Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

Cannabis Expression Atlas: a comprehensive resource for integrative analysis of Cannabis sativa L. gene expression

Cannabis sativa L., a plant originating from Central Asia, is a versatile crop with applications spanning textiles, construction, pharmaceuticals, and food products. This study aimed to compile and analyze publicly available Cannabis RNA-Seq data and develop an integrated database tool to help advance Cannabis research in various topics such as fiber production, cannabinoid biosynthesis, sex determination, and plant development. We identified 515 publicly available RNA-Seq samples that, after stringent quality control, resulted in a high-quality dataset of 394 samples. Utilizing the Jamaican Lion genome as reference, we constructed a comprehensive database and developed the Cannabis Expression Atlas (https://cannatlas.venanciogroup.uenf.br/), a web application for visualization of gene expression, annotation, and functional classification. Key findings include the quantification of 27,640 Cannabis genes and their classification into seven expression categories: not-expressed, low-expressed, housekeeping, tissue-specific, group-enriched, mixed, and expressed-in-all tissues. The study revealed substantial variability and coherence in gene expression across different tissues and chemotypes. We found 2,382 tissue-specific genes, including 177 transcription factors. The Cannabis Expression Atlas constitutes a valuable tool for exploring gene expression patterns and offers insights into Cannabis biology, supporting research in plant breeding, genetic engineering, biochemistry, and functional genomics.

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research

Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. The Tripal platform was used to host public genome assemblies, gene annotations, quantitative trait loci and genetic maps, gene and protein expression data, metabolic profiles and their sample attributes. Single nucleotide polymorphisms were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service Application Programming Interface (API), developed on top of existing Tripal modules, returns generic tables of samples, properties and values. Use cases demonstrate the API's utility for various omics analyses, enabling researchers to perform multi-omics analyses efficiently.

Availability and implementation

The web portal can be accessed at www.icgrc.info.

Assessing the adaptive role of cannabidiol (CBD) in Cannabis sativa defense against cannabis aphids

Cannabis sativa is known for having unique specialized or secondary metabolites, cannabinoids that are derived from an extension of the terpene pathway in the Cannabis lineage and includes more than 100 other similar metabolites. Despite the assumption that cannabinoids evolved as novel herbivory defense adaptations, there is limited research addressing the role of cannabinoids in C. sativa responses to insect herbivores. Here we investigated the role of cannabidiol (CBD), the predominant cannabinoid in hemp, in plant defense against cannabis aphid (Phorodon cannabis), one of the most damaging pests of hemp. We hypothesize that insect feeding may induce changes in cannabinoids as an adaptive strategy for defense. We found that mean fecundity, net reproductive rate (R0) and adult longevity of cannabis aphids was reduced on the high cannabinoid cultivar compared to the low- cannabinoid cultivar in whole plant assays. In contrast, supplementation of CBD in artificial feeding assays increased aphid fecundity from day 1 to day 3. Additionally, aphid feeding did not impact cannabinoid levels in leaf tissues with the exception of Δ9-tetrahydrocannabinol (THC). This suggests that other cannabinoids and/or metabolites such as terpenes are causing the observed decrease in aphid performance in the whole plant assays. In addition to cannabinoids, C. sativa also possesses a range of defense mechanisms via phytohormone signaling pathways that are well described in other plant species. Indeed, cannabis aphid feeding significantly increased levels of the major phytohormones, salicylic acid, jasmonic acid, and abscisic acid, which are known to be involved in plant defense responses against aphid species. These results highlight the interplay between cannabinoid synthesis and phytohormone pathways and necessitate further investigation into this complex interaction.

Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple (Acer saccharum Marshall) saplings

Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of the United States and is economically important for its hardwood and syrup production. Sugar maple trees are highly vulnerable to changing climatic conditions, especially drought, so understanding the physiological, biochemical, and molecular responses is critical. The sugar maple saplings were subjected to drought stress for 7, 14, and 21 days and physiological data collected at 7, 14, and 21 days after stress (DAS) showed significantly reduced chlorophyll and Normalized Difference Vegetation Index with increasing drought stress time. The drought stress-induced biochemical changes revealed a higher accumulation of malondialdehyde, proline, and peroxidase activity in response to drought stress. Transcriptome analysis identified a total of 14,099 differentially expressed genes (DEGs); 328 were common among all stress periods. Among the DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, and ERF), chloroplast-related and stress-responsive genes such as peroxidases, membrane transporters, kinases, and protein detoxifiers were predominant. GO enrichment and KEGG pathway analysis revealed significantly enriched processes related to protein phosphorylation, transmembrane transport, nucleic acids, and metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, and carotenoid biosynthesis in response to drought stress. Time-series transcriptomic analysis revealed changes in gene regulation patterns in eight different clusters, and pathway analysis by individual clusters revealed a hub of stress-responsive pathways. In addition, qRT-PCR validation of selected DEGs revealed that the expression patterns were consistent with transcriptome analysis. The results from this study provide insights into the dynamics of physiological, biochemical, and gene responses to progressive drought stress and reveal the important stress-adaptive mechanisms of sugar maple saplings in response to drought stress.

Expression of Genes Involved in ABA and Auxin Metabolism and LEA Gene during Embryogenesis in Hemp

The level of phytohormones such as abscisic acid (ABA) and auxins (Aux) changes dynamically during embryogenesis. Knowledge of the transcriptional activity of the genes of their metabolic pathways is essential for a deeper understanding of embryogenesis itself; however, it could also help breeding programs of important plants, such as Cannabis sativa, attractive for the pharmaceutical, textile, cosmetic, and food industries. This work aimed to find out how genes of metabolic pathways of Aux (IAA-1, IAA-2, X15-1, X15-2) and ABA (PP2C-1) alongside one member of the LEA gene family (CanLea34) are expressed in embryos depending on the developmental stage and the embryo cultivation in vitro. Walking stick (WS) and mature (M) cultivated and uncultivated embryos of C. sativa cultivars 'KC Dora' and 'USO 31' were analyzed. The RT-qPCR results indicated that for the development of immature (VH) embryos, the genes (IAA-1, IAA-2) are likely to be fundamental. Only an increased expression of the CanLea34 gene was characteristic of the fully maturated (M) embryos. In addition, this feature was significantly increased by cultivation. In conclusion, the cultivation led to the upsurge of expression of all studied genes.

Effects of short-term environmental stresses on the onset of cannabinoid production in young immature flowers of industrial hemp (Cannabis sativa L.)

BACKGROUNDS

Cannabis sativa L. produces at least 120 cannabinoids. Although genetic variation is the main factor in cannabinoid production, the effects of short-term environmental stresses in the early flowering stage remains largely unknown.

METHODS

To investigate the effects of short-term environmental stresses on the onset of cannabinoid production in young immature flowers, a hemp variety, Green-Thunder (5-8% CBD/mg of dry weight), was treated with mechanical damage, insect herbivory, extreme heat, or drought stress for 5-7 days during the first 2 weeks of flowering. Three hemp tissues, including flowers, leaves, and stems, were collected from hemp grown under these stress conditions at multiple time points during the first 2 weeks after transition to the short photoperiod and analyzed using high pressure liquid chromatography to quantify phytocannabinoids including cannabigerolic acid (CBGA), cannabigerol (CBG), cannabidiolic acid (CBDA), cannabidiol (CBD), Δ-tetrahydrocannabinolic acid (THCA), Δ-tetrahydrocannabinol (THC), and cannabinol (CBN).

RESULTS

The 5 days of mechanical wounding did not affect the production of any of the cannabinoids during the initial stage of flowering. However, after 5 days of herbivore treatment, there was a significant difference in concentration between day 1 and day 6 of CBGA (control: 308 μg/g; treatment - 24 μg/g), CBG (control: 69 μg/g; treatment: 52 μg/g), and CBD (control: 755 μg/g; treatment: 194 μg/g) between the control and treatment plants. The 7 days of heat treatment at 45-50 oC significantly reduced the production of CBGA during this observed window (control: 206 μg/g; treatment: 182 μg/g) and CBG (control: 21 μg/g; treatment: - 112 μg/g). Notably, the largest change was observed after 7 days of drought stress, when plants showed a 40% greater accumulation of CBG (control: 336 μg/g; treatment: 622 μg/g), and a significant decrease (70-80%) in CBD (control: 1182 μg/g; treatment: 297 μg/g) and THC amounts (control: 3927 μg/g; treatment: 580 μg/g).

CONCLUSIONS

Although this observation is limited in the early flowering stage, the common field stresses are adequate to induce changes in the cannabinoid profiles, particularly drought stress being the most impactful stress for hemp flower initiation with the altering the cannabinoid production by decreasing CBD and THC accumulation while increasing CBG by 40%.

Selection and validation of reference genes for normalization of qRT-PCR data to study the cannabinoid pathway genes in industrial hemp

There has been significant interest in researching the pharmaceutical applications of Industrial hemp since its legalization three years ago. The crop is mostly dioecious and known for its production of phytocannabinoids, flavonoids, and terpenes. Although many scientific reports have showed gene expression analysis of hemp through OMICs approaches, unreliable reference genes for normalization of qRT-PCR data make it difficult to validate the OMICs data. Four software packages: geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the differential gene expression patterns of 13 candidate reference genes under osmotic, heavy metal, hormonal, and UV stresses. EF-1α ranked as the most stable reference gene across all stresses, TUB was the most stable under osmotic stress, and TATA was the most stable under both heavy metal stress and hormonal stimuli. The expression patterns of two cannabinoid pathway genes, AAE1 and CBDAS, were used to validate the reliability of the selected reference genes. This work provides useful information for gene expression characterization in hemp and future research in the synthesis, transport, and accumulation of secondary metabolites.

Response of essential oil hemp (Cannabis sativa L.) growth, biomass, and cannabinoid profiles to varying fertigation rates

Five essential oil hemp (Cannabis sativa L.) cultivars (Cherry Blossom, Cherry Blossom (Tuan), Berry Blossom, Cherry Wine, and Cherry Blossom × Trump) were treated with six fertigation treatments to quantify the effects of synthetic fertilizer rates and irrigation electrical conductivity on plant growth, biomass accumulation, and cannabinoid profiles. Irrigation water was injected with a commercial 20-20-20 fertilizer at rates of 0, 50, 150, 300, 450, and 600 ppm nitrogen equating to 0.33 (control), 0.54, 0.96, 1.59, 2.22, and 2.85 dS m-1, respectively. Plants were grown under artificial lighting (18 hr) to maintain vegetative growth for eight weeks, followed by an eight-week flowering period. High linear relationship between chlorophyll concentrations and SPAD-502 measurements validated the utilization of SPAD meters to rapidly identify nutrient deficiency in essential oil hemp. Cultivars expressed significant variation in plant height and cannabinoid profiles (% dry mass), in concurrence with limited biomass and cannabinoid (g per plant) yield variation. Cherry Blossom was the best performing cultivar and Cherry Wine was the least productive. Variation in plant growth, biomass, and cannabinoid concentrations were affected to a greater extent by fertilizer rates. Optimal fertilizer rates were observed at 50 ppm N, while increased fertilizer rates significantly reduced plant growth, biomass accumulation, and cannabinoid concentrations. Increased fertilizer rates (> 300 ppm N) resulted in compliant THC levels (< 0.3%), although when coupled with biomass reductions resulted in minimal cannabinoid yields. Additionally, CBD concentration demonstrated higher sensitivity to increased fertilizer rates (> 300 ppm N) compared to THC and CBG (> 450 ppm N). The results of this study can serve as a guide when using fertigation methods on essential oil hemp cultivars; although results may differ with cultivar selection, environmental conditions, and management practices.

Physiological and transcriptome analyses for assessing the effects of exogenous uniconazole on drought tolerance in hemp (Cannabis sativa L.)

Uniconazole (S-(+)-uniconazole), a plant growth retardant, exerts key roles in modulating growth and development and increasing abiotic stress tolerance in plants. However, the underlying mechanisms by which uniconazole regulates drought response remain largely unknown. Here, the effects of exogenous uniconazole on drought tolerance in hemp were studied via physiological and transcriptome analyses of the drought-sensitive industrial hemp cultivar Hanma No. 2 grown under drought stress. Exogenous uniconazole treatment increased hemp tolerance to drought-induced damage by enhancing chlorophyll content and photosynthesis capacity, regulating activities of enzymes involved in carbon and nitrogen metabolism, and altering endogenous hormone levels. Expression of genes associated with porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins, photosynthesis, starch and sucrose metabolism, nitrogen metabolism, and plant hormone signal transduction were significantly regulated by uniconazole compared with that by control (distilled water) under drought stress. Numerous genes were differentially expressed to increase chlorophyll content, enhance photosynthesis, regulate carbon-nitrogen metabolism-related enzyme activities, and alter endogenous hormone levels. Thus, uniconazole regulated physiological and molecular characteristics of photosynthesis, carbon-nitrogen metabolism, and plant hormone signal transduction to enhance drought resistance in industrial hemp.

Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco.

Impact of Nitrogen Nutrition on Cannabis sativa: An Update on the Current Knowledge and Future Prospects

Nitrogen (N) availability represents one of the most critical factors affecting cultivated crops. N is indeed a crucial macronutrient influencing major aspects, from plant development to productivity and final yield of lignocellulosic biomass, as well as content of bioactive molecules. N metabolism is fundamental as it is at the crossroad between primary and secondary metabolic pathways: Besides affecting the synthesis of fundamental macromolecules, such as nucleic acids and proteins, N is needed for other types of molecules intervening in the response to exogenous stresses, e.g. alkaloids and glucosinolates. By partaking in the synthesis of phenylalanine, N also directly impacts a central plant metabolic 'hub'-the phenylpropanoid pathway-from which important classes of molecules are formed, notably monolignols, flavonoids and other types of polyphenols. In this review, an updated analysis is provided on the impact that N has on the multipurpose crop hemp (Cannabis sativa L.) due to its renewed interest as a multipurpose crop able to satisfy the needs of a bioeconomy. The hemp stalk provides both woody and cellulosic fibers used in construction and for biocomposites; different organs (leaves/flowers/roots) are sources of added-value secondary metabolites, namely cannabinoids, terpenes, flavonoids, and lignanamides. We survey the available literature data on the impact of N in hemp and highlight the importance of studying those genes responding to both N nutrition and abiotic stresses. Available hemp transcriptomic datasets obtained on plants subjected to salt and drought are here analyzed using Gene Ontology (GO) categories related to N metabolism. The ultimate goal is to shed light on interesting candidate genes that can be further studied in hemp varieties growing under different N feeding conditions and showing high biomass yield and secondary metabolite production, even under salinity and drought.

Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis

Cannabinoids are the main medicinal compounds of interest in the plant Cannabis sativa, that are primarily synthesised in the glandular trichomes; found on female floral buds. The content, composition and yield of secondary metabolites (cannabinoids and terpenoids) is influenced by the plant's genetics and environment. Some initial gene expression experiments have been performed from strains of this plant species that contrasted in cannabinoid production, however the present knowledge about detailed trichome transcriptomics in this species is limited. An extensive transcriptome atlas was generated by RNA sequencing using root, shoot, flower and trichome tissues from a female plant strain (Cannbio-2) and was enhanced with the addition of vegetative and reproductive tissues from a male cannabis plant. Differential gene expression analysis identified genes preferentially expressed in different tissues. Detailed trichomics was performed from extractions specifically from glandular trichomes as well as female floral tissues at varying developmental stages, to identify stage-specific differentially expressed genes. Candidate genes involved in terpene and cannabinoid synthesis were identified and the majority were found to have an abundant expression in trichomes. The comprehensive transcriptome is a significant resource in cannabis for further research of functional genomics to improve the yield of specialised metabolites with high pharmacological value.