Linkage drag refers to:
Linkage drag describes physical association along chromosome between desired donor gene and neighboring deleterious or undesirable genes inherited together due to limited recombination near centromere or introgression segment. When donor parent contributes disease resistance gene for example, flanking chromosomal region spanning several megabases containing genes for poor quality, late maturity, low yield, or bitterness is co-transferred because crossing over between closely linked loci is rare per meiosis, frequency proportional to map distance in centimorgans. Until recombination breaks linkage, undesirable alleles hitchhike with selection for target gene, imposing yield penalty and quality defects observed in early backcross lines and near-isogenic lines. Breaking drag requires large backcross populations, additional rounds of meiosis, and marker-assisted background selection with flanking markers to select rare recombinants where only small donor interval retained. Molecular mapping revealed drag often extends 10-20 cM around introgressed QTL causing persistent penalty. High density SNP arrays and whole genome sequencing now allow precise quantification of drag size in megabases and identification of deleterious alleles linked to target; genome editing using CRISPR Cas9 offers future strategy to introduce only desired allele without drag, bypassing introgression and recombination limitations entirely in crop improvement programs.
Ref: Hospital F. Linkage drag – theoretical; Young & Tanksley 1989 RFLP study of drag. Nature Biotechnology