Cannabis (Cannabis sativa L.) stands as a historically significant and culturally important plant, embodying economic, social, and medicinal relevance for human societies. However, years of prohibition and stigmatization have hindered the cannabis research community, which is hugely undersized and suffers from a scarcity of understanding of cannabis genetics and how key traits are expressed or inherited. In this study, we conducted a comprehensive phenotypic characterization of 176 drug-type cannabis accessions, representative of Canada’s legal market. We assessed germination methods, evaluated various traits including agronomic, morphological, and cannabinoid profiles, and uncovered significant variation within this population. Notably, the yield displayed a negative correlation with maturity-related traits but a positive correlation with the fresh biomass. Additionally, the potential THC content showed a positive correlation with maturity-related traits but a negative correlation with the yield. Significant differences were observed between the plants derived from regular female seeds and feminized seeds, as well as between the plants derived from cuttings and seeds for different traits. This study advances our understanding of cannabis cultivation, offering insights into germination practices, agronomic traits, morphological characteristics, and biochemical diversity. These findings establish a foundation for precise breeding and cultivar development, enhancing cannabis’s potential in the legal market.

Differential gene expression profiles of various cannabis calli including non-embryogenic and embryogenic (i.e., rooty and embryonic callus) were examined in this study to enhance our understanding of callus development in cannabis and facilitate the development of improved strategies for plant regeneration and biotechnological applications in this economically valuable crop. A total of 6118 genes displayed significant differential expression, with 1850 genes downregulated and 1873 genes upregulated in embryogenic callus compared to non-embryogenic callus. Notably, 196 phytohormone-related genes exhibited distinctly different expression patterns in the calli types, highlighting the crucial role of plant growth regulator (PGRs) signaling in callus development. Furthermore, 42 classes of transcription factors demonstrated differential expressions among the callus types, suggesting their involvement in the regulation of callus development. The evaluation of epigenetic-related genes revealed the differential expression of 247 genes in all callus types. Notably, histone deacetylases, chromatin remodeling factors, and EMBRYONIC FLOWER 2 emerged as key epigenetic-related genes, displaying upregulation in embryogenic calli compared to non-embryogenic calli. Their upregulation correlated with the repression of embryogenesis-related genes, including LEC2, AGL15, and BBM, presumably inhibiting the transition from embryogenic callus to somatic embryogenesis. These findings underscore the significance of epigenetic regulation in determining the developmental fate of cannabis callus. Generally, our results provide comprehensive insights into gene expression dynamics and molecular mechanisms underlying the development of diverse cannabis calli. The observed repression of auxin-dependent pathway-related genes may contribute to the recalcitrant nature of cannabis, shedding light on the challenges associated with efficient cannabis tissue culture and regeneration protocols.

Genome‐wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a given trait in crop species. Assessing genetic variants other than single‐nucleotide polymorphisms (SNPs) could alleviate this problem. In this study, we tested the potential of structural variant (SV)‐ and k ‐mer‐based GWAS in soybean by applying these methods as well as conventional SNP/indel‐based GWAS to 13 traits. We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k ‐mer‐based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k ‐mer‐based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to Phytophthora sojae . In our dataset, SV‐based GWAS did not add value compared to k ‐mer‐based GWAS and may not be worth the time and computational resources invested. Despite promising results, significant challenges remain regarding the downstream analysis of k ‐mer‐based GWAS. Notably, better methods are needed to associate significant k ‐mers with sequence variation. Our results suggest that coupling k ‐mer‐ and SNP/indel‐based GWAS is a powerful approach for discovering candidate genes in crop species.

In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [ Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome‐wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole‐genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single‐nucleotide polymorphism (SNP) including Glyma.15G217100 , which encodes a major latex protein (MLP)‐like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant ( R ) allele compared with those carrying the susceptible ( S ) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker‐assisted selection.

SUMMARY: Cannabis sativa L. exhibits pronounced sexual plasticity in which both XX and XY plants can undergo floral phenotypic sex reversal in response to ethylene modulation, yet the underlying molecular mechanisms remain poorly defined. Here, we present the most extensive multi‐omic analysis of ethylene‐induced sex change in C. sativa to date, integrating over 130 RNA‐seq libraries, ethylene pathway metabolite quantification, and whole‐genome sequencing across three XX and XY genotypes. Treatments with silver thiosulfate and ethephon induced more than 80% phenotypic conversion, but transcriptomic responses diverged sharply between XX and XY plants. Profiling 47 ERGs revealed 14 high‐confidence candidates, including CsACS1 , CsACO5 , CsERF1 , and CsMTN , with sex‐specific and temporal expression patterns that show dynamic ethylene mediation of plasticity. Early transcriptional activation occurred prior to the emergence of flowers, within 18 h of sex‐change treatments and the photoperiod‐induced transition to flowering. As opposite‐sex floral tissues emerged, ethylene‐related gene expression shifted accordingly within developing floral organs, with distinct sets of genes stabilizing the opposite‐sex phenotype in XX and XY plants. Several candidates were located in non‐recombining regions of the X chromosome or were absent from the Y chromosome, and most exhibited low nucleotide diversity, consistent with functional constraint. These results provide a high‐resolution view of ethylene‐responsive sexual plasticity in cannabis and show that the shared capacity for sex reversal in XX and XY plants is implemented through distinct regulatory trajectories that produce opposite‐sex floral phenotypes. This work expands the mechanistic understanding of sex expression in dioecious species and identifies candidate genes relevant to the development of sex‐stable cultivars.