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To allow for a broad survey of subtle metabolic shifts in wine caused by rootstock and irrigation, an integrated metabolomics-based workflow followed by quantitation was developed. This workflow was particularly useful when applied to a poorly studied variety cv. Chambourcin. Allowing volatile metabolites that otherwise may have been missed with a targeted analysis to be included, this approach allowed deeper modeling of treatment differences which then could be used to identify important compounds. Wines produced on a per vine basis, over two years, were analyzed using SPME-GC-MS/MS. From the 382 and 221 features that differed significantly among rootstocks in 2017 and 2018 respectively, we tentatively identified 94 compounds by library search and retention index, with 22 confirmed and quantified using authentic standards. Own-rooted Chambourcin differed from other root-systems for multiple volatile compounds with fewer dif-ferences among grafted vines. For example, the average concentration of β-Damascenone present in own-rooted vines (9.49 µg/L) was significantly lower in other rootstocks (8.59 µg/L), whereas mean Linalool was significantly higher in 1103P rootstock compared to own-rooted. β-Damascenone was higher in regulated deficit irrigation (RDI) than other treatments. The workflow outlined not only was shown to be useful for scientific investigation, but also in creating a protocol for analysis that would ensure differences of interest to industry are not missed.

SummaryIn many perennial crops, grafting the root system of one individual to the shoot system of another individual has become an integral part of propagation performed at industrial scales to enhance pest, disease, and stress tolerance and to regulate yield and vigor. Grafted plants offer important experimental systems for understanding the extent and seasonality of root system effects on shoot system biology.Using an experimental vineyard where a common scion ‘Chambourcin’ is growing ungrafted and grafted to three different rootstocks, we explore associations between root system genotype and leaf phenotypes in grafted grapevines across a growing season. We quantified five high-dimensional leaf phenotyping modalities: ionomics, metabolomics, transcriptomics, morphometrics, and physiology and show that rootstock influence is subtle but ubiquitous across modalities.We find strong signatures of rootstock influence on the leaf ionome, with unique signatures detected at each phenological stage. Moreover, all phenotypes and patterns of phenotypic covariation were highly dynamic across the season.These findings expand upon previously identified patterns to suggest that the influence of root system on shoot system phenotypes is complex and broad understanding necessitates volumes of high-dimensional, multi-scale data previously unmet.

Grapevine (Vitis spp.) contains a wealth of phytochemicals that have received considerable attention due to health-promoting properties and biological activities as phytoalexins. To date, the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited. Here, metabolic quantitative trait locus (mQTL) mapping was conducted using grapevine stems of a segregating F2 population. Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry (LC-HRMS), resulting in the detection of 1317 ions/features. In total, 19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software, resulting in the identification of four mQTLs. Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18, accounting for phenotypic variances of 29.0% and 38.4%. Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18. This 2.8-Mbp region contains 48 genes with R-gene motifs, including variants of TIR, NBS, and LRR, that might potentially confer resistance to powdery mildew, downy mildew, or other pathogens. The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites, including phytoalexins. In addition, haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.