Abstract
A chromosome segment designated as Wz found to positively affect resistance of to black shank disease caused by Phytophthora nicotianae was previously introgressed from Nicotiana rustica into cultivated tobacco (N. tabacum). DNA markers associated with this region can aid in efforts to pyramid multiple mechanisms of black shank resistance into single new tobacco cultivars. In order to identify DNA markers associated with Wz, we generated RNA-seq data from roots of nearly isogenic lines (NILs) differing for the presence/absence of the alien genomic region. Analysis of SNPs, INDELs, and differentially expressed genes that distinguished the NILs suggested that the N. rustica Wz introgression replaced an approximately 65 Mb region of N. tabacum chromosome 19. The utility of a subset of derived Kompetitive Allele Specific PCR (KASP) and Cleaved Amplified Polymorphic Sequence (CAPS) markers for predicting the presence of Wz was verified using segregating populations and F3:4 families that were evaluated for field black shank resistance. The new markers are useful for overall efforts to develop tobacco cultivars containing novel gene combinations affecting soil-borne pathogen resistance.
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