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 lagging behind in understanding Cannabis genetics and trait inheritance compared to other major crops. To address this gap, we conducted a comprehensive genome-wide association study (GWAS) of nine key agronomic and morphological traits, using a panel of 176 drug-type Cannabis accessions from the Canadian legal market. Utilizing high-density genotyping-by-sequencing (HD-GBS), we successfully generated dense genotyping data in Cannabis, resulting in a catalog of 800 K genetic variants, of which 282 K common variants were retained for GWAS analysis. Through GWAS analysis, we identified 18 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These findings lay a solid foundation for an innovative cannabis research, leveraging genetic markers to inform breeding programs aimed at meeting diverse needs in the industry.

Exploring ethylene-related genes in Cannabis sativa: implications for sexual plasticity

KEY MESSAGE

Presented 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. 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.

k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean

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.

Comprehensive Phenotypic Characterization of Diverse Drug-Type Cannabis Varieties from the Canadian Legal Market

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.

Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis

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.

Optimization of in vitro and ex vitro Agrobacterium rhizogenes-mediated hairy root transformation of soybean for visual screening of transformants using RUBY

In vitro and ex vitro Agrobacterium rhizogenes-mediated hairy root transformation (HRT) assays are key components of the plant biotechnology and functional genomics toolkit. In this report, both in vitro and ex vitro HRT were optimized in soybean using the RUBY reporter. Different parameters including A. rhizogenes strain, optical density of the bacterial cell culture (OD₆₀₀), co-cultivation media, soybean genotype, explant age, and acetosyringone addition and concentration were evaluated. Overall, the in vitro assay was more efficient than the ex vitro assay in terms of the percentage of induction of hairy roots and transformed roots (expressing RUBY). Nonetheless, the ex vitro technique was deemed faster and a less complicated approach. The highest transformation of RUBY was observed on 7-d-old cotyledons of cv. Bert inoculated for 30 minutes with the R1000 resuspended in ¼ B5 medium to OD₆₀₀ (0.3) and 150 µM of acetosyringone. The parameters of this assay also led to the highest percentage of RUBY through two-step ex vitro hairy root transformation. Finally, using machine learning-based modeling, optimal protocols for both assays were further defined. This study establishes efficient and reliable hairy root transformation protocols applicable for functional studies in soybean.

3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a "standard" ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500-1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.

The SoyaGen Project: Putting Genomics to Work for Soybean Breeders

The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.

Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL

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.