BSA-Seq discovery of stripe rust resistance with incomplete dominance in wild emmer wheat

Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to identify new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single gene to which we applied bulked segregant analysis sequencing (BSA-Seq) to rapidly characterize the underlying genetic locus. From short-read whole-genome resequencing of fully resistant versus susceptible F2 plants, we identified a 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used to design genetic markers for recombinant screening, further refining the interval of the resistance gene, temporary designated as YrPI487260, to 2.3-3.3 Mb in tetraploid wheat genomes. This interval contains 34 candidate genes encoding for protein domains involved in disease resistance responses. Further analysis revealed resistance is incompletely dominant, with homozygous alleles conferring full resistance.