I'm not sure how else you would be choosing strong genes?
The genotype are the ones to breed.
In a DNA, it consist of thousands of genes (Genomes), most of these genes are common to both plants and animals(including human). The markers are what separate plant from animals. The markers(Genomes) separate a tomato from cannabis. And supposedly, there is a marker that separate Og Kush from White Widow.
There's no way you can breed based on the genomes....unless you own a or have access to gene sequencing operation, well you can pay for the analysis. If you have, then you might as well play with genetic manipulation.
However you don't have everything analyze every time you have to breed (unless you're Bill Gates) and this is where Phenotypes comes handy. Phenotypes are just the physical expression of those genes (Genotype). Not all of them are express physically but for breeding purposes genes that are express physically are good enough to achieve what we want to produce.
Seems easy enough.
The problem with breeding is not the genetic make-up of your parent material.....The problem lies in the method/technique of breeding <<=== this alone here is responsible for the mess our cannabis is in.
There are 2 major mode of breeding
1. Inbreeding or Line Breeding
2. Outcrossing
A breeding program can be either or the combination of both
Our cannabis breeding problem is 2 front
1. Those who practice Inbreeding....would inbred the same bloodline, often brother with sister multiple times. Obviously, there is a great chance that 2 same bad genes (or alleles if you really want to be technical) will be pass to the offspring. Remember that some genes are not express physically? Some of these genes might have something to do with low yield or vulnerability to disease, etc.. Later on, you would wonder why such a great bloodline after a few generations suddenly start dying during a temperature change while its great grand-parent is able to handle such issue. This issue is called inbreeding depression/coeffiecient. There are techniques, that would minimize the chance of this happening and still maintain healthy offsprings both in phenotype and genotype.
2. Outcrossing....this is the common breeding practice we have. Why? Because its the easiest and no brainer and comes with benefit (pollen chuckers). The benefit of Outcrossing is called Heterosis. When you cross two unrelated strain, you created a hybrid (F1). If your hybrid goes through heterosis, then your growth is better than average, your yield is much better than average.....in other words everything is better. There's no denying that. And this is whether intentionally or ignorantly, breeders start to hype their F1, because it is simply better (potency, frosty, whatever). In terms of its genetic make up, all the gene pairings are complementary to each other (Genetic diversity). The problem here is the moment you have the plant cross with something else....you lose your original hybrid and start a new F1 again (a hybrid of a hybrid), now whether you have heterosis or not, depends on the new genetic makeup. F1 is good for production only and not for breeding. If you need to stabilize your F1, you need to learn Inbreeding properly.
