Grapevine scion gene expression is driven by rootstock and environment interaction.

BACKGROUND: Grafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings. RESULTS: In the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment. CONCLUSIONS: Our results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.

Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines.

Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study how genetically distinct root systems influence the elemental composition of a common shoot system. We measured elemental composition of over 7,000 leaves in the grapevine cultivar "Chambourcin" growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition, and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.

Increases in vein length compensate for leaf area lost to lobing in grapevine.

PREMISE: Leaf lobing and leaf size vary considerably across and within species, including among grapevines (Vitis spp.), some of the best-studied leaves. We examined the relationship between leaf lobing and leaf area across grapevine populations that varied in extent of leaf lobing. METHODS: We used homologous landmarking techniques to measure 2632 leaves across 2 years in 476 unique, genetically distinct grapevines from five biparental crosses that vary primarily in the extent of lobing. We determined to what extent leaf area explained variation in lobing, vein length, and vein to blade ratio. RESULTS: Although lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. CONCLUSIONS: For leaves with different extents of lobing but the same area, the more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.

Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season.

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.

Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density.

Inflorescence architecture provides the scaffold on which flowers and fruits develop, and consequently is a primary trait under investigation in many crop systems. Yet the challenge remains to analyse these complex 3D branching structures with appropriate tools. High information content datasets are required to represent the actual structure and facilitate full analysis of both the geometric and the topological features relevant to phenotypic variation in order to clarify evolutionary and developmental inflorescence patterns. We combined advanced imaging (X-ray tomography) and computational approaches (topological and geometric data analysis and structural simulations) to comprehensively characterize grapevine inflorescence architecture (the rachis and all branches without berries) among 10 wild Vitis species. Clustering and correlation analyses revealed unexpected relationships, for example pedicel branch angles were largely independent of other traits. We identified multivariate traits that typified species, which allowed us to classify species with 78.3% accuracy, versus 10% by chance. Twelve traits had strong signals across phylogenetic clades, providing insight into the evolution of inflorescence architecture. We provide an advanced framework to quantify 3D inflorescence and other branched plant structures that can be used to tease apart subtle, heritable features for a better understanding of genetic and environmental effects on plant phenotypes.

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard.

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine 'Chambourcin' (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in 'Chambourcin' grown ungrafted as well as grafted to three different rootstocks ('SO4', '1103P' and '3309C') across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on 'Chambourcin' leaf morphology, ionomics, and gene expression.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections.

PREMISE OF THE STUDY: Grapes are one of the most economically important berry crops worldwide, with the vast majority of production derived from the domesticated Eurasian species Vitis vinifera. Expansion of production into new areas, development of new cultivars, and concerns about adapting grapevines for changing climates necessitate the use of wild grapevine species in breeding programs. Diversity within Vitis has long been a topic of study; however, questions remain regarding relationships between species. Furthermore, the identity of some living accessions is unclear. METHODS: This study generated 11,020 single nucleotide polymorphism (SNP) markers for more than 300 accessions in the USDA-ARS grape germplasm repository using genotyping-by-sequencing. Resulting data sets were used to reconstruct evolutionary relationships among several North American and Eurasian Vitis species, and to suggest taxonomic labels for previously unidentified and misidentified germplasm accessions based on genetic distance. KEY RESULTS: Maximum likelihood analyses of SNP data support the monophyly of Vitis, subg. Vitis, a Eurasian subg. Vitis clade, and a North American subg. Vitis clade. Data delineate species groups within North America. In addition, analysis of genetic distance suggested taxonomic identities for 20 previously unidentified Vitis accessions and for 28 putatively misidentified accessions. CONCLUSIONS: This work advances understanding of Vitis evolutionary relationships and provides the foundation for ongoing germplasm enhancement. It supports conservation and breeding efforts by contributing to a growing genetic framework for identifying novel genetic variation and for incorporating new, unsampled populations into the germplasm repository system.

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences.

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.

Digital Morphometrics of Two North American Grapevines (Vitis: Vitaceae) Quantifies Leaf Variation between Species, within Species, and among Individuals.

Recent studies have demonstrated that grapevine (Vitis spp.) leaf shape can be quantified using digital approaches which indicate phylogenetic signal in leaf shape, discernible patterns of developmental context within single leaves, and signatures of local environmental conditions. Here, we extend this work by quantifying intra-individual, intraspecific, and interspecific variation in leaf morphology in accessions of North American Vitis riparia and V. rupestris in a common environment. For each species at least four clonal replicates of multiple genotypes were grown in the Missouri Botanical Garden Kemper Center for Home Gardening. All leaves from a single shoot were harvested and scanned leaf images were used to conduct generalized Procrustes analysis, linear discriminant analysis, and elliptical Fourier analysis. Leaf shapes displayed genotype-specific signatures and species distinctions consistent with taxonomic classifications. Leaf shape variation within genotypes and among clones was the result of pest and pathogen-induced leaf damage that alters leaf morphology. Significant trends in leaf damage caused by disease and infestation were non-random with respect to leaf position on the shoot. Digital morphometrics is a powerful tool for assessing leaf shape variation among species, genotypes, and clones under common conditions and suggests biotic factors such as pests and pathogens as important drivers influencing leaf shape.

Comprehensive Methods for Leaf Geometric Morphometric Analyses.

Leaf morphometrics are used frequently by several disciplines, including taxonomists, systematists, developmental biologists, morphologists, agronomists, and plant breeders to name just a few. Leaf shape is highly variable and can be used for identifying species or genotypes, developmental patterning within and among individuals, assessing plant health, and measuring environmental impacts on plant phenotype. Traditional leaf morphometrics requires hand tools and access to specimens, but modern efforts to digitize botanical collections make digital morphometrics a readily accessible and scientifically rigorous option. Here we provide detailed instructions for performing some of the most informative digital geometric morphometric analyses available: generalized Procrustes analysis, elliptical Fourier analysis, and shape features. This comprehensive procedure for leaf shape analysis is comprised of six main sections: A) scanning of material, B) acquiring landmarks, C) analysis of landmark data, D) isolating leaf outlines, E) analysis of leaf outlines, and F) shape features. This protocol provides a detailed reference for applying landmark and outline analysis to leaf shape as well as describing leaf shape features, thus empowering researchers to perform high throughput phenotyping for diverse applications.

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes.

Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.

Latent developmental and evolutionary shapes embedded within the grapevine leaf.

Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other. We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity. Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.

A curious case of anti-D antibody titer.

RhD alloimmunization remains a threat to 1% of the 10% of RhD-negative women in the United States who are giving birth to RhD-positive fetuses despite routine antenatal and postpartum administration of Rh(o)D immune globulin (RhIG). This report examines the clinical course of an RhD-negative woman who developed a high anti-D antibody titer during her pregnancy while carrying an RhD-positive female fetus yet had a negative antibody screen at the time she gave birth. Although she delivered a healthy newborn unaffected by hemolytic disease, subsequent pregnancies will be treated as though she is RhD alloimmunized. The discussion below includes possible causes for the abrupt rise in this woman's anti-D antibody titer, a review of the complex Rh system and cellular anamnestic response, and current fetal surveillance for hemolytic disease of the fetus and newborn.

Shotgun proteomic analysis of vaginal fluid from women in late pregnancy.

Liquid chromatography and tandem mass spectrometry without prior fractionation (shotgun proteomics) were used to analyze vaginal fluid from patients admitted for signs and symptoms of preterm labor. The patients had an average age of 26.3 +/- 5.9 years, a gestational age of 30.5 +/- 2.5 weeks, and a median cervical dilation of 1 cm (range, 0-6 cm). None of the patients exhibited signs of vaginal infection at the time of enrollment. Shotgun proteomics yielded reproducible identifications (R = 0.973) of more than 40 proteins in vaginal fluid samples, such as plasma proteins, epithelial structural proteins, and several immunoregulatory proteins, including some that were previously linked to intra-amniotic infection. This initial characterization of the vaginal fluid proteome using a nonbiased, high-throughput technique yields reproducible results in late pregnancy. The presence of host defense proteins in vaginal fluid suggests that this technique may be useful for future study of inflammation-related preterm birth.

Detection of intra-amniotic infection in a rabbit model by proteomics-based amniotic fluid analysis.

OBJECTIVE: This study was undertaken to identify intra-amniotic infection caused by several different organisms in a rabbit model by using proteomics. STUDY DESIGN: Twenty infected and 18 uninfected amniotic fluid samples were subjected to proteomic analysis by surface-enhanced laser desorption ionization (SELDI-TOF, Ciphergen Biosystems, Fremont, Calif), 1- and 2-dimensional gel electrophoresis, and tandem mass spectrometry (MS/MS). RESULTS: Detailed SELDI-TOF spectra revealed a constitutive 4.0 kd peak in all animals. Infected samples also displayed a signature double peak at 3.6 kd. A SELDI-TOF signature profile for intra-amniotic infection predicted positive amniotic fluid and/or fetal cultures with a sensitivity of 90% and specificity of 83%. Similar proteomic profiles were obtained regardless of the infecting organism. The 3.6 kd peak appeared to contain rabbit calgranulin C and rabbit calcyclin, members of the S100 family of calcium binding proteins. CONCLUSION: Amniotic fluid proteomic analysis was able to detect intra-amniotic infection in this experimental rabbit model. S100 proteins may be involved in the host inflammatory response to intra-amniotic infection.

Infection and preterm birth.

As many as 50% of spontaneous preterm births are infection-associated. Intrauterine infection leads to a maternal and fetal inflammatory cascade, which produces uterine contractions and may also result in long-term adverse outcomes, such as cerebral palsy. This article addresses the prevalence, microbiology, and management of intrauterine infection in the setting of preterm labor with intact membranes. It also outlines antepartum treatment of infections for the purpose of preventing preterm birth.

Use of microbial cultures and antibiotics in the prevention of infection-associated preterm birth.

OBJECTIVE: The purpose of this study was to summarize recent evidence regarding infection-associated preterm birth and to make appropriate recommendations. Antepartum treatment of lower genital tract infection or bacterial colonization has been found to reduce the incidence of preterm birth in the case of asymptomatic bacteriuria and bacterial vaginosis in selected patients but has been proved to be ineffective for vaginal colonization with organisms such as Ureaplasma urealyticum and group B streptococcus. STUDY DESIGN: This is a clinical opinion based on a review of recent data related to 1) the association between lower genital tract infection and preterm birth and 2) antibiotic trials to prevent preterm birth. RESULTS: Antepartum treatment of lower genital tract infection or bacterial colonization has been found to reduce the incidence of preterm birth in the case of asymptomatic bacteriuria and bacterial vaginosis in selected patients, but has been proven to be ineffective for vaginal colonization with organisms such as Ureaplasma urealyticum and group B streptococcus. Large well-designed trials have shown that the routine administration of antibiotics to women with preterm labor and intact membranes is not beneficial; however, antibiotic regimens including macrolides are recommended for preterm premature rupture of the membranes. CONCLUSION: Large well-designed trials have shown that the routine administration of antibiotics to women with preterm labor and intact membranes is not beneficial; however, antibiotic regimens that include macrolides are recommended for preterm premature rupture of the membranes.

Cardiac disease in pregnancy.

This article reviews the complications, management and prognosis of cardiac disease in pregnancy.