What topics does this cannabis study cover?

This study covers research on: Endocannabinoid, Terpenes, Neuroprotection.

Where was this research published?

Published in G3 (Bethesda, Md.) on December 30, 2025.

Scientific illustration for A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.

Endocannabinoid Terpenes Neuroprotection

A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.

G3 (Bethesda, Md.) • December 30, 2025 • Highly Relevant

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AI Summary

Researchers have developed a new technique for understanding the genetic blueprint of cannabis plants, focusing on two popular cultivars: Punto Rojo (a Colombian landrace) and Cherry Pie #16 (a Colorado CBD-rich clone). Using long-read DNA sequencing technology from Oxford Nanopore, they separated out the genetic material inherited from each parent plant in an F1 hybrid cross. This "trio-binning" approach allowed them to create high-quality, complete genome assemblies while keeping the paternal and maternal genetic contributions separate—something that's valuable for breeders wanting to understand which traits come from which parent.

The study revealed significant structural variations and copy number differences between the two cultivars, particularly in genes related to disease resistance and the production of cannabinoids and other secondary metabolites (the compounds that give cannabis its therapeutic and recreational effects). These genetic differences could explain why different cannabis strains produce different levels of CBD, THC, and other beneficial compounds, and why some strains might be more resistant to diseases than others. The researchers demonstrated that this approach is cost-effective and practical, requiring only a single DNA sequencing run with modest coverage depth (18x per haplotype).

For the cannabis industry and researchers, this work provides a blueprint for understanding the genetic basis of important traits like CBD production and disease resistance. By identifying the structural variations between cultivars, breeders can better understand which genetic factors control the characteristics they're interested in, potentially leading to faster development of improved varieties. This genetic insight could help explain phenotypic variation across different cannabis strains and support more informed breeding decisions.

💡 Key Findings

Trio-binning approach successfully separated maternal and paternal genome contributions from an F1 cannabis hybrid cross, enabling high-quality haplotype-resolved genome assemblies with good contiguity using modest sequencing coverage (18x per haplotype)

High

95%

Extensive structural variations and copy number differences exist between Punto Rojo and Cherry Pie cultivars, particularly in genes related to disease resistance and secondary metabolite synthesis

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90%

The identified genetic structural variations likely contribute to phenotypic differences between cannabis strains, including differences in cannabinoid production and disease resistance traits

High

85%

Trio-binning is a cost-effective approach for cannabis genome analysis that requires only a single PromethION flow cell sequencing run, making it accessible for breeding programs

High

90%

📄 Original Abstract

With the advent of long-read DNA sequencing technologies, assembling eukaryotic genomes has become routine; however, properly phasing the maternal and paternal contributions, which is of great value for breeding programs, remains technically challenging. Here, we use the trio-binning approach to separate Oxford Nanopore reads derived from a Cannabis F1 wide cross, made between the Colombian landrace Punto Rojo and the Colorado CBD clone Cherry Pie #16. Reads were obtained from a single PromethION flow cell, generating assemblies with coverage of just 18 × per haplotype, but with good contiguity and gene completeness, demonstrating that it is a cost-effective approach for genome-wide and high-quality haplotype phasing. Evaluated through the lenses of disease resistance and secondary metabolite synthesis, both being traits of interest for the Cannabis industry, we report copy number and structural variation that, as has recently been shown for other major crops, may contribute to phenotypic variation along several relevant dimensions.

Paper Type

📄 Research

Publication

Journal: G3 (Bethesda, Md.)
Published: December 30, 2025
PMID: 41467882
DOI: 10.1093/g3journal/jkaf286

Authors (3)

Brett Pike Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Distrito Capital 110231, Colombia.
Alexander Kozik Genome Center and Department of Plant Sciences, University of California, Davis, California, CA 95616, United States.
Wilson Terán Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Distrito Capital 110231, Colombia.