Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties
Abstract
:1. Introduction
2. Results and Discussion
2.1. In-Silico Modeling and Selection of Restriction Endonuclease Combinations for Complexity Reduction
2.2. PCA and DAPC of Complete Variant Sets Can Distinguish Cannabis Varieties
2.3. Cannabis Varieties Can Be Identified by a Minimal Number of SNPs Highly Associated with the LTR Class of Retroelement
3. Conclusions
4. Materials and Methods
4.1. In-Silico Restriction Digest of Cannabis Genome Assemblies
4.2. Plant Material and DNA Extraction
4.3. Restriction Endonuclease Digestion of Genomic DNA
4.4. Sample Preparation and DNA Sequencing
4.5. Read Mapping
4.6. Determination of In-Silico and Sequenced Fragment Overlap
4.7. Variant Calling
4.8. Principal Component Analysis and Discriminant Analysis of Principal Components
4.9. Calculating Pairwise Genetic Distance between Varieties Using Nei’s Genetic Distance
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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AK | BV | Bu | CJ | CBD1 | CBD2 | MB | Mot | SDA | THC1 | |
AK | 0 | 0.0388 | 0.0444 | 0.0463 | 0.0575 | 0.0575 | 0.0349 | 0.0407 | 0.0538 | 0.0423 |
BV | 0.0388 | 0 | 0.052 | 0.0475 | 0.0697 | 0.0695 | 0.0514 | 0.0125 | 0.0556 | 0.0573 |
Bu | 0.0444 | 0.052 | 0 | 0.0472 | 0.0589 | 0.0573 | 0.0425 | 0.0495 | 0.057 | 0.0506 |
CJ | 0.0463 | 0.0475 | 0.0472 | 0 | 0.0664 | 0.0662 | 0.0478 | 0.0503 | 0.0572 | 0.0529 |
CBD1 | 0.0575 | 0.0697 | 0.0589 | 0.0664 | 0 | 0.0095 | 0.0599 | 0.0689 | 0.0665 | 0.06 |
CBD2 | 0.0575 | 0.0695 | 0.0573 | 0.0662 | 0.0095 | 0 | 0.0597 | 0.0673 | 0.066 | 0.0594 |
MB | 0.0349 | 0.0514 | 0.0425 | 0.0478 | 0.0599 | 0.0597 | 0 | 0.0536 | 0.0552 | 0.0455 |
Mot | 0.0407 | 0.0125 | 0.0495 | 0.0503 | 0.0689 | 0.0673 | 0.0536 | 0 | 0.0531 | 0.0538 |
SDA | 0.0538 | 0.0556 | 0.057 | 0.0572 | 0.0665 | 0.066 | 0.0552 | 0.0531 | 0 | 0.0512 |
THC1 | 0.0423 | 0.0573 | 0.0506 | 0.0529 | 0.06 | 0.0594 | 0.0455 | 0.0538 | 0.0512 | 0 |
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Oultram, J.M.J.; Pegler, J.L.; Symons, G.M.; Bowser, T.A.; Eamens, A.L.; Grof, C.P.L.; Korbie, D.J. Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties. Int. J. Mol. Sci. 2022, 23, 14531. https://doi.org/10.3390/ijms232314531
Oultram JMJ, Pegler JL, Symons GM, Bowser TA, Eamens AL, Grof CPL, Korbie DJ. Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties. International Journal of Molecular Sciences. 2022; 23(23):14531. https://doi.org/10.3390/ijms232314531
Chicago/Turabian StyleOultram, Jackson M. J., Joseph L. Pegler, Greg M. Symons, Timothy A. Bowser, Andrew L. Eamens, Christopher P. L. Grof, and Darren J. Korbie. 2022. "Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties" International Journal of Molecular Sciences 23, no. 23: 14531. https://doi.org/10.3390/ijms232314531