Linkage Drag – Why an Introgressed Gene Brings Its Neighbours Along

Linkage drag is the piece of foreign genome that stays attached to an introgressed gene and cannot be shaken off. The name describes exactly what happens: the target gene is brought in, and it drags its neighbours with it.

Why a gene cannot move on its own

Suppose an old landrace resists a fungus, and that property is wanted in an existing variety that otherwise has everything going for it. You cross the two, pick the offspring carrying the resistance, and cross those back to your own variety. Then you repeat. Building a foreign trait into an existing variety this way is called introgression; in everyday terms, crossing something in.

On paper the landrace disappears fast: after the first round three quarters of the genome come from your own variety again on average, after the second seven eighths. That average, however, holds for the genome as a whole.

The reason lies in how genetic material is passed on. Genes sit in a row along chromosomes, and when gametes form, those chromosomes are not shuffled gene by gene but cut and rejoined at only a few places. This cutting is called recombination. An offspring therefore inherits not a collection of individual genes but whole stretches at once.

That sets the trap. In every round you select the plants carrying the target gene – and unavoidably select the stretch it sits in along with it. While the rest of the donor genome halves with every cross, the immediate surroundings of the target gene persist. They shrink only when a cut happens to fall close enough to the target, and such plants are rare.

How large the dragged piece stays

In a worked simulation on oilseed rape that piece averaged 15.9 million base pairs after the first backcross and 5.4 million after the second. For scale: one haploid chromosome set of cannabis runs to roughly 750 million base pairs. On that order, the dragged piece amounts to about two percent of an entire genome – sitting precisely where nothing foreign was wanted.

It becomes starker further along. After three backcrosses followed by selfing, 98 % of all remaining donor genome came from that single segment. The rest of the landrace had gone; its neighbourhood around the target gene had not.

Why position decides more than the number of rounds

Recombination does not happen at the same rate everywhere. Some stretches are cut often, others almost never. Where the target gene sits in an exchange-friendly region, the same segment in the same simulation shrinks to a fraction of a megabase, that is, to a small remainder.

How extreme the difference can be shows in the best-studied cannabis case. The stretch holding the CBDA synthase sits inside a gene-poor, recombination-poor block of roughly 39 million base pairs. Among 99 offspring examined, not one cut occurred there. A region like that travels as a block: whatever lies inside comes along whole or not at all.

For planning this means that before fixing the number of generations, the question of where the wanted trait actually sits has to be settled. Five rounds at an unfavourable position achieve less than two at a favourable one.

What can be done about it

The usual move is markers to the left and right of the target gene. You check not only whether a plant carries the target but also whether the two flanking positions already come from your own variety. If both hold, the cut in that plant fell close to the target. Such plants are rare, but among a few hundred offspring they turn up.

That shrinks the segment; it does not remove it. Where no recombination occurs at all, even the best marker cannot help – the plant it is looking for simply does not exist.

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