Kannapedia – New Data Visualizations


Growers Network wanted to let breeders and geneticists know about a service provided by Medicinal Genomics, known as Kannapedia. Kannapedia allows you to compare genetic similarities between different cannabis strains to produce your ideal combination!

The following is an article produced by a contributing author. Growers Network does not endorse nor evaluate the claims of our contributors, nor do they influence our editorial process. We thank our contributors for their time and effort so we can continue our exclusive Growers Spotlight service.


Disclaimer

This Contributors article has been reproduced with permission from Medicinal Genomics. The original article can be found here.


Kannapedia – New Data Visualizations


Earlier this week, Medicinal Genomics made some exciting updates to Kannapedia, the website that houses genetic data from the cannabis cultivars sequenced with their StrainSEEK Strain Identification and Registration Service.

They added new data visualizations and genetic distance tables that make it easy to compare cannabis cultivars in the Kannapedia database. Cultivars that were sequenced with their StrainSEEK Version 2 panel now also include a table that compares them to cultivars published in Phylos Bioscience’s Open Cannabis Project.

Medicinal Genomics can do this because they designed the assay to include loci from the other public cannabis genomic datasets (Phylos, Lynch, Sawler). StrainSEEK is the only cannabis strain sequencing service that can do this.

Read more about the updates below.


New Phylotree

The targeted approach we are using for StrainSEEK delivers 25,000-50,000 SNPs across the genome with a concentrated contribution from chemotype-related genes. The higher SNP density enables Marker Assisted Selection.

This phylotree is derived using the intersecting high-quality SNPs from StrainSEEK V1 and StrainSEEK V2. The SNPs with the higher information content in StrainSEEKV1 were carried over into StrainSEEK V2 for backwards compatibility during the upgrade.

View the Phylotree here.


Strain Rarity Visualization

Each strain page now includes a Strain Rarity Visualization, which shows how distant the cultivar is from the other cultivars in the Kannapedia database.

The y-axis represents genetic distance, getting farther as you go up. The width of the visualization at any position along the y-axis shows how many strains there are in the database at that genetic distance. So, a common strain will have a more bottom-heavy shape, while uncommon and rare cultivars will have a visualization that is generally shifted towards the top.


Heterozygosity Visualization

Each Strain Page also shows how the cultivars heterozygosity compares to others in the database.

The bell curve in the heterozygosity visualization shows the distribution of heterozygosity levels for cannabis cultivars in the Kannapedia database. The green line shows where this particular strain fits within the distribution. Heterozygosity is associated with heterosis (aka hybrid vigor) but also leads to the production of more variable offspring. When plants have two genetically different parents, heterozygosity levels will be higher than if it has been inbred or backcrossed repeatedly.


Most Genetically Distant Strains Dot Plot

Medicinal Genomics added a new table and dot plot which shows the 10 cultivars that are most distant.

This can be useful information for breeders who are interested in creating new and interesting cultivars. Breeding with genetically distant cultivars will produce diverse phenotypes, which will likely have high heterozygosity or hybrid vigor.


Nearest Genetic Relatives in Phylos Dataset

Finally, Medicinal Genomics added a table that compares genetic data from cultivars sequenced with the StrainSEEK Version 2 panel to cultivars that were sequenced by Phylos and published to the Open Cannabis Project.

They can do this because they designed the assay to include loci from the other public cannabis genomic datasets (Phylos, Lynch, Sawler). StrainSEEK is the only cannabis strain sequencing service that can do this.

As result, samples sequenced with this method can be cross compared to all data that is public as of 2017. StrainSEEK version 2 delivers more than 10 times the genetic information than other tests on the market. and as a result is the most comprehensive sequencing tool. More data means you can better protect your strain from patents, better determine if your strain is unique, better identify genetic markers for breeding, and much more.

Learn more about our StrainSEEK Strain Identification and Registration Service and sequence your cultivar today!



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Resources:

  1. Want to get in touch with Medicinal Genomics? They can be reached via the following methods:
    1. Website: https://www.medicinalgenomics.com/
    2. Phone: 866-574-3582
    3. Email: [email protected]

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About the Author

Ben is the Marketing Manager at Medicinal Genomics (MGC) and enjoys the challenge of trying to simplify the amazing science performed in the MGC lab into content for the layman. Ben also maintains Kannapedia.net and helps to organize and execute MGCs annual CannMed Conference. Prior to joining MGC Ben worked as an writer and editor. He earned his journalism degree from the University of New Hmapshire.