Hyperspectral imaging and cnn for on‐the‐go, non‐destructive assessment of grape composition in the vineyard

Vitis champinii cultivars Ramsey and Dog-ridge are main choices for rootstocks to adapt viticulture in semi-arid and arid regions thanks to their distinctive tolerance to drought and salinity. However, genetic studies on non-vinifera rootstocks have heavily relied on the grapevine (Vitis vinifera) reference genome, which difficulted the assessment of the genetic variation between rootstock species and grapevines. In the present study, this limitation is addressed by introducing a novo phased genome assembly and annotation of Vitis champinii. This new Vitis champinii genome was employed as reference for mapping RNA-seq reads from the same species under drought and salt stresses, and for comparison the same reads were also mapped to the Vitis vinifera PN40024.V4 reference genome. A significant increase in alignment rate was gained when mapping Vitis champinii RNA-seq reads to its own genome, compared to the Vitis vinifera PN40024.V4 reference genome, thus revealing the expression levels of genes specific to Vitis champinii. Moreover, differences in coding sequences were observed in ortholog genes between Vitis champinii and Vitis vinifera, which therefore challenges previous differential expression analyses performed between contrasting Vitis genotypes on the same gene from the Vitis vinifera genome. Genes with possible implications in drought and salt tolerance have been identified across the genome of Vitis champinii, and the same genomic data can potentially guide the discovery of candidate genes specific from Vitis champinii for other traits of interest, therefore becoming a valuable resource for rootstock breeding designs, specially towards increased drought and salinity due to climate change.

Soil is a reservoir of microorganisms playing important roles in biogeochemical cycles and interacting with plants whether in the rhizosphere or in the root endosphere. The composition of the microbial communities thus impacts the plant health. Rhizodeposits (such as sugar, organic and amino acids, secondary metabolites, dead root cells …) are released by the roots and influence the communities of rhizospheric microorganisms, acting as signaling compounds or carbon sources for microbes. The composition of root exudates varies depending on several factors including genotypes. As most of the cultivated grapevines worldwide are grafted plants, the aim of this study was to explore the influence of rootstock and scion genotypes on the microbial communities of the rhizosphere and the root endosphere. The work was conducted in the GreffAdapt plot (55 rootstocks x 5 scions), in which the 275 combinations have been planted into 3 blocks designed according to the soil resistivity. Samples of roots and rhizosphere of 10 scion x rootstock combinations were first collected in May among the blocks 2 and 3. The quantities of bacteria, fungi and archaea have been assessed in the rhizosphere by quantitative PCR, and by cultivable methods for bacteria and fungi. The communities of bacteria, fungi and arbuscular mycorrhizal fungi (AMF) was analyzed by Illumina sequencing of 16S rRNA gene, ITS and 28S rRNA gene, respectively. The level of mycorrhization was also evaluated using black ink coloration of newly formed roots harvested in October. The level of bacteria, fungi and archaea was dependent on rootstock and scion genotypes. A block effect was observed, suggesting that the soil characteristics strongly influenced the microorganisms from the rhizosphere and root endosphere. High-throughput sequencing of the different target genes showed different communities of bacteria, fungi and AMF associated with the scion x rootstock combinations. Finally, all the combinations were naturally mycorrhized. The root mycorrhization intensity was influenced by the rootstock genotype, but not by the scion one. Altogether, these results suggest that both rootstock and scion genotypes influence the rhizosphere and root endophytic microbiomes. It would be interesting to analyze the biochemical composition of the rhizodeposition of these genotypes for a better understanding of the processes involved in the modulation of these microbiomes. Moreover, crossing our data with the plant agronomic characteristics could provide insights into their roles on plant fitness.

The work shows the results of a year of experimentation (2020) in a Syrah variety vineyard in La Roda (Castilla-La Mancha, Spain). The trial approach was on a randomized block design with two factors: Irrigation (I) and Pruning (P).
Irrigation schedules were adjusted to apply amounts close to 1,500 m3/ha. With this provision, 2 different irrigation treatments were proposed: I1) Start of irrigation from pea-sized grape to post-harvest (providing at least 20 % of the total amount of irrigation water to be provided post-harvest); I2) Start of irrigation from pea-sized grape to harvest (usual irrigation practice in the study area). Pruning was proposed with two treatments, one at the end of January (P1), which is pruning on a conventional date; and P2) pruning carried out at the beginning of budding. In total, 4 repetitions were designed with 4 elementary plots, each one of them representing one of the proposed treatments (I1P1; I1P2; I2P1; I2P2). In total, 16 plots were worked on and each elementary plot consisted of 30 strains, distributed in 3 lines.
The productive response was evaluated with the yield results of the harvest harvested at 23 ºBrix. The qualitative response was measured in the musts through the indices of technological (acidity, pH and potassium) and phenolic maturity and aromatic compounds in free and glycosylated fractions. The treatments tested had, in general, an effect on the different variables analyzed.

Increasing temperatures worldwide are expected to cause a change in spatial distribution of plant species along elevational gradients and there are already observable shifts to higher elevations as a consequence of climate change for many species. Not only naturally growing plants, but also agricultural cultivations are subject to the effects of climate change, as the type of cultivation and the economic viability depends largely on the prevailing climatic conditions. A shift to higher elevations therefore represents a viable adaptation strategy to climate change, as higher elevations are characterized by lower temperatures. This is especially important in the case of viticulture because a certain wine-style can only be achieved under very specific climatic conditions. Although there are several studies investigating climatic suitability within winegrowing regions or longitudinal shifts of winegrowing areas, little is known about how fast vineyards move to higher elevations, which may represent a viable strategy for winegrowers to maintain growing conditions and thus wine-style, despite the effects of climate change. We therefore investigated the change in the spatial distribution of vineyards along an elevational gradient over the past 20 years in the mountainous wine-growing region of Alto Adige (Italy). A dataset containing information about location and planting year of more than 26000 vineyard parcels and 30 varieties was used to perform this analysis. Preliminary results suggest that there has been a shift to higher elevations for vineyards in general (from formerly 700m to currently 850 m a.s.l., with extreme sites reaching 1200 m a.s.l.), but also that this development has not been uniform across different varieties and products (i.e. vitis vinifera vs hybrid varieties and still vssparkling wines). This is important for climate change adaptation as well as for rural development. Mountain areas, especially at mid to high elevations, are often characterized by severe land abandonment which can be avoided to some degree if economically viable and sustainable land management strategies are available.

In Champagne, the vine adaptation to different climatic and technical changes during these last 20 years can be seen through physiological balance disruptions. These disruptions emphasize the general grapevine decline. Since the 2000s, among other nitrogen stress indicators, the must nitrogen has been decreasing. The combination of restricted mineral fertilizers and herbicide use, the growing variability of spring rainfall, the increasing thermal stress as well as the soil type heterogeneity are only a few underlying factors that trigger loss of physiological balance in the vineyards. It is important to weigh and quantify the impact of these factors on the vine. In order to do so, the Comité Champagne uses two key-tools: networking and modelization. The use of quantitative and harmonized ecophysiological indicators is necessary, especially in large spatial scales such as the Champagne appellation. A working group with different professional structures of Champagne has been launched by the Comité Champagne in order to create a common ecophysiology protocol and thus monitor the vine physiology, yearly, around 100 plots, with various cultural practices and types of soil. The use of crop modelling to follow the vine physiological balance within different pedoclimatic conditions enables to understand the present balance but also predict the possible disruptions to come in future climatic scenarios. The physiological references created each year through the working group, benefit the calibration of the STICS model used in Champagne. In return, the model delivers ecophysiology indicators, on a daily scale and can be used on very different types of soils. This study will present the bottom-up method used to give accurate information on the impacts of soil, climate and cultural practices on vine physiology.