Genomic sequencing combined with marker-assisted breeding effectively eliminates potential linkage drag of a target gene: a case study in tobacco

Linkage drag frequently impedes the utilization of beneficial genes from wild species in crop improvement. The <i>N</i> gene from <i>Nicotiana glutinosa</i> confers strong resistance to tobacco mosaic virus (TMV) but introduces linkage drag when introgressed into cultivated tobacco (<i>Nicotiana tabacum</i>). To address this issue, we sequenced the TMV-resistant flue-cured tobacco line 0970A and carried out comparative genomic analysis. Additionally, we used molecular markers to screen a BC₄F₁ population derived from the cross between 0970A and an elite flue-cured tobacco variety CB-1 (recurrent parent). As a result of sequencing 0970A, the <i>N</i> gene was located at the end of chromosome Nt11. The comparative genomic analysis showed that 0970A inherited approximately 3.74 Mb of <i>N. glutinosa</i> DNA (<i>N</i>-fragment) from its donor, Coker 176. From screening the BC₄F₁ population with molecular markers, a recombinant was identified. This recombinant had a significantly reduced <i>N</i>-fragment (~270 kb), which minimized the linkage drag while still maintaining resistance to TMV. This research indicates that the combination of genome sequencing and marker-assisted breeding can be successfully applied to reduce linkage drag. The findings offer valuable resources for breeding tobacco with resistance to TMV.