Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California.

BACKGROUND: Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. RESULTS: To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. CONCLUSIONS: These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity.

Many threatened plants have low genetic diversity, which may reduce their capacity for genetically based adaptation, increasing their extinction risk. Non-genetic variation (e.g. epigenomic modifications such as DNA methylation) and plasticity may facilitate the persistence of threatened plants, yet are rarely incorporated into conservation assessments. We present a case study investigating variation and plasticity in DNA methylation and phenotypic traits in four genetically depauperate species of Leavenworthia (Brassicaceae), including one widespread species and one asexual, threatened species. We grew individuals from several maternal lines and populations per species in contrasting watering treatments, measured phenotypic traits and analysed DNA methylation using whole-genome bisulphite sequencing. We addressed four questions: (1) How do patterns of DNA methylation differ within and among species? (2) Within species, how do phenotypic traits and patterns of DNA methylation vary in response to drought? (3) Does variation in DNA methylation correspond to phenotypic variation? (4) What are the implications for conservation? We found that taxa were epigenomically distinct and that each species exhibited variation in DNA methylation among populations that could be relevant for conservation. Within species, the DNA methylation response to environmental stress corresponded to its phenotypic response. Species differed in their DNA methylation and phenotypic responses to environmental stress, with the extent of plasticity possibly related to species geographic range size. We also found phenotypic and DNA methylation variation in the asexual, threatened species that may be relevant for conservation. Our results suggest that variation in DNA methylation may promote the persistence of genetically depauperate threatened plants, highlighting its potential as a novel conservation target to reduce extinction risk.

Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits.

Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.

Sainfoin (Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations.

Sainfoin (Onobrychis spp.) is a perennial forage legume that is also attracting attention as a perennial pulse with potential for human consumption. The dual use of sainfoin underpins diverse research and breeding programs focused on improving sainfoin lines for forage and pulses, which is driving the generation of complex datasets describing high dimensional phenotypes in the post-omics era. To ensure that multiple user groups, for example, breeders selecting for forage and those selecting for edible seed, can utilize these rich datasets, it is necessary to develop common ontologies and accessible ontology platforms. One such platform, Crop Ontology, was created in 2008 by the Consortium of International Agricultural Research Centers (CGIAR) to host crop-specific trait ontologies that support standardized plant breeding databases. In the present study, we describe the sainfoin crop ontology (CO). An in-depth literature review was performed to develop a comprehensive list of traits measured and reported in sainfoin. Because the same traits can be measured in different ways, ultimately, a set of 98 variables (variable = plant trait + method of measurement + scale of measurement) used to describe variation in sainfoin were identified. Variables were formatted and standardized based on guidelines provided here for inclusion in the sainfoin CO. The 98 variables contained a total of 82 traits from four trait classes of which 24 were agronomic, 31 were morphological, 19 were seed and forage quality related, and 8 were phenological. In addition to the developed variables, we have provided a roadmap for developing and submission of new traits to the sainfoin CO.

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.

Interspecific Hybridization and Island Colonization History, not Rarity, Most Strongly Affect the Genetic Diversity in Diospyros a Clade of Mascarene-Endemic Trees.

Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species.

Crop genetic erosion: understanding and responding to loss of crop diversity.

Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.

Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops.

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.

Re-imagining crop domestication in the era of high throughput phenomics.

De novo domestication is an exciting option for increasing species diversity and ecosystem service functionality of agricultural landscapes. Genomic selection (GS), the application of genomic markers to predict phenotypic traits in a breeding population, offers the possibility of rapid genetic improvement, making GS especially attractive for modifying traits of long-lived species. However, for some wild species just entering the domestication pipeline, especially those with large and complex genomes, a lack of funding and/or prior genome characterization, GS is often out of reach. High throughput phenomics has the potential to augment traditional pedigree selection, reduce costs and amplify impacts of genomic selection, and even create new predictive selection approaches independent of sequencing or pedigrees.

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.

The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia.

PREMISE: Annual and perennial life history transitions are abundant among angiosperms, and understanding the phenotypic variation underlying life span shifts is a key endeavor of plant evolutionary biology. Comparative analyses of trait variation and correlation networks among annual and perennial plants is increasingly important as new herbaceous perennial crops are being developed for edible seed. However, it remains unclear how seed to vegetative growth trait relationships correlate with life span. METHODS: To assess the relative roles of genus and life span in predicting phenotypic variation and trait correlations, we measured seed size and shape, germination proportion, and early-life-stage plant height and leaf growth over 3 mo in 29 annual and perennial, herbaceous congeneric species from three legume genera (Lathyrus, Phaseolus, and Vicia). RESULTS: Genus was the strongest predictor of seed size and shape variation, and life span consistently predicted plant height and leaf number at single time points. Correlation networks revealed that annual species had significant associations between seed traits and vegetative traits, whereas perennials had no significant seed-vegetative associations. Each genus also differed in the extent of integration between seed and vegetative traits, as well as within-vegetative-trait correlation patterns. CONCLUSIONS: Genus and life span were important for predicting aspects of early-life-stage phenotypic variation and trait relationships. Differences in phenotypic correlation may indicate that selection on seed size traits will impact vegetative growth differently depending on life span, which has important implications for nascent perennial breeding programs.

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems.

Grafting connects root and shoot systems of distinct individuals, bringing microbial communities of different genotypes together in a single plant. How do root system and shoot system genotypes influence plant microbiota in grafted grapevines? To address this, we utilized clonal replicates of the grapevine 'Chambourcin', growing ungrafted and grafted to three different rootstocks in three irrigation treatments. Our objectives were to (1) characterize the microbiota (bacteria and fungi) of below-ground compartments (roots, adjacent soil) and above-ground compartments (leaves, berries), (2) determine how rootstock genotype, irrigation, and their interaction influences grapevine microbiota in different compartments, and (3) investigate abundance of microorganisms implicated in the late-season grapevine disease sour rot (Acetobacterales and Saccharomycetes). We found that plant compartment had the largest influence on microbial diversity. Neither rootstock genotype nor irrigation significantly influenced microbial diversity or composition. However, differential abundance of bacterial and fungal taxa varied as a function of rootstock and irrigation treatment; in particular, Acetobacterales and Saccharomycetes displayed higher relative abundance in berries of grapevines grafted to '1103P' and 'SO4' rootstocks and varied across irrigation treatments. This study demonstrates that grapevine compartments retain distinct microbiota and identifies associations between rootstock genotypes, irrigation treatment, and the relative abundance of agriculturally relevant microorganisms in the berries.

RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees.

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Comparative Analysis of Early Life Stage Traits in Annual and Perennial Phaseolus Crops and Their Wild Relatives.

Herbaceous perennial species are receiving increased attention for their potential to provide both edible products and ecosystem services in agricultural systems. Many legumes (Fabaceae Lindl.) are of special interest due to nitrogen fixation carried out by bacteria in their roots and their production of protein-rich, edible seeds. However, herbaceous perennial legumes have yet to enter widespread use as pulse crops, and the response of wild, herbaceous perennial species to artificial selection for increased seed yield remains under investigation. Here we compare cultivated and wild accessions of congeneric annual and herbaceous perennial legume species to investigate associations of lifespan and cultivation with early life stage traits including seed size, germination, and first year vegetative growth patterns, and to assess variation and covariation in these traits. We use "cultivated" to describe accessions with a history of human planting and use, which encompasses a continuum of domestication. Analyses focused on three annual and four perennial species of the economically important genus Phaseolus. We found a significant association of both lifespan and cultivation status with seed size (weight, two-dimensional lateral area, length), node number, and most biomass traits (with cultivation alone showing additional significant associations). Wild annual and perennial accessions primarily showed only slight differences in trait values. Relative to wild forms, both cultivated annual and cultivated perennial accessions exhibited greater seed size and larger overall vegetative size, with cultivated perennials showing greater mean trait differences relative to wild accessions than cultivated annuals. Germination proportion was significantly lower in cultivated relative to wild annual accessions, while no significant difference was observed between cultivated and wild perennial germination. Regardless of lifespan and cultivation status, seed size traits were positively correlated with most vegetative traits, and all biomass traits examined here were positively correlated. This study highlights some fundamental similarities and differences between annual and herbaceous perennial legumes and provides insights into how perennial legumes might respond to artificial selection compared to annual species.

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.

Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution.

Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.

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.