I know quite a bit in general but as good as nothing when it comes to hands on plant breeding and especially cannabis breeding ....
I just finished watching this video... very insightful and very helpful. it tickles my brain and makes me want to go back to school. He talks about and shows how gene sequencing and marker assisted selection by way of various molecular methods, can actually identify linked genes then using the sequencing/mapping to select plants which contain the marker gene that is known to be linked to the desirable trait... then use proven breeding methods to cross and work the lines toward homozygosity (ideally using gene marker techs each step of the way) and notice that even with all these high tech advantages he still mentions HUGE populations .... but obviously this kind of stuff goes way way way beyond the scope of probably 99.99999999% of people interested in playing with cannabis genetics.
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There are soooo many stories and tales about hollow stems, purpling and so on which allegedly are linked to potency and alike that I still wonder if one of these 'byproduct phenotypes' could actually serve as visible marker and not just a molecular marker (i.e. invisible to the naked eye) as you mentioned it above. There are always some linked but unrelated traits (at least for some time) and drawing a rudimentary gene map with the poor man's markers should also be possible (but maybe not useful).
One huge problem I see with the scientific approach, besides time and space, are costs. Unless you're one of the dozen or so top selling seed banks, you don't get enough money from seed sells alone... and selling weed only work for a very few.