Biology subjects

Babaei, M.

Publications and source records attributed to Babaei, M..

8 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↗

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↗

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↗

bioRxiv2022

Nonuniform structural properties of wings confer sensing advantages

Sensory feedback is essential to both animals and robotic systems for achieving coordinated, precise movements. Mechanosensory feedback, which provides information about body deformation and position in space, depends not only on the properties of sensors but also on the structure in which they are embedded. In insects, wing structure plays a particularly important role in flapping flight: in addition to generating aerodynamic forces, wings provide mechanosensory feedback necessary for guiding flight while undergoing dramatic deformations over the course of each wingbeat. However, the role that wing structure plays in determining mechanosensory information is relatively unexplored. Insect wings exhibit characteristic stiffness gradients, with greatest stiffness at the base and leading edge and lowest stiffness at the tip of the trailing edge. Additionally, wings are subject to both aerodynamic and structural damping. The sensory consequences of stiffness gradients and damping are unknown. Here we examine how both the nonuniform stiffness profile of a wing and its damping impacts sensory performance, using finite elements analysis combined with sensor placement optimization approaches. We show that wings with nonuniform stiffness exhibit several advantages over uniform stiffness wings, resulting in higher accuracy of rotation detection and lower sensitivity to the placement of sensors on the wing. Moreover, we show that higher damping generally improves the accuracy with which body rotations can be detected. These results contribute to our understanding of the evolution of the nonuniform stiffness patterns in insect wings, as well as suggest design principles for robotic systems.

neuroscience↗

bioRxiv2019

Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation

Biological and biochemical functions of immunity transcription factor NF-{kappa}B in basal metazoans are largely unknown. Herein, we characterize transcription factor NF-{kappa}B from the demosponge Amphimedon queenslandica (Aq), in the phylum Porifera. Structurally and phylogenetically, the Aq-NF-{kappa}B protein is most similar to NF-{kappa}B p100 and p105 among vertebrate proteins, with an N-terminal DNA-binding/dimerization domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile more similar to human NF-{kappa}B proteins than Rel proteins. Aq-NF-{kappa}B also resembles the mammalian NF-{kappa}B protein p100 in that C-terminal truncation results in translocation of Aq-NF-{kappa}B to the nucleus and increases its transcriptional activation activity. Overexpression of a human or sea anemone I{kappa}B kinase (IKK) can induce C-terminal processing of Aq-NF-{kappa}B in vivo, and this processing requires C-terminal serine residues in Aq-NF-{kappa}B. Unlike human NF-{kappa}B p100, however, the C-terminal sequences of Aq-NF-{kappa}B do not effectively inhibit its DNA-binding activity when expressed in human cells. Tissue of another demosponge, a black encrusting sponge, contains NF-{kappa}B site DNA-binding activity and an NF-{kappa}B protein that appears mostly processed and in the nucleus of cells. NF-{kappa}B DNA-binding activity and processing is increased by treatment of sponge tissue with LPS. By transcriptomic analysis of A. queenslandica we identified likely homologs to many upstream NF-{kappa}B pathway components. These results present a functional characterization of the most ancient metazoan NF-{kappa}B protein to date, and show that many characteristics of mammalian NF-{kappa}B are conserved in sponge NF-{kappa}B, but the mechanism by which NF-{kappa}B functions and is regulated in the sponge may be somewhat different.

cell biology↗

bioRxiv2018

CRISPR/Cas9-based Editing of a Sensitive Transcriptional Regulatory Element to Achieve Cell Type-Specific Knockdown of the NEMO Scaffold Protein

The use of alternative promoters for the cell type-specific expression of a given mRNA/protein is a common cell strategy. NEMO is a scaffold protein required for canonical NF-{kappa}B signaling. Transcription of the NEMO gene is primarily controlled by two promoters: one (promoter B) drives NEMO transcription in most cell types and the second (promoter A) is largely responsible for NEMO transcription in liver cells. Herein, we have used a CRISPR/Cas9-based approach to disrupt a core sequence element of promoter B, and this genetic editing essentially eliminates expression of NEMO mRNA and protein in 293T human kidney cells. By cell subcloning, we have isolated targeted 293T cell lines that express no detectable NEMO protein, have defined genomic alterations at promoter B, and do not support canonical NF-{kappa}B signaling in response to treatment with tumor necrosis factor (TNF). Nevertheless, non-canonical NF-{kappa}B signaling is intact in these NEMO-deficient cells. Expression of ectopic NEMO in the edited cells restores downstream NF-{kappa}B signaling in response to TNF. Targeting of the promoter B element does not substantially reduce NEMO expression (from promoter A) in the human SNU-423 liver cancer cell line. We have also used homology directed repair (HDR) to fix the promoter B element in a 293T cell clone. Overall, we have created a strategy for selectively eliminating cell type-specific expression from an alternative promoter and have generated 293T cell lines with a functional knockout of NEMO. The implications of these findings for further studies and for therapeutic approaches to target canonical NF-{kappa}B signaling are discussed.

molecular biology↗