Forging a New Frontier in Cannabis

Written By: Christopher Pauli

Our lives depend on plants, for food, clothes and beauty. And there are so many mysteries to explore. For instance:

Why can a plant produce both male and female flowers when it appears genetically to be female?

Can we determine the tissue-specific gene expression profiles of any organism?

The Agricultural Genomics Foundation sponsors a research project at the University of Colorado Boulder that focuses on transcriptomics, or the study of RNA, the next genetic frontier for the Cannabis plant. With numerous transcriptomes sequenced, AGF is aiming to expand upon its previous work in the genome to include RNA data that will help us better understand how gene expression controls the plant.

The genes expressed are called RNA, or ribonucleic acid, which collectively referred to as the transcriptome. By comparing the differences between these transcriptomes in different areas on the plant, we can understand genetically why one branch of a plant does something different than another.  This new genetic frontier is groundbreaking to be applied in Cannabis sciences since we can apply the most cutting genetics to one of the most demanded plants in the world.    

With advances in RNA-sequencing capabilities, we are able to move past DNA, which has been the focus of most genetic research to date. DNA, or the genome, encodes all of the genes you can express at any time throughout your life, and can be used to study mutations that can be predictive of disease.

Every sexual-reproducing organism inherits one copy of their genes from their mother and one from their father, that allows for either one of the two alleles, or gene copies, to be expressed depending on which one(s) they inherit; however, both alleles would be considered part of the genome.  While the genome of every cell is the same, there are some vast differences between a heart cell and a skin cell, but how is this true if they contain the same genes? This is because the mRNA, or message, that is created from the DNA to be translated into proteins varies between the cells,  and that is what determines what the cell is doing. The mRNA only includes the genes that were expressed at the time of the extraction, which RNA extractions includes other RNAs, such as tRNA and rRNA, that are isolated from the mRNA after the extraction.

So why have we looked at DNA in the past, and what can RNA tell us?  Scientists first published a journal article about RNA-sequencing in 2008; however, the progress of creating standardized protocols and benchmarks has been slow to say the least. Understanding the differences between the expressed genes of two tissues of the same plant can allow scientists to better understand the mechanism of gene expression causing the observed phenotype, or physical features. Experiments using mRNA could allow us to understand how male and female flowers are produced on the same plant (hermaphrodites), the production of secondary metabolites (cannabinoids and terpenes), and the genetic basis of many of the physical and chemical differences we observe in the Cannabis species.

There are many barriers and biases to consider when attempting to undertake an mRNA-based project. RNAases, the enzyme that degrades mRNA, are everywhere and can be difficult to remove from the clean area where the extractions take place. Furthermore, the gene expression profile in plants changes rapidly due to environmental cues, such as photoperiod fluctuation and temperature, as well as physical and chemical stresses from nutrients and soil mixtures, which also make it difficult for a consistent comparison between samples. However, by overcoming these obstacles, the Agricultural Genomics Foundation (AGF) is leading the Cannabis mRNA studies to understand the foundational sciences that underlie this magnificent plant.

With the notorious instability of RNA, other research groups have focused on the gene expression profiles of Cannabis at different time points and areas within the plant using  publicly available data produced by the University of Toronto. With this publically available data in addition to the numerous cannabis transcriptomes AGF has extracted and sequenced, we can begin to explain some of the mysteries that puzzle Cannabis scientists.

Understanding transcriptomics can let us understand why male and female flowers are produced on the same plant. We can better understand the genome that allows for breeders to be more selective and produce higher quality plants for the consumers. By applying science to Cannabis, AGF scientists are beginning to gain the ability to determine and select for any gene expressed throughout the plant.