A SNP (pronounced "snip") is a single position in the genome where individuals differ by one DNA letter: some plants carry an A there, others a G. Each SNP is a locus with, usually, two alleles. They are abundant, stable and cheap to read in bulk, which makes them the standard marker for modern genotyping.
In practice
A SNP panel reads hundreds to tens of thousands of positions at once. Comparing two cuts across a large panel gives a confident answer on whether they are the same genotype. Studies of North American cannabis used SNP panels to map population structure and show that commercial labels do not match genetic groups well (Henry et al. 2020).
Most SNPs have no known effect on traits; they are markers, not causes. A few sit in or near genes that matter, such as the synthase loci, and can be used to predict a trait in seedlings.
Don't confuse with
- Mutation: the event that originally created a SNP; a SNP is the resulting variation in the population.
- Gene: a SNP is one letter; a gene spans thousands.
- Microsatellite (SSR): an older marker type based on short repeated sequences.
A locus is the fixed position on a chromosome where a particular gene or DNA marker sits; the plural is loci.An allele is one version of a gene; a diploid cannabis plant carries two alleles at each locus, one from each parent, which may be the same or different.Genotyping is reading a plant's DNA at selected markers to identify it, compare it with other plants, check sex or chemotype, or estimate its ancestry.The genotype is the set of alleles a plant actually carries, either at one locus or across its whole genome, as opposed to the traits you can see.A gene is a stretch of DNA that carries the instructions for one functional product, usually a protein such as an enzyme, and is the basic unit of inheritance.A seedling is a young cannabis plant from emergence of the cotyledons until it has several sets of true leaves, typically the first 2-3 weeks.Marker-assisted selection is choosing seedlings or parents by testing DNA markers linked to wanted traits, so plants can be selected before they flower.A QTL (quantitative trait locus) is a region of the genome statistically linked to variation in a quantitative trait such as yield or flowering time.
