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Abstract PremiseThe selection ofArabidopsisas a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural‐ or ecological‐based model species were rejected, in favor of building knowledge in a species that would facilitate genome‐enabled research. MethodsHere, we examine the ability of models based onArabidopsisgene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested onArabidopsisdata achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained onArabidopsisdata, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64. ResultsThe identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance fromArabidopsis.k‐nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants. DiscussionOur data‐driven results highlight that the assertion that knowledge fromArabidopsisis translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis onArabidopsisand prioritize plant diversity. 

Abstract PremiseStudies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf shapes, quantifying variation in leaf shape and the effects of environmental factors on leaf shape has proven challenging. MethodsTo investigate leaf shape variation in a species with inconsistently shaped leaves, we used geometric morphometric modeling and deterministic techniques to analyze approximately 500 digitized specimens ofCapsella bursa‐pastoriscollected throughout the continental United States over 100 years. We generated a morphospace of the leaf shapes and modeled leaf shape as a function of environment and time. ResultsLeaf shape variation ofC. bursa‐pastoriswas strongly associated with temperature over its growing season, with lobing decreasing as temperature increased. While we expected to see changes in variation over time, our results show that the level of leaf shape variation was consistent over the 100 years. ConclusionsOur findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation. 

Societal Impact StatementThe cultural significance of the grapevine is undeniable. However, we fail to acknowledge how the grapevine has and continues to influence the most pressing political questions of our time. From the beginning of the Conquest, Indigenous peoples were forced to plant the vine, Spain burned the vines Miguel Hidalgo used to teach the poor, and César Chávez and the Delano grape strike demanded justice for agricultural laborers. From theGrito de DolorestoSí se puede, we demonstrate how the continuing relationship between Mexico and the grapevine influences debates surrounding labor, immigration, and human rights in the United States and throughout the world. To enhance the reach of this work, a Spanish language version of the paper is available in the Supporting Information (see Translation_ES). SummaryThe wild grapevine species (Vitisspp.) that comprise the pedigrees of rootstocks, the Americas as the source (and solution) to thePhylloxeracrisis that decimated European vineyards, and California as a premier wine‐growing region are the topics that usually frame the history of grapes in North America. This Anglo‐American perspective ignores that domesticated grape varieties were first introduced to North America in what is now Mexico and the singular contributions of Mexican labor to the California wine economy that continue to influence politics. Here, we highlight the neglected history of grapevines in Mexico and argue that the politics of labor that played out during the Conquest never ceased and still shape debates surrounding immigration. Beginning with Hernán Cortés, Indigenous peoples were forced to plant grapevines and when they were successful, they were abruptly forbidden by Spain to grow grapes. This interference influenced Miguel Hidalgo, who taught the poor viticulture as a trade and who would lead the Mexican War of Independence and pay with his life. The grapevine continued its journey north to California, where Franciscans established the missions and cultivated the Mission grapes, which had lasting impacts on the genetics of grapevine varieties. Finally, it was the Delano grape strike that coalesced César Chávez and the United Farm Workers to demand justice for agricultural laborers that is the foundation of the California wine economy and still shapes the current political debate of immigration, labor, and human rights between the United States and Mexico. 

Societal Impact StatementThe innumerable effects of terroir—including climate, soil, microbial environment, biotic interactions, and cultivation practice—collectively alter plant performance and production. A more direct agricultural intervention is grafting, in which genetically distinct shoot and root genotypes are surgically combined to create a chimera that alters shoot performance at a distance. Selection of location and rootstock are intentional decisions in viticulture to positively alter production outcomes. Here, we show that terroir and rootstock alter the shapes of grapevine leaves in commercial vineyards throughout the California Central Valley, documenting the profound effects of these agricultural interventions that alter plant morphology. SummaryEmbedded in a single leaf shape are the latent signatures of genetic, developmental, and environmental effects. In viticulture, choice of location and rootstock are important decisions that affect the performance and production of the shoot. We hypothesize that these effects influence plant morphology, as reflected in leaf shape.We sample 1879 leaves arising from scion and rootstock combinations from commercial vineyards in the Central Valley of California. Our design tests 20 pairwise contrasts between Cabernet Sauvignon and Chardonnay scions from San Joaquin, Merced, and Madera counties from vines grafted to Teleki 5C, 1103 Paulsen, and Freedom rootstocks.We quantify clear differences between Cabernet Sauvignon and Chardonnay leaves. However, we also detect a separate, statistically independent source of shape variance that affects both Cabernet Sauvignon and Chardonnay leaves similarly. We find that this other shape difference is associated with differences in rootstock and location.The shape difference that arises from rootstock and location affects the basal part of the leaf near the petiole, known as the petiolar sinus, and affects its closure. This shape effect is independent from previously described shape differences that arise from genetic, developmental, or size effects. 

Abstract BackgroundBud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch’s Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch’s Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch’s Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets. ResultsThe Dakapo and Merlot cases of Witch’s Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch’s Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968–974 unique genetic mutations in our two Witch’s Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch’s Broom impacting the gene GSVIVG01008260001. ConclusionsThe Witch’s Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch’s Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine. 

Abstract Interdisciplinarity is used to integrate and synthesize new research directions between scientific domains, but it is not the only means by which to generate novelty by bringing diverse perspectives together. Internationality draws upon cultural and linguistic diversity that can potentially impact interdisciplinarity as well. We created an interdisciplinary class originally intended to bridge computational and plant science that eventually became international in scope, including students from the United States and Mexico. We administered a survey over 4 years designed to evaluate student expertise. The first year of the survey included only US students and demonstrated that biology and computational student groups have distinct expertise but can learn the skills of the other group over the course of a semester. Modeling of survey responses shows that biological and computational science expertise is equally distributed between US and Mexico student groups, but that nonetheless, these groups can be predicted based on survey responses due to subspecialization within each domain. Unlike interdisciplinarity, differences arising from internationality are mostly static and do not change with educational intervention and include unique skills such as working across languages. We end by discussing a distinct form of interdisciplinarity that arises through internationality and the implications of globalizing research and education efforts. 

Abstract Speciation is a complex process typically accompanied by significant genetic and morphological differences between sister populations. In plants, divergent floral morphologies and pollinator differences can result in reproductive isolation between populations. Here, we explore floral trait differences between two recently diverged species, Gilia yorkii and G. capitata. The distributions of floral traits in parental, F1, and F2 populations are compared, and groups of correlated traits are identified. We describe the genetic architecture of floral traits through a quantitative trait locus analysis using an F2 population of 187 individuals. While all identified quantitative trait locus were of moderate (10–25%) effect, interestingly, most quantitative trait locus intervals were non-overlapping, suggesting that, in general, traits do not share a common genetic basis. Our results provide a framework for future identification of genes involved in the evolution of floral morphology. 

Abstract South American coca (Erythroxylum coca and E. novogranatense) has been a keystone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half-century, global demand for its alkaloid cocaine has driven intensive agriculture of this plant and placed it in the center of armed conflict and deforestation. To monitor the changing landscape of coca plantations, the United Nations Office on Drugs and Crime collects annual data on their areas of cultivation. However, attempts to delineate areas in which different varieties are grown have failed due to limitations around identification. In the absence of flowers, identification relies on leaf morphology, yet the extent to which this is reflected in taxonomy is uncertain. Here, we analyze the consistency of the current naming system of coca and its four closest wild relatives (the “coca clade”), using morphometrics, phylogenomics, molecular clocks, and population genomics. We include name-bearing type specimens of coca's closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the statistical analyses illuminate that rounder and more obovate leaves of certain varieties could be associated with the subtle domestication syndrome of coca. Our phylogenomic data indicate extensive gene flow involving E. gracilipes which, combined with morphometrics, supports E. gracilipes being retained as a single species. Establishing a robust evolutionary-taxonomic framework for the coca clade will facilitate the development of cost-effective genotyping methods to support reliable identification. 

Summary The iconic, palmately compound leaves ofCannabishave attracted significant attention in the past. However, investigations into the genetic basis of leaf shape or its connections to phytochemical composition have yielded inconclusive results. This is partly due to prominent changes in leaflet number within a single plant during development, which has so far prevented the proper use of common morphometric techniques.Here, we present a new method that overcomes the challenge of nonhomologous landmarks in palmate, pinnate, and lobed leaves, usingCannabisas an example. We model corresponding pseudo‐landmarks for each leaflet as angle‐radius coordinates and model them as a function of leaflet to create continuous polynomial models, bypassing the problems associated with variable number of leaflets between leaves.We analyze 341 leaves from 24 individuals from nineCannabisaccessions. Using 3591 pseudo‐landmarks in modeled leaves, we accurately predict accession identity, leaflet number, and relative node number.Intra‐leaf modeling offers a rapid, cost‐effective means of identifyingCannabisaccessions, making it a valuable tool for future taxonomic studies, cultivar recognition, and possibly chemical content analysis and sex identification, in addition to permitting the morphometric analysis of leaves in any species with variable numbers of leaflets or lobes. 

Societal Impact StatementGrapevine leaves are emblematic of the strong visual associations people make with plants. Leaf shape is immediately recognizable at a glance, and therefore, this is used to distinguish grape varieties. In an era of computationally enabled machine learning‐derived representations of reality, we can revisit how we view and use the shapes and forms that plants display to understand our relationship with them. Using computational approaches combined with time‐honored methods, we can predict theoretical leaves that are possible, enabling us to understand the genetics, development, and environmental responses of plants in new ways. SummaryGrapevine leaves are a model morphometric system. Sampling over 10,000 leaves using dozens of landmarks, the genetic, developmental, and environmental basis of leaf shape has been studied and a morphospace for the genusVitispredicted. Yet, these representations of leaf shape fail to capture the exquisite features of leaves at high resolution.We measure the shapes of 139 grapevine leaves using 1672 pseudo‐landmarks derived from 90 homologous landmarks with Procrustean approaches. From hand traces of the vasculature and blade, we have derived a method to automatically detect landmarks and place pseudo‐landmarks that results in a high‐resolution representation of grapevine leaf shape. Using polynomial models, we create continuous representations of leaf development in 10Vitisspp.We visualize a high‐resolution morphospace in which genetic and developmental sources of leaf shape variance are orthogonal to each other. Using classifiers,Vitis vinifera,Vitisspp., rootstock and dissected leaf varieties as well as developmental stages are accurately predicted. Theoretical eigenleaf representations sampled from across the morphospace that we call synthetic leaves can be classified using models.By predicting a high‐resolution morphospace and delimiting the boundaries of leaf shapes that can plausibly be produced within the genusVitis, we can sample synthetic leaves with realistic qualities. From an ampelographic perspective, larger numbers of leaves sampled at lower resolution can be projected onto this high‐resolution space, or, synthetic leaves can be used to increase the robustness and accuracy of machine learning classifiers.