Several crops have been studied in this evolutionary context , but there are at least two emerging issues. The first is the speed at which domestication occurs. One view, supported primarily by archaeological evidence, is that domestication is a slow process that takes millennia . Another view, based on genetic evidence and population modeling , argues that domestication occurs much more rapidly. The gap between these two views has been bridged, in part, by a recent study of African rice. The study used population genomic data to infer that a bottleneck occurred during domestication ∼3.5 kya and also that the bottleneck was preceded by a long, ∼14,000-y decline in the effective population size of the progenitor population . The authors hypothesized that the protracted Ne decline reflects a period of low-intensity management and/or cultivation before modern domestication. While an intriguing hypothesis, it is not yet clear whether other crops also have demographic histories marked by protracted Ne declines. The second emerging issue is the “cost of domestication” , which refers to an increased genetic load within cultivars. This cost originates partly from the fact that the decreased Ne during a domestication bottleneck reduces the efficacy of genome-wide selection , which may in turn increase the frequency and number of slightly deleterious variants . The characterization of deleterious variants is important because they may be fitting targets for crop improvement . Consistent with a cost of domestication, black plastic planting pots annual crops are known to contain an increase in derived, putatively deleterious variants relative to their wild progenitors . However, it is not yet clear whether these deleterious variants increase genetic load and whether this phenomenon applies to perennial crops. The distinction between annual and perennial crops is crucial because perennial domestication is expected to differ from annual domestication in at least three aspects .
The first is clonal propagation; many perennials are propagated clonally but most annuals are not. Clonal propagation maintains genetic diversity in desirous combinations but also limits opportunities for sexual recombination . The second aspect is time. As a result, the number of sexual generations is much reduced for perennials relative to annual crops, even for perennials that were domesticated relatively early in human agricultural history. The third aspect is the severity of the domestication bottleneck. A meta-analysis has documented that perennial crops retain 95% of neutral variation from their progenitors, on average, while annuals retain an average of 60% . This observation suggests that many perennial crops have not experienced severe domestication bottlenecks; as a consequence, their domestication may not come with a cost. Here we study the domestication history of the grapevine , which is the most economically important horticultural crop in the world . Grapes have been a source of food and wine since their hypothesized domestication ∼8.0 kya from their wild progenitor, V. vinifera ssp. sylvestris . The exact location of domestication remains uncertain, but most lines of evidence point to a primary domestication event in the Near East . Domestication caused morphological shifts that include larger berry and bunch sizes, higher sugar content, altered seed morphology, and a shift from dioecy to a hermaphroditic mating system . There is interest in identifying the genes that contribute to these morphological shifts. For example, several papers have attempted to identify the gene that are responsible for the shift to hermaphroditism, which were mapped to an ∼150-kb region on chromosome 2 . Historically, genetic diversity among V. vinifera varieties has been studied with simple sequence repeats . More recently, a group genotyped 950 vinifera and 59 sylvestris accessions with a chip containing 9,000 SNPs .
Their data suggest that grape domestication led to a mild reduction of genetic diversity, indicating that grape is a reasonable perennial model for studying the accumulation of deleterious variation in the absence of a pronounced bottleneck. Still more recent studies have used whole genome sequencing to assess structural variation among grape varieties . Surprisingly, however, WGS data have not been used to investigate the population genomics of grapes. Here we perform WGS on a sample of vinifera cultivars and on putatively wild sylvestris accessions to focus on three sets of questions. First, what do the data reveal about the demographic history of cultivated grapes, specifically, the timing and severity of a domestication bottleneck? Second, what genes bear the signature of selection in vinifera, and do they provide insights into the agronomic shifts associated with domestication? Finally, do domesticated grapes have more derived, putatively deleterious variants relative to sylvestris, or have the unique features of perennial domestication permitted an escape from this potential cost?There is natural spatial variability present in vineyards due to the variations in soil characteristics and topography . Soil characteristics are too complex to be thoroughly surveyed effortlessly. With traditional destructive methods, it is difficult to obtain enough comprehensive information from the soil pits at the field scale. These soil characteristics may directly affect the water availability for grapevines, which eventually determine the physiological performance of the plants . However, there is no variable management practices currently available to accommodate the natural spatial variability. Thus, the spatial variability derived from vineyard soils will inevitably be expressed in the whole plant physiology at the cost of homogeneity of vineyard productivity and quality. We previously reported the spatial variation of midday stem water potential affecting grapevine carbon assimilation and stomatal conductance of grapevine . The resultant variations in whole plant physiology were associated to flavonoid composition and concentration at the farm gate. However, there is a lack of information about the effects on the chemical composition in the final wine, which would ultimately determine wine quality as perceived by consumers.
Georeferenced proximal sensing tools can capture the spatial and temporal variability in vineyards, making it possible to supervise and manage variations at the field scale . Previous studies showed that soil bulk electrical conductivity may be used to evaluate many soil attributes, including soil moisture content, salinity, and texture . Soil electromagnetic induction sensing has been used in precision agriculture to acquire soil bulk EC at the field scale due to its non-invasive and prompt attributes . Although research had been conducted on the relationships between soil electrical properties with plant water status, they were mostly point measurements and the results were rarely interpolated to whole fields. There were only a few studies that investigated the EMI sensing and soil-plant water relationships over a vineyard . Previous research suggested that the connection between soil water content and soil bulk EC could have relied on specific soil profiles, and needed to include soil physical and chemical properties to complete this connection . Nevertheless, there is evidence that soil bulk EC may still be useful not only to identify the variability in soil, but also in the plant response affected by vineyard soils such as yield, plant physiology, and grape berry chemistry . Plant available water is a determinant factor on grapevine physiology, black plastic pots for plants together with nitrogen availability in semi-arid regions . Wine grapes are usually grown under a moderate degree of water deficits as yields were optimized at 80% of crop evapotranspiration demand with sustained deficit irrigation . Water deficits would limit leaf stomatal conductance and carbon assimilation rate that sustain grapevines’ vegetative and reproductive growth and development . When grapevines are under water deficits, carbohydrates repartitioned into the smaller berries would enhance berry soluble solids content . Sucrose and fructose, which are the major components of total soluble solids in grape berry, can act as a signaling factor to stimulate anthocyanin accumulation . The effects on grapevine physiology and berry composition also depend on the phenological stages they occur and how severe and prolonged the water deficits are . Flavonoids are the most critical compounds dictating many qualitative traits in both grape berries and wine . The variations in environmental factors could alter the concentration and biosynthesis of flavonoids and can be extrapolated spatially within the same vineyard, including water deficits , solar radiation , and air temperature . Among flavonoid compounds, anthocyanins are responsible for the color of berry skin as well as wine . Moderate water deficits during growing season can increase anthocyanin concentration in berry skin and wine . However, water deficits can impair plant temperature regulation through evaporative cooling . They may also inhibit berry growth by limiting berry size and altering berry skin weight . Thus, in some cases it may be uncertain if water deficit promotes anthocyanins biosynthesis or reduces berry growth, or contributes to anthocyanin degradation . Applying water deficit on grapevines can contribute to greater proportion in tri-hydroxylated over dihydroxylated anthocyanins due to the up-regulation of F30 5 0 H . Another major class in flavonoids, proanthocyanidins, are polymers of flavan-3-ol monomers and they contributes mainly toward astringency or bitterness in wine . Compared to anthocyanins, water deficits showed mild effects on proanthocyanidins . However, water deficits with great severity can still alter the concentration and composition of proanthocyanidins in both berries and wine .
Selective harvest is one of the targeted management strategies to minimize the spatial variation in berry chemistry in vineyards . By differentially harvesting or segregating the fruits into batches prior to vinification, the berry composition can be artificially set at a more uniform stage with minimal variations . In our previous work, we reported the use of plant water status to determine the spatial variation of grape berry flavonoids . The goal of this study was to deduce if the spatial variability of soil bulk EC and differences in soil texture can be related to plant physiology and grape and wine composition. The specific objective of the study was to determine if the spatial variability of proximally sensed vineyard soil bulk EC would affect plant water status, and if this relation would affect leaf gas exchange, components of yield, berry composition, and flavonoids in both berries and wine. The study was conducted in a commercial vineyard in 2016 and 2017 with Cabernet Sauvignon grapevines grafted on 110R located in Healdsburg, CA, United States. In this vineyard, grapevines were planted at 1.83 m × 3.35 m . The grapevines were trained to a high quadrilateral, horizontally split trellis with two bilateral cordons. They were spur pruned with two buds per spur, and seven spurs per meter of the cordon. Irrigation was applied uniformly with a drip irrigation system, starting at fruitset to the end of veraison at 50% ETc . There were two emitters per grapevine, delivering 3.8 L·h −1 of water. Weather data was obtained from the California Irrigation Management Information System station to measure precipitation, air temperature, and reference evapotranspiration .An equidistant 33 m × 33 m grid with 35 experimental units was used for on-site measurements and berry samplings. Each experimental unit consisted of five plants. The locations of each central plant in these five plant experimental units were registered as the grid nodes with a GPS , wirelessly connected to a Trimble Pro 6T DGNSS receiver .Soil bulk EC was assessed with EM38 in 2016 when the vineyard soil was at field capacity condition. Both vertical dipole mode and horizontal dipole mode were used to assess EC at two depths, including deep soil and shallow soil . The instrument was calibrated according to manufacturer instructions. The device was placed on a PVC sled and driven through the vineyard with an allterrain vehicle along the inter-rows. A distance of approximately 0.5 m from the vehicle to the device was maintained to avoid interference with the vehicle. A stratified grid was used to collect soil samples corresponding to the two depths at which we measured soil bulk EC. Soil texture was assessed according to the soil analysis method: hydrometer analysis in the North American Proficiency Testing program. Geostatistical analysis was performed in the R language by using package “gstat” 1.1-6 . The bulk EC data were filtered by Tukey’s rule to remove outliers either below the first quartile by 1.5 inter-quartile range or above the third quartile by 1.5 inter-quartile range. To further remove the outliers, the data were filtered by the speed that the vehicle was driving, which was between 3.2 km per hour to 8.0 km per hour. Variograms were assessed by “automap” package 1.0-14 , and fitted to perform kriging.