Breaking linkage drag

Linkage drag refers to the (usually undesirable) effects of genes linked to the genes or QTL we are trying to introgress. If a desirable QTL for trait X lies close to an undesirable gene affecting trait Y, you will want to “break” the linkage drag – that is, separate the good QTL from the bad.

Overcoming linkage drag requires passing the material through meiosis again, and searching for recombinants (possibly rare) between the target QTL (which is tracked by the DNA markers used originally to identify it) and the undesirable gene/QTL, such that you can select a plant that has the desirable QTL but not the undesirable one.

Here a QTL that increases yield is near a QTL that increases grain shattering. In the next population, you would look for a plant that still had the positive allele at Marker B, but has lost the grain shattering allele at Marker C.