are used not only for wine but also for fresh fruit, dried fruit, and juice production. Wine is by far the major product of grapes, and the focus of this chapter is on wine grape cultivars. Grapevine cultivars of Vitis vinifera L. have a reputation for producing premium quality wines. These premium quality wines are produced from a small number of cultivars that enjoy a high level of consumer acceptance and are firmly entrenched in the market place because of varietal name branding and the association of certain wine styles and regions with specific cultivars. In light of this situation, grapevine improvement by a transgenic approach is attractive when compared to a classical breeding approach. The transfer of individual traits as single genes with a minimum disruption to the original genome would leave the traditional characteristics of the cultivar intact. However, a reliable transformation system is required for a successful transgenic approach to grapevine improvement. There are three criteria for achieving an efficient Agrobacterium-mediated transformation system: (1) the production of highly regenerative transformable tissue, (2) optimal cocultivation conditions for both grapevine tissue and Agrobacterium, and (3) an efficient selection regime for transgenic plant regeneration. In this chapter, we describe a grapevine transformation system that meets these criteria. We also describe a protocol for the production of transformed roots suitable for functional gene studies and for the production of semi-transgenic grafted plants.

Background We consider data from a time course microarray experiment that was conducted on grapevines over the development cycle of the grape berries at two different vineyards in South Australia. Although the underlying biological process of berry development is the same at both vineyards, there are differences in the timing of the development due to local conditions. We aim to align the data from the two vineyards to enable an integrated analysis of the gene expression and use the alignment of the expression profiles to classify likely developmental function. Results We present a novel alignment method based on hidden Markov models (HMMs) and use the method to align the motivating grapevine data. We show that our alignment method is robust against subsets of profiles that are not suitable for alignment, investigate alignment diagnostics under the model and demonstrate the classification of developmentally driven genes. Conclusions The classification of developmentally driven genes both validates that the alignment we obtain is meaningful and also gives new evidence that can be used to identify the role of genes with unknown function. Using our alignment methodology, we find at least 1279 grapevine probe sets with no current annotated function that are likely to be controlled in a developmental manner.

Soils in some major Australian viticultural regions are generally high in potassium content, which is in contrast to viticultural regions in other parts of the world. There is a considerable body of evidence, both from commercial experiences and research results, that the widely adopted high vigour, root-knot nematode tolerant rootstock varieties contribute to negative impacts on wine quality associated with high potassium uptake, high pH and malate levels. Previous findings have shown that in a given year, grafted vine grape juice pH at harvest is highly correlated with the ungrafted rootstock petiole potassium level at anthesis. We demonstrated that this relationship is also present when multiple years of juice pH and ungrafted rootstocks petioles are compared. The mean harvest pH of ?Chardonnay? grafted on 6 commer¬cial rootstocks from 4 vineyards over two consecutive years had a strong correlation (adjusted R2= 0.755) with the 2 year mean potassium content of the ungrafted rootstocks in the field. Likewise, the 8 year mean pH of a rootstock trial with 5 commercial rootstock and 14 experimental rootstocks with ?Shiraz? scions was highly correlated (adjusted R2= 0.502) with the 2 year mean petiole potassium content of the ungrafted field grown rootstocks. To facilitate accelerated breeding of new rootstocks, we have developed a glasshouse based assay for the early selection of rootstocks with low potassium transport to aerial tissues. We demonstrated that the 8 year mean juice pH of grafted vines is also correlated with the ungrafted vine petiole potassium content for plants grown in the glasshouse with supplemented levels of potassium (adjusted R2= 0.501). In addition, we are also screening vines in the glasshouse for resistance to the root-knot nematode Meloidogyne javanica. We are currently screening potential and commercial germplasm for resistance to M. javanica, and have identified a Vitis cinerea accession that transmits resistance as a single dominant gene.

The FLESHLESS BERRY (Flb) somatic variant identified in the grapevine cultivar Ugni Blanc develops grape berries without flesh, suggesting a role for the altered gene in differentiation of flesh cells. Here we describe identification of the molecular defect responsible for this phenotype. Using a combination of genetic and transcriptomic approaches, we detected the insertion of a miniature inverted-repeat transposable element in the promoter region of the PISTILLATA-like (VvPI) gene, the grapevine homologue of Arabidopsis PISTILLATA. The transposon insertion causes specific ectopic expression of the corresponding VvPI allele during early fruit development, causing expression of genes specific for petal and stamen development within the fruit. A causal relationship between the insertion and the phenotype was demonstrated by phenotypic and molecular analyses of somatic revertants showing that ectopic expression and mutant phenotype were always linked to the presence of the transposon insertion. The various phenotypic effects of the flb mutation on ovary morphology, fruit set and fruit development, depending on the cell lineage affected, are presented for each phenotype, offering new insights into floral and fleshly fruit development. The results highlight the importance of VvPI repression after fertilization to achieve normal fleshy fruit development, and the complex genetic, genomic and cellular interactions required for the flower to fruit transition in grapevine.

The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR-NB-LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated resistance to Uncinula necator (MrRUN1) and resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south-eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1-mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR-NB-LRR genes at this locus share a common ancestor.

Anthropogenically induced change in soil redistribution plays an important role in the soil organic carbon (SOC) budget. Uncertainty of its impact is large because of the dearth of recent soil redistribution estimates concomitant with changing land use and management practices. An Australian national survey used the artificial radionuclide caesium‐137 (137Cs) to estimate net (1950s–1990) soil redistribution. South‐eastern Australia showed a median net soil loss of 9.7 t ha−1 yr−1. We resurveyed the region using the same 137Cs technique and found a median net (1990–2010) soil gain of 3.9 t ha−1 yr−1 with an interquartile range from −1.6 t ha−1 yr−1 to +10.7 t ha−1 yr−1. Despite this variation, soil erosion across the region has declined as a likely consequence of the widespread adoption of soil conservation measures over the last ca 30 years. The implication of omitted soil redistribution dynamics in SOC accounting is to increase uncertainty and diminish its accuracy.

BACKGROUND:Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification.RESULTS:We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification.CONCLUSIONS:We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable.

The Eurasian winegrape Vitis vinifera has little or no genetic resistance to the major fungal pathogens, powdery mildew (Erysiphe necator) and downy mildew (Plasmopora viticola). These pathogens were first introduced into French vineyards from North America in the 1800s before spreading to all major grape producing regions of the world. As a result, grape production is highly dependent on the use of fungicides. With the increasing financial and environmental costs of chemical application and the emergence of fungicide-resistant strains, the introduction of natural genetic resistance against these fungal pathogens is a high priority for viticultural industries worldwide. We are utilising a number of different molecular approaches to increase our understanding of the basis of resistance to these important major fungal pathogens and to identify potential new sources of genetic resistance. This review will outline the progress and the potential of each of these different molecular strategies to the generation of fungal-resistant grapevine germplasm.