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Significance Genome-wide association (GWA) mapping is a powerful tool for identification of genetic variants underlying complex traits. However, existing methods typically perform GWA mapping within a single species; methods allowing the description of the genomic landscape of interspecies interactions are only beginning to be developed. Here, we present a method to simultaneously perform GWA mapping on two interacting species. We applied our approach to theArabidopsis thaliana–Xanthomonas arboricola pathosystem and identified candidate genes conferring host–pathogen specificity. By integrating the whole-genome sequence data available for pairs of interacting species, we can decipher the genetic architecture of complex traits in finer detail than has previously been possible.

Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes