Linkage is the tendency of genes that are close together on a chromosome to be inherited as a unit. They break apart only when crossing over (recombination) happens between them during meiosis, and the closer they are, the rarer that is.
In practice
Linkage helps and hurts. It helps marker-assisted selection: a DNA marker tightly linked to a trait gene predicts the trait in seedlings. It hurts when an unwanted trait rides along with a wanted one. Breeders call that linkage drag: you backcross a trait into a line and a chunk of the donor chromosome comes with it, sometimes carrying poorer vigour or an off aroma.
In cannabis the region around the THCA and CBDA synthase genes is a well-studied case. It is a stretch of repeats and duplicated synthase copies with little recombination, so it tends to move as a block (Laverty et al. 2019; Grassa et al. 2021).
Distance is measured in centimorgans (cM): 1 cM ≈ 1% recombination per generation between two loci.
Don't confuse with
- Independent assortment: the default for genes on different chromosomes.
- Sex linkage: genes on the X or Y chromosome, inherited with sex.
- Pleiotropy: one gene affecting several traits; linkage is two genes travelling together.
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 chromosome is one long DNA molecule packaged with proteins that carries many genes; cannabis normally has 10 pairs, nine autosome pairs plus an X/Y sex pair.Marker-assisted selection is choosing seedlings or parents by testing DNA markers linked to wanted traits, so plants can be selected before they flower.THCA (tetrahydrocannabinolic acid) is the acid cannabinoid that drug-type cannabis makes in its trichomes; heat or time decarboxylates it into THC, losing about 12% of its mass.CBDA synthase is the trichome enzyme that converts CBGA into CBDA; it competes with THCA synthase, and its alleles largely decide whether a plant is CBD-dominant.The stretch is the rapid increase in height in the first two to three weeks after switching to flower, when many cultivars grow 1.5 to 3 times taller.Independent assortment is Mendel's rule that alleles of genes on different chromosomes are passed to gametes independently of each other, creating new trait combinations.Pleiotropy is when a single gene affects two or more apparently unrelated traits, so selecting on one trait changes the others too.A locus is the fixed position on a chromosome where a particular gene or DNA marker sits; the plural is loci.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.Introgression is the movement of genes from one population or type into another through hybridisation followed by repeated backcrossing.
