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Summary  Crop plant partial resistance to plant pathogens controlled by quantitative trait loci (QTL) is desirable in cultivar development programmes because of its increased durability. Mechanisms underlying such resistance are difficult to study. We performed RNA‐seq analyses for tobacco ( Nicotiana tabacum ) nearly isogenic lines (NILs) with and without favourable allele(s) at  Phn7.1 , a major QTL influencing partial resistance to the soil‐borne pathogens  Phytophthora nicotianae  and  Ralstonia solanacearum . Based upon combined analyses of transcriptome‐based sequence variation and gene expression profiles, we concluded that allelic variability at the  Phn7.1  locus was likely generated from homoeologous exchange, which led to deletion of low‐expressing members of the  SAR8.2  gene family and duplication of high‐expressing  SAR8.2  genes from a different subgenome of allotetraploid tobacco. The high expression of endogenous  Phn7.1 ‐associated  SAR8.2  genes was correlated with observed resistance to  P .  nicotianae . Our findings suggest a role for genomic rearrangements in the generation of favourable genetic variability affecting resistance to pathogens in plants.

Homoeologous chromosome exchange explains the creation of a QTL affecting soil‐borne pathogen resistance in tobacco