When introgressing, for example, resistance genes from wild species, unwanted donor segments can hitchhike along with your gene of interest—a phenomenon known as linkage drag.

A structured marker-assisted breeding pipeline can help minimize this while retaining the resistance.

Here’s how:

1. Foreground selection:
Start by selecting individuals that carry the target gene itself using a trait-linked marker in the first round of backcrossing (Bc1). This ensures all selected plants express the desired trait.

2. Recombinant selection:
Use markers flanking the target QTL on both sides to identify recombination events. For example, if markers are 5 cM from the QTL, roughly 5 recombinants are expected per 100 individuals at the first backcross (BC1).

Step 1: Screen BC1 progeny for the trait marker, then select recombinants on one side of the QTL.
Step 2: In BC2, repeat the process on the other side to recover recombinants from that side.

3. Result: By combining foreground and flanking-marker selection, you retain the target gene while minimizing linked donor DNA.

💡Tip: The number of individuals to screen depends on the genetic distance of your flanking markers, and the optimal selection scheme should balance available genotyping resources and DNA extraction capacity.

Takeaway: Structured marker-assisted selection allows precise introgression of desired traits with minimal linkage drag, speeding up the development of improved varieties.

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How can marker-assisted breeding remove flanking donor DNA while keeping the target gene?