Emery, B. F. | Search bioRxiv

bioRxiv2025

Unraveling Cross-Cellular Communication in Cannabis sativa Sex Determination: A Network Ontology Transcript Annotation (Nota) Analysis.

Cannabis sativa L. (marijuana, hemp, cannabis) is an angiosperm species currently evolving sex chromosomes. Genetic mechanisms, primarily an XY chromosome system, dictate cannabis sex expression in dioecious populations. However, sexual expression is also governed by the interplay of hormone regulatory gene networks, influenced by both genetic and environmental factors. Within the species, some populations exhibit dioecy, monoecy, or a gradient of both. Dioecious individuals produce exclusively male or female flowers, while monoecious plants bear both male and female flowers. Remarkably, through interruption of phytohormone signal transduction via abiotic stressors, genetically male or female cannabis are able to produce flowers of the opposite sex. Previous transcriptomic analysis have identified genes associated with masculinization through the application of phytohormone signal disruption using silver thiosulfate treatment. We analyzed transcriptomic data from cannabis treated with colloidal silver to similarly induce masculinization. Using Nota (Network Ontology Transcript Annotation), a multilayer network analysis (random walk with restart) tool, we identified candidate genes involved in sex-determination. Nota and a companion program Jack facilitate multi-layer network analyses, enabling discovery and annotation of gene-trait associations. Our findings highlight Notas robust application to enrich the genetic architecture of complex traits, particularly in non-model systems like cannabis, and complex traits such as sex determination. Our analyses identified genes associated with cell wall morphogenesis and embryogenic tissue homeostasis, indicating that silver ion treatment perturbs phytohormone signal transduction through metal ion imbalance. In this reproductive strategy, cannabis is able to make use of its widely investigated sex-determining genetic architecture to navigate transient changes in co-expression and cross-cellular signaling driving embryogenic cell wall re-patterning.

systems biology↗

bioRxiv2020

Global relationships between crop diversity and nutritional stability

Nutritional stability - a food systems capacity to provide sufficient nutrients despite disturbance - is a critical feature of sustainable agriculture, especially in light of ongoing climate change. Yet, measuring nutritional stability has proven challenging. Addressing this challenge will help identify resilient food systems, detect shortcomings in nutrient availability, and evaluate if stability-focused interventions actually work. We develop a novel approach that uses 55 years of crop data across 184 countries to assemble over 22,000 bipartite crop-nutrient networks. We then quantify the tolerance of these networks to disturbance simulated via sequential crop loss (Fig. 1) and evaluate patterns of crop diversity and nutritional stability across countries, over time and between crop supply scenarios (imports versus in country production). We observe a positive, saturating relationship between crop diversity and nutritional stability across countries; however there is substantial variability between countries over time. Next, despite crop diversity gains since 1961, nutritional stability has remained stagnant or decreased in all regions except Asia. A decline in the average number of nutritional links per network (range: -3 to -18% across regions) and the aforementioned saturating relationship explain this counter-intuitive finding. Finally, we find that imports increase crop diversity and improve or sustain stability, indicating that nutrient availability is market exposed in many countries, particularly developing states. Although applied globally, our approach is applicable across levels of organization, from household intake to sub-national production, and provides a way forward for understanding the contributions of crop diversity to the stability of nutrients available for human consumption. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/227520v1_fig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@d6712forg.highwire.dtl.DTLVardef@a0cc45org.highwire.dtl.DTLVardef@c2d6bforg.highwire.dtl.DTLVardef@1a0a459_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO A new approach for understanding nutritional stability. The robustness of networks, such as a crop-nutrient network (a), can be gauged through assembling attack tolerance curves (b & c), whereby as nodes (i.e. crops) are eliminated constituent nutrients are lost. Of course, removal order matters (b vs c), therefore permuted combinations of crop loss generate average loss curves (see Methods). We use the area under this curve as our measure of nutritional stability (RN). Crop-nutrient networks with few redundant connections are susceptible to crop removal and can experience rapid nutrient loss (e.g. Maldives; d), whereas countries with a diverse food supply are more robust (e.g. China; e). This unitless metric is generalizable across different levels of aggregation (e.g. individual, household, community, national food system). C_FIG

ecology↗