Genomic Characterization of a Sexual Cross of Phytophthora infestans

The oomycete Phytophthora infestans, a diploid, eukaryotic, and filamentous microbe, causes the devastating late blight disease of potato and tomato. The phenotypes of P. infestans lineages in nature have been shaped by sexual reproduction, in addition to asexual variation. The contribution of sexual reproduction is hypothesized to be affected by interisolate variation in ploidy (ranging from diploidy to tetraploidy) and other forms of structural variation. To better understand how sexual reproduction affects traits relevant to plant pathogenicity, we crossed two diploid strains, generated 120 progeny, and scored asexual sporangia production, pathogenicity on potato tubers, and resistance to the fungicide metalaxyl. After sequencing the parents and progeny, SNPs segregating in the cross were identified and tested for association with the three traits. This identified genomic intervals associated with some of the traits. The analysis is being supplemented with expression level polymorphism analysis. To evaluate other mechanisms that may contribute to genetic variation, a genome-wide analysis was performed of copy number variation and loss of heterozygosity, including gene conversion events. The results indicate that both mendelian and non-mendelian events contribute to variation resulting from sexual reproduction.