Development, validation, and utility of species-specific diagnostic markers for detection of Peronospora belbahrii

• Published in: Phytopathology 2022-08, Vol.112 (8), p.1667-1675
• Main Authors: Standish, Jeff, Góngora-Castillo, Elsa, Bowman, Megan J, Childs, Kevin, Tian, Miaoying, Quesada-Ocampo, Lina
• Format: Article
• Language: English
• ISSN: 0031-949X; 1943-7684
• DOI: 10.1094/PHYTO-09-21-0393-R

is an oomycete and cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed, therefore, identifying in seed-lots before sale or planting, or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next generation sequencing reads for , and publicly available DNAseq and RNAseq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict -specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of , host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used to develop a highly sensitive probe-based real-time qPCR assay that could detect in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and for identifying -contaminated seed-lots, to mitigate the effects of future basil downy mildew epidemics.