Biology subjects

Harris, Z. N.

Publications and source records attributed to Harris, Z. N..

10 recordsLinked to original sources

bioRxiv2026

Conserved Rhizosphere Microbiomes and Metabolic Functions Across Diverse Grapevine Rootstocks: Implications for Plant Elemental Composition

BackgroundWhile grapevine rootstocks are essential to commercial viticulture, researchers still lack a complete understanding of how these root systems and their associated microbiomes influence the vines mineral nutrition. Previous research has shown that rootstocks with similar pedigrees, reflecting the limited number of parental genotypes in the breeding pool, affect both the vines elemental profile and microbiome composition. Here, we extend this work by surveying a broader diversity of rootstock genotypes representing distinct parentage groups across multiple scions and by assessing both functional and taxonomic associations between the rhizosphere metagenome and vine elemental composition. ResultsWe used a rootstock diversity trial with ten rootstock genotypes grafted to one of two scions to simultaneously characterize the rhizosphere metagenome and elemental composition of both berries and roots. We found that elemental composition varied strongly among vine compartments, while scion and rootstock had comparatively minor effects. Berries of Cabernet Sauvignon contained higher concentrations of boron, potassium, and phosphorus than those of Chardonnay. Only three elements in root tissues differed among rootstock genotypes, and these differences were unrelated to genetic relatedness among rootstocks. Rhizosphere microbiome composition was also conserved across rootstocks, suggesting that diverse genotypes recruit a consistent microbial community with similar functional potential. By linking rhizosphere microbiome profiles with root elemental composition, we found that Streptomyces and Mesorhizobium were significantly associated with elemental patterns, showing negative correlations with a principal component heavily loaded for molybdenum, cadmium, potassium, and iron. ConclusionsOur findings suggest that vine compartment exerts a dominant influence on elemental composition, while rootstock genotypes have comparatively modest effects. Despite the overall conservation of the rhizosphere microbiome, specific microbial taxa were linked to elemental variation, highlighting potential microbe-element associations that may influence nutrient dynamics in the grapevine rhizosphere. These results provide a foundation for disentangling how root-associated microbes contribute to vine mineral nutrition, or vice versa, across diverse rootstock genotypes.

plant biology↗

bioRxiv2025

Leveraging High-dimensional Seed Colorspace in Phenomic Selection Models for Herbaceous Perennial Crops

Herbaceous perennial crops, which only recently entered the domestication pipeline, offer the potential of ecological benefits in agricultural systems but remain underdeveloped, partly due to slow breeding cycles. Early-stage phenomic selection, the process of using high-dimensional secondary traits to predict target traits, may accelerate improvement. We evaluated whether seed traits derived from image scans could be used to predict germination traits in three perennial crop candidate species: sainfoin (Onobrychis viciifolia), intermediate wheatgrass (Thinopyrum intermedium), and silflower (Silphium integrifolium). Over 20,000 seeds were scanned, and PlantCV was used to extract 692 hue, saturation, and value (HSV) color features along with five morphological traits. We demonstrated that seed color, morphology, and germination traits were all influenced by maternal family, but patterns of correlation between germination traits and color and morphology traits are complex. To enable prediction from high-dimensional seed traits, we constructed relationship matrices from combinations of HSV and morphology features for use in phenomic selection models to predict germination proportion and timing. Model performance varied by trait, species, and cohort, and in many cases, predictions were significantly better than chance. HSV features, when combined with morphology, often yielded the most accurate predictions, with performance reaching a maximum of r = 0.33. These results demonstrate the potential of low-cost, image-based phenomic data to inform early-stage selection and support the development of sustainable perennial crops. Plain language summaryMany of the worlds most important crops (e.g., wheat, maize, soy) live for less than one year, leaving soil bare for many months and subject to erosion. Longer-lived (perennial) alternatives to these crops have the potential to support a more sustainable agricultural system by improving soil health and reducing the need for chemical inputs. However, perennial herbaceous plants were not domesticated by early farmers, and now lag behind annual crops in development. They take longer to breed and often lack the genetic resources needed for modern breeding approaches. In this study, we tested whether simple seed images derived from color scanners could be used to predict key traits like germination proportion and timing in emerging perennial crops. We found that seed color and shape varied by maternal family and that color, especially when combined with seed size and shape, could help predict germination performance. These predictions were significantly better than chance. This work shows that low-cost, image-based seed data can support early-stage selection in breeding programs, especially for undeveloped perennial crops, helping save time, reduce cost, and accelerate progress toward more sustainable agriculture.

plant biology↗

bioRxiv2025

A leaf phenomics approach to estimating below-ground traits in North American Licorice

Premise of the studyThousands of years of selective breeding has prioritized above-ground yield, with little regard for changes happening below-ground. Despite their central role in plant success and resilience, our knowledge of roots lags behind above-ground structures. Accurately phenotyping root traits is often labor-intensive, expensive, and destructive. In order to advance understanding of the fundamental biology underlying root systems, and to integrate hard-to-measure root traits into breeding programs, high-throughput non-destructive methods are required. MethodsThis study uses American licorice (Glycyrrhiza lepidota Pursh.), a perennial legume with a rich ethnobotanical history, as a model to investigate root system phenotypes. We assess root traits across multiple populations, analyze relationships between above- and below-ground phenotypes, and test the use of multidimensional leaf traits, including spectral reflectance, in predicting root traits. Key resultsAmerican licorice displays significant variation in root traits across source populations and strong correlations between above- and below-ground traits. Leaf spectral reflectance and elemental composition show promise in modeling below-ground traits, though the isometric relationship between plant size and root traits complicates model accuracy. ConclusionsThese findings demonstrate the use of high-dimensional leaf traits as a proxy for root traits, with potential applications for understanding foundational questions in plant biology and in breeding programs targeting the below-ground structures of perennial herbaceous species. Further optimization and larger studies are needed to improve predictive models.

plant biology↗

bioRxiv2023

Genome assembly of the hybrid grapevine Vitis Chambourcin

Background Chambourcin is a French-American interspecific hybrid grape variety grown in the eastern and midwestern United States and used for making wine. Currently, there are few genomic resources available for hybrid grapevines like Chambourcin. ResultsWe assembled the genome of Chambourcin using PacBio HiFi long-read sequencing, Bionano optical map sequencing and Illumina short read sequencing. We produced an assembly for Chambourcin with 26 scaffolds with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. 33,791 gene models were predicted, of which 81% (27,075) were functionally annotated using Gene Ontology and KEGG pathway analysis. We identified 16,056 common orthologs between Chambourcin gene models, V. vinifera PN40024 12X.v2, VCOST.v3, Shine Muscat (Vitis labruscana x V. vinifera) and V. riparia Gloire. A total of 1,606 plant transcription factors representing 58 different gene families were identified in Chambourcin. Finally, we identified 304,571 simple sequence repeats (SSRs), repeating units of 1-6 base pairs in length in the Chambourcin genome assembly. ConclusionsWe present the genome assembly, genome annotation, protein sequences and coding sequences reported for Chambourcin. The Chambourcin genome assembly provides a valuable resource for genome comparisons, functional genomic analysis and genome-assisted breeding research.

bioinformatics↗

bioRxiv2023

Grapevine scion gene expression is driven by rootstock and environment interaction

BACKGROUNDGrafting 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. RESULTSIn 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. CONCLUSIONSOur 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.

plant biology↗

bioRxiv2022

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 genotype, 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 the role of the root system in the elemental composition of the shoot system. We measured elemental composition of over 7000 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.

plant biology↗

bioRxiv2021

Comparative population genomics in two sympatric species of Strophostyles (Fabaceae) with contrasting life histories

PREMISE OF THE STUDYLife history is an important predictor of population genetic variation, although this link remains unexplored in numerous important plant lineages. One such lineage is the legume genus Strophostyles, which contains both annual and herbaceous perennial vines native to eastern North America. Specifically, it remains to be determined whether Strophostyles species with different life histories show different patterns of genetic differentiation and diversity, as well as if these species hybridize across their range. METHODSHere we sampled the perennial Strophostyles helvola and annual S. leiosperma in five sites across a latitudinal transect in the central United States, including three sites where the species occur in sympatry. Using genotyping-by-sequencing, we identified 5556 polymorphic SNPs across 166 individuals. KEY RESULTSThere is no evidence that Strophostyles helvola and S. leiosperma hybridize in the populations examined. Within species, Strophostyles helvola (perennial) displays admixture among populations, while S. leiosperma (annual) does not, although both species show more genetic diversity among rather than within populations. Patterns of genetic diversity are varied across populations of both species, with both heterozygote excess and deficiency. CONCLUSIONSThe complex patterns of genetic differentiation and diversity warrant further investigation of life history and population dynamics in Strophostyles, particularly mating system and modes of gene flow. This study exemplifies the diversity of population genetic patterns even within a small genus, and it reinforces the need to characterize such diversity in non-model systems to gain a more complete understanding of how life history contributes to population genetics.

plant biology↗

bioRxiv2020

Root system influence on high dimensional leaf phenotypes over the grapevine growing season

O_LIIn 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. C_LIO_LIUsing 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. C_LIO_LIWe 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. C_LIO_LIThese 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. C_LI

plant biology↗

bioRxiv2020

Grapevine microbiota reflect diversity among compartments and complex interactions within and among root and shoot systems

BackgroundWithin an individual plant, different compartments (e.g. roots, leaves, fruits) host distinct communities of microorganisms due to variation in structural characteristics and resource availability. Grafting, which joins the root system of one individual with the shoot system of a second genetically distinct individual, has the potential to bring the microbial communities of different genotypes together. An important question is the extent to which unique root system and shoot system genotypes, when grafted together, influence the microbiota of the graft partner. Our study sought to answer this question by utilizing an experimental vineyard composed of Chambourcin vines growing ungrafted and grafted to three different rootstocks, replicated across three irrigation treatments. We characterized bacterial and fungal communities in roots, leaves, and berries, as well as surrounding soil. Our objectives were to (1) characterize the microbiota of compartments within the root system (roots and adjacent soil) and the shoot system (leaves and berries), (2) determine the influence of rootstock genotypes, irrigation, and their interaction on the microbiota of aboveground and belowground compartments, and (3) investigate the distribution of microorganisms implicated in the late-season grapevine bunch rot disease sour rot (Acetobacterales and Saccharomycetes). ResultsCompartments were significantly differentiated in bacterial and fungal richness and composition. Abundance-based machine learning accurately predicted the compartment and differential abundance analysis showed a large portion of taxa differed significantly across compartments. Rootstock genotypes did not differ significantly in microbial community richness or composition; however, individual microbial taxa exhibited significant differences in abundance based on rootstock and irrigation treatment. The relative abundance of Acetobacterales and Saccharomycetes in the berry was influenced by complex interactions among rootstock genotype and irrigation. ConclusionOur results indicate that grapevine compartments retain distinct core microbiota regardless of the rootstock to which they are grafted. While rootstock genotype generally had a subtle impact on global patterns of microbial diversity, we found associations between rootstock genotypes and specific groups of microorganisms. Further experimental validation is needed in order to understand how associations with these microorganisms impacts a vines susceptibility to sour rot upon damage and whether the characteristics of wine are impacted.

plant biology↗

bioRxiv2018

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 use 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 own-rooted as well as grafted to three different rootstocks ( SO4, 1103P and 3309C) across two years and three different irrigation treatments. Results described here demonstrate that 1) the largest source of variation in leaf shape stems from the interaction of rootstock by irrigation; 2) leaf position, but also rootstock and rootstock by irrigation interaction, are the primary sources of variation in leaf ion concentrations; and 3) gene expression in scion leaves exhibited significantly different patterns of gene expression from ungrafted vines, and these expression patterns were rootstock-specific. Our work provides an initial description of the subtle and complex effect of grafting on Chambourcin leaf morphology, ionomics and gene expression in grapevine scions. Further work across multiple years, environments and additional phenotypes is required in order to determine how the relationship between the rootstock and the scion can best be leveraged for adapting grapevines to a changing climate.

plant biology↗