Biology subjects

Torkamaneh, D.

Publications and source records attributed to Torkamaneh, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Volatile profiling and estimated odor-activity analysis of commercial drug-type cannabis accessions

Volatile organic compounds (VOCs) define the distinctive aroma of cannabis and critically influence consumer preference, cultivar authentication, and breeding programs. However, systematic characterization of VOC diversity across commercial drug-type cultivars remains limited. This study presents a comprehensive volatilomics-based phenotypic characterization of 165 commercial drug-type cannabis accessions using gas chromatography with flame ionization detection and mass spectrometry (GC-FID/MS). We identified 61 high-confidence VOCs assigned to three biosynthetic classes: terpenoids (n = 45), fatty acid-derived volatiles (n = 12) and amino acid-derived volatiles (n = 4), resolved into 12 subclasses. Analysis of variance revealed highly significant among-accession differences for all compounds (p < 0.001; 2 = 0.67-0.97), with repeatability estimates averaging 0.81 (range 0.50-0.95). Unsupervised clustering partitioned accessions into three distinct chemotypes (n = 90, 53, and 22), supported by principal component and t-SNE analyses. Machine learning-based feature selection identified a consensus panel of 12 discriminative compounds (camphene, -fenchene, sabinene, -terpinene, ({+/-})-limonene, -humulene, linalool, endo-fenchol, {Delta}3-carene, -thujene, {gamma}-terpinene and -phellandrene) that recovered the chemotype assignment of 32 of 33 held-out accessions. Estimated odor-activity screening ranked prenylthiol, -pinene, ({+/-})-limonene, linalool and myrcene highest among the odor-active compounds. All three chemotypes shared a prenylthiol-dominated core (67-77% of summed OAV) and were distinguished by the extent and nature of terpenoid modulation of that core: minimally modulated (Cluster ZERO), citrus-floral modulated (Cluster ONE) and pine-terpenic modulated (Cluster TWO). These findings indicate that volatile diversity in this panel can be summarized by three reproducible chemotypes, providing a quantitative basis for accession characterization and a foundation for future breeding and quality-assessment studies.

plant biology↗

bioRxiv2026

Sex chromosome-aware GWAS reveals XY-linked agronomic architecture and breeding targets in cannabis

Cannabis sativa is a dioecious crop whose male plants carry a Y chromosome entirely excluded from every genome-wide association study (GWAS) published to date, despite its direct relevance to agronomic trait variation. Here, we present the first sex chromosome-aware GWAS of cannabis, integrating both ChrX and ChrY across 145 landrace accessions and 27 agronomic traits. By combining SNP-based GWAS with sex-stratified k-mer association analysis, we identified 16 genome-wide significant markers: eight on ChrX controlling traits including stem biomass (CsWSL1; phenotypic variance explained (PVE) 56.4%) and relative growth rate (CsX8; PVE 73.6%), and eight on ChrY controlling male morphology (CsMSML1; PVE 17.18-76.1%) and male-specific flowering (CsMSFL1; PVE 84.08-87.1%). K-mer GWAS yielded 1,838 annotated signal-trait associations representing 1,082 unique genomic windows across the pseudoautosomal, hemizygous X, and male-specific Y regions. The key loci identified here provide a genomic toolkit for marker-assisted paternal selection, flowering-time synchronization, and biomass improvement across dioecious cannabis breeding systems. HIGHLIGHTFirst sex chromosome-aware GWAS of cannabis integrating ChrX and ChrY identifies 16 agronomic loci including CsMSFL1, a near-deterministic regulator of male flowering with 87% phenotypic variance explained.

Plant Biology↗

bioRxiv2026

A pistillate-biased epidermal regulatory program underlies glandular trichome development in Cannabis sativa

Glandular trichomes are specialized epidermal structures on Cannabis sativa L. inflorescences that synthesize and store cannabinoids and terpenoids, making them central to the species economic and medicinal value. Although trichome development is a multistage genetic process, its regulatory basis in C. sativa remains poorly understood, particularly with respect to sexual dimorphism and sex plasticity. Here, we combined orthologybased gene discovery with transcriptomic profiling to investigate trichome development across four floral phenotypes: female flowers (FF), male flowers (MF), induced male flowers on XX plants (IMF), and induced female flowers on XY plants (IFF). Using trichome development-related genes from Arabidopsis thaliana, a model for unicellular non-glandular trichome development, and Solanum lycopersicum, a model for multicellular glandular trichomes, we identified and mapped 53 candidate C. sativa trichome development regulator genes (CsTDRGs). The CsTDRG set did not support a simple Arabidopsis- or tomato-like model, but instead included Arabidopsis-like epidermal fate components, including MBW-related regulators and GL2, alongside tomato-like multicellular trichome regulators, including MIXTA-like, HD-ZIP IV, WOX, MTR, GRAS, and hormone-associated candidates. RNA-seq analysis showed that CsTDRG expression was more strongly associated with floral phenotype than chromosomal sex. Genes with preferential expression in pistillate tissues were CsTT8, CsMYC1/GL3, CsGL2, CsYABBY4 and CsMIXTA-like1/MYB106, whereas CsMTR1, CsGRAS9, and CsCKX3 were upregulated in male (MF and IMF) flower. These findings suggest that sexually dimorphic trichome development in C. sativa reflects differential regulation of a shared developmental toolkit that combines conserved epidermal fate components with multicellular and glandular trichome regulatory modules.

developmental biology↗

bioRxiv2026

Ethylene-Gibberellin Crosstalk Drives Phenotypic Sex Changes in Cannabis sativa

Abstract/SummarySex expression in Cannabis sativa is determined by XX/XY sex chromosomes but remains plastic, with ethylene inhibition inducing male flowers on XX plants and ethylene release inducing female flowers on XY plants. Although ethylene is a central regulator of this process, the contribution of gibberellin signaling to cannabis sex reversal remains poorly defined. Here, we reconstructed the GA biosynthesis, regulation, and signaling pathway in C. sativa and profiled GA-related gene expression during chemically induced sex reversal. Orthology-based searches identified 50 putative C. sativa GA-related genes, widely distributed across the genome, with the X chromosome harboring 11 genes, including six within the non-recombining region. Transcriptomic analyses across vegetative baseline, early post-treatment leaves, and developing flowers showed that expression profiles were broadly similar between XX and XY plants at day 0, weakly perturbed at day 1, and strongly structured by floral phenotype at day 14. Early responses were limited to downregulation of CsGA3ox1 in ethephon-treated XY plants and CsGASA1 in STS-treated XX plants. By day 14, sex reversal was associated with differential expression of key genes, including CsGA1, multiple GA20ox orthologs, CsGID1B, CsSLY2, and several GASA genes, indicating broad remodeling of GA regulation. Our findings position the GA pathway as a downstream module of ethylene-driven sex reversal in C. sativa, with GA activity tracking floral sexual identity, extending the framework of sexual plasticity beyond ethylene, and identifying candidate genes for functional validation and the development of sex-stable cultivars.

developmental biology↗

bioRxiv2026

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction

BackgroundDuckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridisation, chromosomal rearrangements, and selective gene-family remodelling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. ResultsHere we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterisation of an unresolved hybrid lineage (L. aequinoctialis x) that harbours a previously uncharacterised 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random programme of gene loss: effector-triggered immunity (ETI) components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Zostera marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones and flavonols are retained or expanded despite overall genome compaction. ConclusionThese findings illustrate how the return to aquatic environments following terrestrialisation shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.

genomics↗

bioRxiv2025

Predicting flowering time using integrated morphophysiological and genomic data with machine learning models

Indigenous Cannabis Sativa populations have adapted to diverse environments, resulting in genetic and phenotypic diversity. Understanding the mechanisms underlying flowering time variation is crucial for optimizing cultivation and breeding. This study employed a novel approach combining temporal phenotypic analysis, genomic data, and machine learning (ML) to identify key features associated with early, medium, and late flowering in cannabis landraces. We collected weekly data on six morphophysiological traits--stem diameter, height, growth rate, node number, internode length, and SPAD chlorophyll index--from 25 cannabis landrace populations 13 weeks for female plants and 11 weeks for male plants. Additionally, 145 accessions were genotyped using high-density genotyping-by-sequencing, resulting in 233,624 high-quality single nucleotide polymorphisms (SNPs). A comprehensive ML framework integrating mutual information (MI), recursive feature elimination (RFE), random forest (RF), and support vector machine (SVM), was used to investigate 234,002 features, encompassing SNPs, morphophysiological traits, and environmental factors. This approach identified 53 key features--22 genetic variants and 31 morphophysiological traits--that effectively distinguish between early, medium, and late flowering types with an accuracy of 96.6%. The identified SNPs were distributed across multiple chromosomes, including chromosomes 08, 09, and X. Notably, key loci like AutoFlower3 (CsFT3) (on chromosome 08) and CircadianFloweringLocus1 (CsCFL1) (on chromosome 09) were identified, with several SNPs located within or near annotated genes. These findings contribute significantly to the understanding of cannabis chronobiology and support the development of "smart crop" strategies by providing valuable markers for early selection and targeted breeding programs aimed at optimizing flowering time under diverse conditions. Key MessageA data-driven machine learning strategy combining genomic and dynamic phenotypic traits enables accurate classification of flowering time in diverse Cannabis landraces.

plant biology↗

bioRxiv2025

Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces

Despite its long history of cultivation and diverse applications, Cannabis sativa remains underexplored at the genomic level, particularly in landrace populations that harbor untapped genetic diversity. In this study, we investigated the genetic architecture of 145 Iranian cannabis landrace accessions, including both male and female plants, using 233K common SNPs and genome-wide association studies (GWAS). Our analysis revealed three genetically distinct subpopulations shaped by geography, climate, and traditional cultivation practices. We identified 91 significant genomic regions associated with 40 phenological, morphological, and phytochemical traits, including 15 key loci with pleiotropic effects linked to multiple traits, including flowering time, plant architecture, biomass accumulation, and cannabinoid biosynthesis. These findings highlight the complex interplay between developmental and metabolic pathways in cannabis. The high heritability of most traits and rapid linkage disequilibrium decay underscore the potential of these landraces for high-resolution mapping and genetic improvement. This work provides a valuable genomic resource for marker-assisted selection, supporting the development of improved cultivars with tailored cannabinoid profiles and agronomic traits.

plant biology↗

bioRxiv2025

Sex-Specific Ethylene Responses and Convergent Plasticity: Multi-Omic Insights into Cannabis Sexual Plasticity

Cannabis sativa L. exhibits remarkable sexual plasticity: both XX and XY individuals can undergo complete phenotypic sex reversal in response to ethylene modulation. While this phenomenon is well documented, the molecular mechanisms remain underexplored. Here, we present the first multi-omic study of hormonally induced sex change in both XX and XY Cannabis plants, integrating transcriptomic profiling, ethylene pathway metabolite quantification, and whole-genome sequencing across three genetically distinct genotypes. Treatments with silver thiosulfate (STS) and ethephon induced >80% phenotypic conversion, but transcriptomic responses diverged sharply between chromosomal sexes. We profiled 47 ethylene-related genes (ERGs) and identified 14 high-confidence candidates--including CsACS1, CsACO5, CsERF1, and CsMTN--with sex-specific, time-dependent expression patterns that support a two-phase model of plasticity: early transcriptional reprogramming followed by stabilization of new floral identities. Several candidate ERGs were in non-recombining regions of the X chromosome or absent from the Y, while most showed low nucleotide diversity, suggesting functional constraint. These findings provide a high-resolution view of ethylene-responsive sex plasticity and demonstrate that convergent floral phenotypes arise from distinct regulatory programs in XX and XY plants. Our work advances the molecular understanding of sexual plasticity in dioecious species and identifies candidate genes for the development of sex-stable cultivars in Cannabis and other crops.

developmental biology↗

bioRxiv2025

DESeq2-MultiBatch: Batch Correction for Multi-Factorial RNA-seq Experiments

RNA sequencing (RNA-seq) experiments frequently encounter batch effects that can significantly distort biological interpretations, particularly in complex, multifactorial studies where biological variables interact with experimental batch conditions. Existing batch correction tools primarily address technical variability and often neglect these critical interaction effects, resulting in incomplete adjustments. To address this gap, we introduce DESeq2-MultiBatch, a novel, lightweight batch correction method implemented entirely within the DESeq2 analytical framework. Unlike conventional approaches, DESeq2-MultiBatch directly leverages DESeq2s internal model estimates to correct raw gene count data, accurately adjusting for experimental batch effects, including interactions with biological variables. Here, we demonstrate that DESeq2-MultiBatch effectively mitigates batch-related variability while preserving genuine biological differences. Benchmarking against widely used methods highlights DESeq2-MultiBatch as a robust, practical solution for improving exploratory data visualization and downstream analyses in multifactorial RNA-seq studies. Availability and implementationhttps://github.com/julienroyulaval/DESeq2-MultiBatch Contactjulien.roy.10@ulaval.ca Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

A Comparison of the Sexual Expression, Biomass, Cannabinoid Content, and Seed Production in XXX and XXY Triploid Cannabis

Cannabis is a multi-billion dollar industry reliant on unpollinated genetically female (XX) plants, as pollination reduces cannabinoid yields and flower quality. The mechanism behind the sexual expression of C. sativa is unclear. This study examines the sexual characteristics of homo- and hetero-gametic triploid cannabis plants (XX(X/Y)) to understand the role of the Y chromosome in cannabis sex determination. Heterogametic triploids were produced by crossing a male diploid C. sativa cv. Durban Poison (2n = 2x = 18 + XY) with a tetraploid female C. sativa cv. Higher Education (2n = 4x = 36 + XXXX) confirmed by flow cytometry and PCR. Measurements include fresh and dry plant weight, dry flower weight, seed counts, seed weights, and cannabinoids quantified using liquid chromatography. Results showed 44.4% of plants were XXY (n = 8), with 75% presenting a monoecious phenotype (n = 6). Of these, 50% produced predominately male flowers (n = 3), while the rest produced predominately female flowers. Plants with predominately female flowers had higher yields and cannabinoids compared to predominantly male plants. XXX genotypes outperformed XXY in several metrics. This study enhances our understanding of C. sativa sex determination and offers insight into breeding and cultivation strategies utilizing triploid cannabis.

plant biology↗

bioRxiv2024

Ethylene sensitivity assay for medicinal and fiber-type Cannabis seedlings reveals a triple-response-like phenotype

As evidence mounts for ethylenes important role in sex determination, understanding ethylene signaling in Cannabis sativa L. (cannabis) has become increasingly vital. This study investigated the response of hemp-type and drug-type Cannabis sativa seedlings to ethylene, revealing a unique paired response phenotype under dark conditions and ethephon treatment, suggesting a more specialized variation of the triple response distinct from that observed in other species. Employing a novel ethephon-based assay, this research bypassed the complexities of using gaseous ethylene, providing a more accessible method for examining ethylene responses. The results showed C. sativa seedlings exhibit marked sensitivity to ethephon at concentrations (125 mg/L, 250 mg/L, and 500 mg/L) lower than those previously reported to influence mature plants, indicating a broad ethylene responsiveness across various genetic backgrounds. Furthermore, the reversal of ethylene-induced phenotypic changes by silver thiosulfate (STS) at all concentrations tested (1, 2, and 3 mM) suggests the conservation of ethylene signaling pathways in C. sativa. Importantly these phenotypic responses were observed in both drug and hemp type cannabis. However, the absence of an exaggerated apical hook in treated seedlings potentially points to a unique regulatory mechanism in response to ethylene in achene-bearing plants. These findings, highlighted by the successful induction of ethylene-sensitive phenotypes, underscore the conserved nature of ethylene signaling in C. sativa. The results highlight the need for further investigations into the regulatory mechanisms of ethylene in cannabis, especially concerning sexual development, opening new pathways for optimized breeding and cultivation practices aimed at enhancing plant growth and reproductive strategies.

plant biology↗

bioRxiv2023

Optimizing ex-vitro one-step RUBY-equipped hairy root transformation in drug- and hemp-type Cannabis

Using synthetic biology techniques to engineer secondary metabolic pathways through hairy root transformation is one of the most advanced approaches used in research. In this study, we optimized an ex-vitro one-step hairy root transformation of the RUBY system in both drug- and hemp-type cannabis, shedding light on its potential applications in secondary metabolite production. Three different strains of A. rhizogenes including (A4, ARqual, and K599) were used. Significant variation in HR induction and transformation efficiency (TE) was observed based on A. rhizogenes strains and seed types. Drug-type seedlings exhibited the highest hairy root induction, increasing by 58.8% compared to hemp-type seedlings. Also, the A4 strain consistently demonstrated the highest transformation efficiency (75%) irrespective of genotype, while the ARqual strain yielded the lowest one (8.33%). In conclusion, our study is the first to present an ex-vitro one-step transformation of both hemp- and drug-type cannabis. In comparison to the in vitro method, our ex-vitro method is simpler, faster, and has a lower risk of contamination, making it an excellent choice for the efficient production of secondary metabolites in cannabis using the CRISPR/Cas system.

plant biology↗

bioRxiv2023

Genetic Insights into Agronomic and Morphological Traits of Drug-Type Cannabis Revealed by Genome-Wide Association Studies

Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research and industry growth. However, years of prohibition have left the cannabis research community underdeveloped and lacking knowledge about cannabis genetics and trait inheritance. To bridge this gap, we conducted a comprehensive genome-wide association study (GWAS), using a panel of 176 drug-type cannabis accessions, curated to represent the Canadian legal market. This pioneering GWAS harnessed the power of high-density genotyping-by-sequencing (HD-GBS), resulting in an exhaustive catalog of 800K genetic variants. These variants served as the bedrock for a GWAS designed to dissect the genetic foundations of nine key traits. To identify the most robust markers associated with these traits, two sophisticated statistical methodologies were used (SUPER and BLINK), ultimately identifying 33 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to a rich trove of putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These markers show great promise for revolutionizing cannabis breeding to meet diverse needs. In doing so, they lay the solid foundation for an innovative cannabis industry poised to reshape the future.

plant biology↗

bioRxiv2023

Comparative Restriction Enzyme Analysis of Methylation (CREAM) Reveals Methylome Variability Within a Clonal In Vitro Cannabis Population

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically consistent products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid production of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to assess a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

plant biology↗

bioRxiv2023

SNPLift: Fast and accurate conversion of genetic variant coordinates across genome assemblies

MotivationThe advent of high-throughput sequencing technologies and the availability of reference genomes have provided an unprecedented opportunity to discover and genotype millions of genetic variants in hundreds or even thousands of samples. Variant calling, the identification of genetic variants from raw sequencing data, is both time-consuming and computationally demanding. Currently, reference genomes are evolving very rapidly and new assembly versions come out more and more frequently. To take advantage of new or improved reference genomes, raw reads alignments, genotype calling, and filtration must typically all be redone. This is a costly and time consuming operation that is not always viable when projects are under time constraints. ResultsHere, we introduce SNPLift, a bioinformatic pipeline that can quickly transfer the coordinate of nucleotide variants (SNPs and Indels) between different versions of reference genomes. We tested SNPLift on nine SNP datasets in VCF format from different species (Homo sapiens, Arabidopsis thaliana, Coregonus clupeaformis, Medicato truncatula, Oriza sativa, Salvelinus namaycush, Solanum lycopersicum, Zea mays, and Glycine max). Depending on the species, we achieved accurate lifting of variants ranging from 92.92% to 99.69%. Importantly, SNPLift significantly reduces the computational resources and time required for variant analysis compared to performing a complete re-analysis using a new reference genome. SNPLift offers a fast and efficient solution to leverage the benefits of updated or improved reference genomes. Availability and implementationSNPLift is available at https://github.com/enormandeau/snplift with its documentation. It contains a script that runs an automated test on a small dataset, composed of 190,443 SNPs in chromosome 1 of Medicago truncatula. SNPLift uses only common tools that are easy to install and works under Linux and MacOS.

genomics↗

bioRxiv2023

Performance analysis of conventional and AI-based variant callers using short and long reads

The accurate detection of variants is essential for genomics-based studies. Currently, there are various tools designed to detect genomic variants, however, it has always been a challenge to decide which tool to use, especially when various major genome projects have chosen to use different tools. Thus far, most of the existing tools were mainly developed to work on short-read data (i.e., Illumina); however, other sequencing technologies (e.g. PacBio, and Oxford Nanopore) have recently shown that they can also be used for variant calling. In addition, with the emergence of artificial intelligence (AI)-based variant calling tools, there is a pressing need to compare these tools in terms of efficiency, accuracy, computational power, and ease of use. In this study, we evaluated the most widely used conventional and AI-based variant calling tools (BCFTools, GATK4, Platypus, DNAscope, and DeepVariant) in terms of accuracy and computational cost using both short-read and long-read data derived from three different sequencing technologies for the same set of samples from the Genome In A Bottle (GIAB) project. The analysis showed that AI-based variant calling tools supersede conventional ones for calling SNVs and INDELs using both long and short reads. In addition, we demonstrate the advantages and drawbacks of each tool while ranking them in each aspect of these comparisons. This study provides best practices for variant calling using AI-based and conventional variant callers with different types of sequencing data.

bioinformatics↗

bioRxiv2023

Soybean-SCN duel: Novel insight into Soybean's Resistant Responses to Heterodera glycines

Soybean cyst nematodes (SCN, Heterodera glycines Ichinohe) are a significant threat to soybean production globally, causing severe yield losses and necessitating the development of effective strategies to combat this devastating nematode disease. This study presents dual RNA-seq analyses of the three most common SCN-resistant lines (Plant Introduction (PI) 437654, 548402, and 88788) and the susceptible line Lee74 against the SCN HG type 1.2.5.7 to identify the mechanisms of resistance and virulence genes involved in resistance breakdown. Transcriptomic and pathway analyses reveal the activation of the phenylpropanoid pathway, MAPK signaling pathway, plant hormone signal transduction, and secondary metabolite pathways in the resistance mechanisms. PI 437654, which exhibited robust resistance (female index, FI=0%), demonstrated unique gene expression associated with cell wall reinforcement, oxidative enzymes, ROS scavengers, and Ca+2 sensors governing the salicylic acid (SA) biosynthesis process, indicating its key defense mechanism. Moreover, using different hosts with varying levels of immunity and a susceptible line provided insights into SCN pathogenesis and how H. glycine overcomes different layers of host immunity by modulating its virulence genes. This research provides novel insights into the molecular mechanisms underlying soybean-SCN interactions and identifies potential targets for developing strategies to manage this devastating nematode disease.

plant biology↗

bioRxiv2023

Exploring Ethylene-Related Genes in Cannabis sativa: Implications for Sexual Plasticity

Sexual plasticity is a phenomenon wherein organisms possess the ability to alter their phenotypic sex in response to environmental and physiological stimuli, without modifying their sex chromosomes. Cannabis sativa L., a medically valuable plant species, exhibits sexual plasticity when subjected to specific chemicals that influence ethylene biosynthesis and signaling. Nevertheless, the precise contribution of ethylene-related genes (ERGs) to sexual plasticity in cannabis remains unexplored. The current study employed Arabidopsis thaliana L. as a model organism to conduct gene orthology analysis and reconstruct the Yang Cycle, ethylene biosynthesis, and ethylene signaling pathways in C. sativa. Additionally, two transcriptomic datasets comprising male, female, and chemically induced male flowers were examined to identify expression patterns in ERGs associated with sexual determination and sexual plasticity. These ERGs involved in sexual plasticity were categorized into two distinct expression patterns: floral organ concordant (FOC) and unique (uERG). Furthermore, a third expression pattern, termed karyotype concordant (KC) expression, was proposed, which plays a role in sex determination. The study revealed that CsERGs associated with sexual plasticity are dispersed throughout the genome and are not limited to the sex chromosomes, indicating a widespread regulation of sexual plasticity in C. sativa. Key MessagePresented here are model Yang cycle, ethylene biosynthesis and signaling pathways in Cannabis sativa. C. sativa floral transcriptomes were used to predict putative ethylene-related genes involved in sexual plasticity in the species.

plant biology↗