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

The Effects of a New Citrus Rootstock Citrus junos cv. Shuzhen No. 1 on Performances of Ten Hybrid Citrus Cultivars

The importance of rootstock in citrus production lies in its crucial role in determining tree growth, environmental stress tolerance, and fruit quality. Citrus junos Siebold ex Tanaka cv. Shuzhen No. 1, a recently developed rootstock, demonstrates excellent graft compatibility and abiotic stress tolerance. The objective of this study was to assess ten hybrid citrus cultivars grafted onto two C. junos rootstock selections, with the aim of determining the potential for industrial utilization of the new citrus rootstock. All graft junctions are mature and well established. Vigorous growth characterized all ten citrus cultivars on Shuzhen No. 1, with the largest tree's height reaching 280.33 cm (Wogan scion) and the widest scion's diameter being 67.52 cm (Chunjian scion). However, the scion-to-rootstock diameter ratio was the lowest at 0.62 (Chunxiang scion). C. junos rootstock selections significantly affected fruit weight (five of ten scions) and fruit color (seven of ten scions) but had negligible impact on peel thickness (nine of ten scions). Furthermore, rootstock type had a significant influence on fruit quality. In conclusion, our findings indicate strong graft compatibility between all scions and C. junos rootstocks, which can impact overall size and fruit quality. Based on these results, Shuzhen No. 1 is recommended as a valuable citrus rootstock.

Emerging Roles of Epigenetics in Grapevine and Winegrowing

Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.

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.

Genome assembly of the hybrid grapevine Vitis 'Chambourcin'

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

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.

Region, vintage, and grape maturity co-shaped the ionomic signatures of the Cabernet Sauvignon wines

The ionic elements in wine and in vineyards are gaining attention due to characterization of the wine traits, wine origin tracing, and vine nutrient judging. In this experiment, 19 elements were detected by inductively coupled plasma mass spectrometry (ICP-MS) in 69 wine samples from 4 regions, 3 vintages, and 3 grape maturity levels. Furthermore, the elements related to vine development, such as N, P, K, Ca, Mg, Cu, Fe, Zn and Cu in the vineyard soil and petioles were determined. Two orthogonal partial least squares discriminant analysis (O2PLS-DA) showed that K, Mn, Co, Sr, B, Si, Pb, Ni, Cu, and Zn were important elements in distinguishing the regions. High-temperature vintages can bring wines with high levels of Sr in wine. Na, Ca, K, Mg, Rb, Al, Rb, Pb and Fe can be used as signature elements to distinguish wines made from 2 grape maturities. And Cu, Zn, and Mn were the key elements used to differentiate the petioles in the 4 regions. Partial square regression (PLSR) analysis showed that soil pH was positively correlated with Al, B, Ba, K, Pb, Mn, Sr and Rb in wine, and K in wine was significantly positively correlated with element K in the soil. In conclusion, the elemental contents in wine are shaped by the combination of origin, vintage and grape maturity, while some key elements can be used as indicators of origin traceability.

Contributions of leaf distribution and leaf functions to photosynthesis and water-use efficiency from leaf to canopy in apple: A comparison of interstocks and cultivars

Grafting has been widely used in horticulture to induce dwarfing and avoid stress-derived limitations on plant growth and yield by affecting plant architecture and leaf functions. However, the respective effects on plant photosynthesis and water use efficiency (WUE) of leaf distribution and functions that depend on both rootstock and scion have not been fully elucidated. This study aimed to (i) clarify the scion × interstock impacts on the variability of leaf photosynthetic traits and WUE, and (ii) decipher the respective effects of leaf distribution and functions on canopy photosynthesis and WUE (WUEc). Leaf gas exchange over light gradients and responses to light, CO₂, temperature, and vapor pressure deficit were measured in two apple cultivars, 'Liquan Fuji' ('Fuji') and 'Regal Gala' ('Gala'), grafted onto rootstocks combined with interstocks: a vigorous (VV, 'Qinguan'), or a dwarf one (VD, M26). The 3D architecture-based RATP model was parameterized to estimate the canopy photosynthesis rate (A_c ), transpiration rate (E _c), and WUEc. Then, virtual scenarios were used to compare the relative contributions of cultivar and interstock to canopy A _c, E _c, and WUE _c. These scenarios changed the leaf distribution and functions of either cultivar or interstock. At the leaf scale, VD trees had significantly higher leaf nitrogen per area but a lower maximum carboxylation rate and dark respiration in both cultivars. In parallel with higher leaf stomatal conductance (g_s ) and transpiration in VD 'Fuji' and similar g_s in VD 'Gala', VD trees showed significantly lower leaf photosynthesis rate and WUE than VV trees. However, lower leaf photosynthetic capacities in VD trees were compensated at the canopy scale, with A _c and WUE _c for 'Fuji' significantly improved in VD trees under both sunny and cloudy conditions, and for 'Gala' significantly improved in VD trees under cloudy conditions compared with VV trees. Switching scenarios highlighted that 'Gala' leaf functions and distribution and VD leaf distributions enhanced A _c and WUE _c simultaneously, irrespective of weather conditions. Up-scaling leaf gas exchange to the canopy scale by utilizing 3D architecture-based modeling and reliable measurements of tree architecture and leaf functional traits provides insights to explore the influence of genetic materials and tree management practices.

Nomogram model predicts the risk of visual impairment in diabetic retinopathy: a retrospective study

BACKGROUND

To develop a model for predicting the risk of visual impairment in diabetic retinopathy (DR) by a nomogram.

METHODS

Patients with DR who underwent both optical coherence tomography angiography (OCTA) and fundus fluorescein angiography (FFA) were retrospectively enrolled. FFA was conducted for DR staging, swept-source optical coherence tomography (SS-OCT) of the macula and 3*3-mm blood flow imaging by OCTA to observe retinal structure and blood flow parameters. We defined a logarithm of the minimum angle of resolution visual acuity (LogMAR VA) ≥0.5 as visual impairment, and the characteristics correlated with VA were screened using binary logistic regression. The selected factors were then entered into a multivariate binary stepwise regression, and a nomogram was developed to predict visual impairment risk. Finally, the model was validated using the area under the receiver operating characteristic (ROC) curve (AUC), calibration plots, decision curve analysis (DCA), and clinical impact curve (CIC).

RESULTS

A total of 29 parameters were included in the analysis, and 13 characteristics were used to develop a nomogram model. Finally, diabetic macular ischaemia (DMI) grading, disorganization of the retinal inner layers (DRIL), outer layer disruption, and the vessel density of choriocapillaris layer inferior (SubVD) were found to be statistically significant (P < 0.05). The model was found to have good accuracy based on the ROC (AUC = 0.931) and calibration curves (C-index = 0.930). The DCA showed that risk threshold probabilities in the (3-91%) interval models can be used to guide clinical practice, and the proportion of people at risk at each threshold probability is illustrated by the CIC.

CONCLUSION

The nomogram model for predicting visual impairment in DR patients demonstrated good accuracy and utility, and it can be used to guide clinical practice.

TRIAL REGISTRATION

Chinese Clinical Trial Registry, ChiCTR2200059835. Registered 12 May 2022, https://www.chictr.org.cn/edit.aspx?pid=169290&htm=4.

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and Ravaz index

Annual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were collected at the beginning (1995 to 1999) and end (2017 to 2020) of the lifetime of a vineyard initially planted in 1991 and removed in 2021. X-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number using a negative exponential model. Early and late wood ring widths, cambium width, and scion trunk radius were correlated with 27 traits. Modeling of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay of later rings, consistently shortening ring width throughout the lifetime of the vine. Ravaz index, juice pH, photosynthetic assimilation and transpiration rates, and instantaneous water use efficiency are correlated with scion trunk radius. Ultimately, our research indicates that rootstocks modulate secondary growth over years, altering physiology and agronomic traits. Rootstocks act in similar but distinct ways from climate to modulate ring width, which borrowing techniques from dendrochronology, can be used to monitor both genetic and environmental effects in woody perennial crop species.

The Expression of Aroma Components and Related Genes in Merlot and Marselan Scion-Rootstock Grape and Wine

Rootstocks were bred and selected from several species in order to enhance the resistance against biotic or abiotic stresses. There are few studies on the effect of rootstocks on aroma and related gene expression. This study focused on the effects of three rootstocks, Kober 5BB (5BB), 1103 Paulsen (1103P), and Selection Oppenheim (SO4), on the aroma and volatile-related gene expression levels of Merlot and Marselan berries and wines. These three rootstocks reduced the total aroma content of Merlot wine. 5BB upregulated VvLoXA and showed increased C6 alcohols. 1103P enhanced the linalool from Merlot berry, with marked upregulation of VvLinNer1. Conversely, rootstocks increased the total aroma content of Marselan berry, verified by the related expression levels of volatile-related genes. For Marselan berry, 5BB and 1103P upregulated five VvGTs and nine genes from the LOX and MEP pathway. 1103P increased the contents of C6 alcohols, C6 aldehydes, and citronellol from Marselan berry. Compared to 5BB and SO4, rootstock 1103P provided berries of better quality and richer aroma volatiles to Merlot and Marselan, while all three of the rootstocks had a significant effect on scion–rootstocks.

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.

Grafting Watermelon Onto Pumpkin Increases Chilling Tolerance by Up Regulating Arginine Decarboxylase to Increase Putrescine Biosynthesis

Low temperature is a major environmental factor that severely impairs plant growth and productivity. Watermelon (Citrullus lanatus) is a chilling-sensitive crop. Grafting of watermelon onto pumpkin rootstock is an effective technique to increase the chilling tolerance of watermelon when exposure to short-time chilling stress. However, the mechanism by which pumpkin rootstock increases chilling tolerance remains poorly understood. Under 10°C/5°C (day/night) chilling stress treatment, pumpkin-grafted watermelon seedlings showed higher chilling tolerance than self-grafted watermelon plants with significantly reduced lipid peroxidation and chilling injury (CI) index. Physiological analysis revealed that pumpkin rootstock grafting led to the notable accumulation of putrescine in watermelon seedlings under chilling conditions. Pre-treat foliar with 1 mM D-arginine (inhibitor of arginine decarboxylase, ADC) increased the electrolyte leakage (EL) of pumpkin-grafted watermelon leaves under chilling stress. This result can be ascribed to the decrease in transcript levels of ADC, ornithine decarboxylase, spermidine synthase, and polyamine oxidase genes involved in the synthesis and metabolism of polyamines. Transcriptome analysis showed that pumpkin rootstock improved chilling tolerance in watermelon seedlings by regulating differential gene expression under chilling stress. Pumpkin-grafted seedling reduced the number and expression level of differential genes in watermelon scion under chilling stress. It specifically increased the up-regulated expression of ADC (Cla97C11G210580), a key gene in the polyamine metabolism pathway, and ultimately promoted the accumulation of putrescine. In conclusion, pumpkin rootstock grafting increased the chilling tolerance of watermelon through transcription adjustments, up regulating the expression level of ADC, and promoting the synthesis of putrescine, which ultimately improved the chilling tolerance of pumpkin-grafted watermelon plants.

Patterns of leaf morphological variation in Quercus frainetto Ten. growing on different soil types in Serbia

Leaf morphology is at a certain level defined by the ways in which plants adapt to different habitats, especially in large trees. In this study, morphological variations in leaf size and shape of the Hungarian oak (Quercus frainetto Ten.) growing on different soil types (lithic leptosol, vertisol, cambisol) were investigated in the central part of Serbia (Sumadija). The information on soil type was obtained using a digitalized soil map of the Republic of Serbia, while leaf traits were characterized by geometric morphometric methods. Landmark analysis and leaf measurements showed significant differences among the analyzed groups, with individuals growing on nutrient-poor, shallow soils having smaller leaves with greater lobation. The observed differences suggest that the levels of soil productivity influence variations in leaf patterns. More studies on a larger sample size and along a broader spatial scale are needed to fully understand the differences in the patterns of leaf morphological variation in Q. frainetto.

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.

Workflow to Investigate Subtle Differences in Wine Volatile Metabolome Induced by Different Root Systems and Irrigation Regimes

To allow for a broad survey of subtle metabolic shifts in wine caused by rootstock and irrigation, an integrated metabolomics-based workflow followed by quantitation was developed. This workflow was particularly useful when applied to a poorly studied red grape variety cv. Chambourcin. Allowing volatile metabolites that otherwise may have been missed with a targeted analysis to be included, this approach allowed deeper modeling of treatment differences which then could be used to identify important compounds. Wines produced on a per vine basis, over two years, were analyzed using SPME-GC-MS/MS. From the 382 and 221 features that differed significantly among rootstocks in 2017 and 2018, respectively, we tentatively identified 94 compounds by library search and retention index, with 22 confirmed and quantified using authentic standards. Own-rooted Chambourcin differed from other root systems for multiple volatile compounds with fewer differences among grafted vines. For example, the average concentration of β-Damascenone present in own-rooted vines (9.49 µg/L) was significantly lower in other rootstocks (8.59 µg/L), whereas mean Linalool was significantly higher in 1103P rootstock compared to own-rooted. β-Damascenone was higher in regulated deficit irrigation (RDI) than other treatments. The approach outlined not only was shown to be useful for scientific investigation, but also in creating a protocol for analysis that would ensure differences of interest to the industry are not missed.

Grapevine rootstocks affect growth-related scion phenotypes

Grape growers use rootstocks to provide protection against pests and pathogens and to modulate viticulture performance such as shoot growth. Our study examined two grapevine scion varieties ('Chardonnay' and 'Cabernet Sauvignon') grafted to 15 different rootstocks and determined the effect of rootstocks on eight traits important to viticulture. We assessed the vines across five years and identified both year and variety as contributing strongly to trait variation. The effect of rootstock was relatively consistent across years and varieties, explaining between 8.99% and 9.78% of the variation in growth-related traits including yield, pruning weight, berry weight and Ravaz index (yield to pruning weight ratio). Increases in yield due to rootstock were generally the result of increases in berry weight, likely due to increased water uptake by vines grafted to a particular rootstock. We demonstrated a greater than 50% increase in yield, pruning weight, or Ravaz index by choosing the optimal rootstock, indicating that rootstock choice is crucial for grape growers looking to improve vine performance.

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.

Compatibility Evaluation and Anatomical Observation of Melon Grafted Onto Eight Cucurbitaceae Species

Melon (Cucumis melo) is one of the top 10 fruits in the world, and its production often suffers due to soil-borne diseases. Grafting is an effective way to solve this problem. However, graft incompatibility between scion and rootstock limits the application of melon grafting. In this study, the melon was grafted onto eight Cucurbitaceae species (cucumber, pumpkin, melon, luffa, wax gourd, bottle gourd, bitter gourd, and watermelon), and graft compatibility evaluation and anatomical observation were conducted. Taking melon homo-grafted plants as control, melon grafted onto cucumber and pumpkin rootstocks was compatible, while melon grafted onto luffa, wax gourd, bottle gourd, bitter gourd, and watermelon rootstocks was incompatible based on the scion dry weight on day 42 after grafting. Meanwhile, we found that starch-iodine staining of scion stem base is an index to predict graft compatibility earlier, on day 14 after grafting. Further, microsection observations showed that there was more cell proliferation at graft junction of melon hetero-grafted combinations; vascular reconnection occurred in all graft combinations. However, excess callose deposited at graft junction resulted in the blockage of photosynthate transport, thus, leading to starch accumulation in scion stem base, and finally graft incompatibility. In addition, undegraded necrotic layer fragments were observed at graft junctions of melon grafted onto incompatible bitter gourd and watermelon rootstocks. The above results provide clues for the selection and breeding of compatible Cucurbitaceae rootstocks of melon and demonstrate that starch accumulation in scion base and callose deposition at graft junction is associated with melon graft compatibility.

The shape of things to come: Topological data analysis and biology, from molecules to organisms

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features-connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub-disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data-driven era where the meaningful interpretation of large data sets is a limiting factor.

Comparative Analysis of Perennial and Annual Phaseolus Seed Nutrient Concentrations

Long-term agricultural sustainability is dependent in part on our capacity to provide productive, nutritious crops that minimize the negative impacts of agriculture on the landscape. Perennial grains within an agroforestry context offers one solution: These plants produce large root systems that reduce soil erosion and simultaneously have the potential to produce nutrients to combat malnutrition. However, nutrient compositions of wild, perennial, herbaceous species, such as those related to the common bean (Phaseolus vulgaris) are not well known. In this study, seed ion and amino acid concentrations of perennial and annual Phaseolus species were quantified using ionomics and mass spectrometry. No statistical difference was observed for Zn, toxic ions (e.g., As) or essential amino acid concentrations (except threonine) between perennial and annual Phaseolus species. However, differences were observed for some nutritionally important ions. For example, Ca, Cu, Fe, Mg, Mn, and P concentrations were higher in annual species; further, ion and amino acid concentrations appear to be largely independent of each other. These results suggest variability in ion and amino acid concentrations exist in Phaseolus. As new crop candidates are considered for ecological services, nutritional quality should be optimized to maximize nutrient output of sustainable food crops.