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

Abstract

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 the Arabidopsis 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.