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Background Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown. Results Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season. Conclusions These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.

With increases in climate extremes resulting in more abiotic and biotic stress on crops such as grapes, it is essential to develop new cultivars that are more robust than the traditional Vitis vinifera but, with the flavor attributes consumers' desire. The interspecific hybrid cultivars developed from crossing V. vinifera with the wild Vitis species do possess cold hardiness and disease resistance, however, the aroma profile of these hybrids are generally less popular in comparison to the V. vinifera grapes. Developing an understanding of the aroma profile of the hybrid grapes is essential to understand how they differ from vinifera cultivars and how viticultural management practices impact their aroma composition. While earlier efforts have been made to determine the volatile profile of hybrid grapes and wines using targeted analysis, we opted for the more inclusive non-targeted metabolomics approach to investigate their differences. The objective of this dissertation is to investigate the aroma profile of two hybrid grapes Norton and Chambourcin, important to the Mid-Western United states, including Missouri, along with the differences during berry development. We also investigated the change in aroma profile of Chambourcin berries due to various viticulture operations, rootstocks, and irrigation using a metabolomics-based approach. To understand consumer preference, differences in aroma between vinifera and interspecific hybrid grapes and wines need to be investigated so that the concentration of the key volatiles can be adjusted by various viticultural and enological practices to make better wine as well as develop cultivars that fit consumer preference better. In Chapter 2, we investigated berry and wine volatile differences between Norton, a popular interspecific hybrid cultivar in Missouri, and Cabernet Sauvignon, a popular Vitis vinifera cultivar known for its wine quality and cultivated worldwide. Berries were sourced from different locations, vintages, and ripening whereas, wines analyzed were commercial wines from different vintages and locations. The volatiles was analyzed using HS-SPME-GCMS and then processed using XCMS online to identify 924, 793, and 1064 metabolic features (M(m/z) T (retention time in minutes)). Multivariate analysis of the significant features (p-value [less than] 0.05 and fold change [greater than] 1.5) demonstrated that the genome of the cultivar is the strongest factor driving differences in free, total and wine volatiles even though there is much variability in the environmental, year, viticultural factors in the berries and wine sampled. Many compounds were identified to be different between two cultivars and some related to plant defense including methyl salicylate and eugenol were found in higher concentrations in Norton. The identified compounds were used as markers to phenotype the F1 population derived from Norton and Cabernet Sauvignon cross. The F1 population demonstrated segregation for the identified compounds with some genotypes demonstrating higher or lower concentrations for the compounds. The future work is to map these volatile compounds using a genetic map to identify regions in genomes that are regulating them, which will accelerate the breeding of cultivars with desired traits from both cultivars. Besides genetics, many viticultural factors such as irrigation management, rootstocks, sun exposure, and hedging have been found to play a pivotal role in manipulating the vine physiology and berry chemistry, thus impacting wine quality. We investigated the impact of rootstocks and irrigation treatments in berry and wine quality using an experimental vineyard planted with Chambourcin own-rooted as well as grafted to three commercial rootstocks (1103P, 3309C, SO4) subjected to three irrigation regimes (full, RDI and none) in a complex experimental design. Since there is no published study on the volatile profile of Chambourcin grapes and wines, and since there is no predefined information on the volatiles that are important in this cultivar, we used a metabolomics-based approach to extract as much information as possible. Chapter 3 of the dissertation aims to study the wine volatiles as impacted by rootstocks and irrigation in a comprehensive and unbiased way. Based on the multivariate analysis, rootstocks had the greatest influence on wine volatiles, but the assortment of compounds was modulated by the season and the irrigation regime. Own-rooted Chambourcin was found to differ from other root-systems for multiple volatile compounds such as Linalool, Ethyl Nonanoate, [beta]-Damascenone, and TDN, whereas fewer differences were detected among grafted vines. Rootstocks were found to increase concentrations of compounds such as Linalool, while, [beta]-Damascenone was found to be highest in own-rooted Chambourcin wines. Significant differences among irrigation regimes were also observed along with the interaction between rootstock and irrigation. [Beta]-Damascenone was higher in RDI than in other treatments. Finding significant differences in wine volatiles due to rootstocks and irrigation, we then investigated the berry volatiles during the course of its development also using the metabolomics-based approach. Volatile compounds present in grapes, as well as aroma precursors, are crucial for wine quality, with their concentrations impacted by a complex interplay between the natural environment (soil conditions, climate, temperature), vineyard management practices (irrigation, pruning, sun exposure) and vine genotypes, including the genomes of both the scion and the rootstocks. Grape-derived volatiles can be free volatiles that are present in grapes as well as aroma precursors which are present as glycosides in grapes and later released during the winemaking processes. Both free and bound volatiles are found to differ during berry development. We investigated the impact that rootstocks and irrigation have on free and total (free + glycosidase releasable) volatiles using the same Chambourcin experiment as described above. Phenology (ripening state) and year were found to be the most significant factors to impact berry volatiles, with berries being more similar in volatile composition at veraison than at harvest, confirming the commonly held view that secondary metabolism in berries reflects the various stresses the vine experiences during the growing season. Rootstocks and irrigation both had a subtle but significant impact on many free and total berry volatiles. Rootstocks were found to be a significant factor impacting free and total volatiles, differentiating own-rooted from grafted vines as well as differentiating between different rootstocks. The fact that rootstocks had only subtle effects on berry volatiles but a major impact on the relative concentration of wine volatiles raises the possibility that the principal manner by which rootstocks modulate wine volatiles may not be the concentration of berry metabolites. It is possible that other factors, such as grape-derived enzymes that modify or release volatile compounds during fermentation, are the ones through which rootstocks primarily influence wine quality. In the final chapter, the basic berry chemistry traits, organic acids, vine yield, and vine midday stem water potential as impacted by rootstocks and irrigation were investigated. Basic berry chemistry and organic acids significantly impact the flavor of the grapes and wines as well as the extraction of many volatiles from berries to wine. The future work is to investigate the relationship between berry and wine volatiles to understand the predictability of wine quality. Also, correlating berry and wine volatiles with many other phenotypes that were collected concurrently as part of the bigger project will be performed. These include remote sensing, hyperspectral data, gene expression, leaf ionomics, leaf morphometrics, epigenetic regulation, and root microbiome that will unfold interesting details about the impact that each of those traits has on berry and wine quality.

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.

With the reduction in the genotyping cost of the sequencing technique, improved statistical methods, and increased computational efficiency, association mapping, especially genome wide association study (GWAS), is widely used to dissect the architecture of the several complex traits. Several review papers and chapters on QTL mapping of disease resistance in maize have been published so far. However, a general review and compilation of the recent GWAS studies in the disease resistance of maize is limited. This chapter compiles and integrates recent studies of the five major diseases of maize using GWAS. The economically important diseases in maize, along with the novel SNPs and QTLs’ hotspots, are highlighted in the chapter. The advantages of association mapping over QTL mapping, along with working model of GWAS, are briefly discussed. At the end, we discuss on the limitation of the GWAS and future perspectives on the identification of novel disease resistance genes.