Next Generation Sequencing (NGS) technologies allow for the collection of large amounts of genetic data from samples. In the Cannabis space, this promises to allow for Whole Genome Sequencing as a basis for in-depth understanding of what genetic traits act to direct critical characteristics, such as chemotypes, growth behaviour, and disease susceptibility and resistance. This can be further refined down for the establishment of key DNA markers of key traits to use in Marker Assisted Selection, supporting breeding programs to establish novel Cannabis varieties with desirable characteristics.
NGS technology can also be employed in the Cannabis environment for “metagenomics” to discover and assess the prevalence and significance of both known and as-yet unrecognized pathogenic microorganisms, including bacteria, fungi, viruses and viroids. As novel pathogens are identified, rapid specific and cost-effective molecular tests can be developed to allow for their monitoring and QA exclusion from nursery tissue culture stock materials to help provide Segra’s customers with the most vigorous juvenile starts, and, consequently, the best growth and product yields possible.
Most current NGS platforms rely on technologies only capable of sequencing a few hundred base pairs at a time. To cover an entire Cannabis variety genome of some ~900 million base pairs, enormous numbers of such short reads must be generated at high per-reaction cost and subsequently overlapped or “tiled” by lengthy, computationally intensive workflows to yield a final full genome sequence and any associated metagenomics data.
Segra has chosen to deploy an alternative disruptive technology known as Nanopore sequencing for its NGS platform. Not only is this platform cheaper to operate per reaction than competing technologies, but the individual read lengths generated routinely run to tens of thousands of base pairs each. This long-read capacity greatly simplifies downstream bioinformatic computational requirements and promises to deliver faster and more compete full variety genomes, with fewer gaps, phasing, and tiling errors than short-read technologies can deliver.
Segra’s Genotyping and Molecular Lab Services Division has recently installed and operationally qualified this technology. Successful preliminary results have been obtained both in generating and assembling Cannabis variety genome sequences, and in metagenomic analysis of samples to identify the full spectrum of known and novel microbiota associated with these Cannabis samples. Ongoing research will further improve on throughput, speed, and accuracy of this process and ensure Segra’s continuing leadership role in the rapidly emerging Cannabis genetic technology space.