Improved Late Blight Management Through Resistance In Tomato, Pathogen Diagnostics, And Understanding Phytophthora Infestans Diversity

Abstract

Late blight, caused by the oomycete Phytophthora infestans, continues to be an important disease of potato and tomato, and host resistance can be an effective management tool. Thirty nine tomato varieties were evaluated for resistance to the currently-predominant clonal lineage of P. infestans in three separate field trials. Varieties with late blight resistance genes Ph-2 + Ph-3, or were homozygous for Ph-3 only, along with three heirloom varieties, showed a high level of resistance. 'Plum Regal F1', which is heterozygous for Ph-3 only, and 'Legend', which has Ph-2 only, showed moderate resistance. When resistant varieties are not planted, early detection of airborne inoculum could be used to improve disease forecasting, inform management decisions, and could be a useful tool for studying late blight epidemiology. Rotorod-style spore trapping coupled with quantitative PCR was tested over seven location-seasons in New York State between 2012 and 2014. Phytophthora infestans was detected from 111 to 6 days prior to late blight symptom observation in four location-seasons, 1 and 6 days after symptom observation in two location-seasons, and was not detected during the seventh location-season. This study demonstrates that although the methods described here are capable of detecting P. infestans inoculum, they do not appear to be a viable approach for informing late blight management decisions under the conditions of this study in New York. In the United States P. infestans exhibits a clonal reproductive lifestyle, and the ability to identify P. infestans lineages has important late blight management implications. Diagnostic single-nucleotide polymorphisms (SNPs) were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate the recently-predominant lineage US-23 from three other lineages. A loop-mediated isothermal amplification assay, which requires less laboratory equipment compared to traditional PCR detection assays, was also developed for rapid detection of P. infestans DNA. Additionally, within-lineage diversity was studied using genotyping-by-sequencing (GBS) on 257 P. infestans isolates belonging to four clonal lineages. SNPs identified through GBS were used to construct neighbor-joining (NJ) trees to investigate relationships among individuals within lineages. NJ trees revealed evidence for regional pathogen dispersal and overwintering, as well as long-distance pathogen dispersal. The relative prominence of clustering by year indicates the importance of long-distance pathogen dispersal in initiating annual late blight outbreaks.