|PURAUANNUR, SAVITHRI - North Carolina State University|
|CANO, LILIANA - North Carolina State University|
|BOWMAN, MEGAN - Michigan State University|
|CHILDS, KEVIN - Michigan State University|
|Gent, David - Dave|
|QUESADA-OCAMPO, LINA - North Carolina State University|
Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2020
Publication Date: 8/11/2020
Citation: Purauannur, S., Cano, L.M., Bowman, M.J., Childs, K.L., Gent, D.H., Quesada-Ocampo, L.M. 2020. The effector repertoire of the hop downy mildew pathogen, Pseudoperonospora humuli. Frontiers in Genetics. 11. https://doi.org/10.3389/fgene.2020.00910.
Interpretive Summary: Downy mildew of hop is an important disease that limits productivity of the crop. Developing varieties of the crop that are naturally resistant to the disease is the most efficient and preferred means of disease management. In this research, we searched the genome of the hop downy mildew pathogen to identify candidate genes associated with alteration of host defense responses, termed effectors. We identified a suite of effectors in the pathogen that are expressed during the infection, consistent across strains of the pathogen, and therefore appear critical to the infection process. The genes identified are candidate targets that may accelerate breeding efforts for disease resistances.
Technical Abstract: Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew of hop, one of the most destructive diseases of cultivated hop and can lead to 100% crop loss in susceptible cultivars. We used the published genome of P. humuli to identify pathogen effectors and analyze transcriptome variation among diverse isolates and during infection of hop leaves. Mining the predicted coding genes of the sequenced isolate OR502AA of P. humuli revealed a secretome of approximately 1,250 genes. A detailed pipeline involving bioinformatics and comparative genomics led to the identification of 296 RXLR and RXLR-like effector-encoding genes. Among the predicted RXLRs, there were several WY-motif-containing effectors that lacked canonical RXLR domains. Transcriptome analysis of sporangia from 12 different isolates collected from various hop cultivars revealed 754 secreted proteins and 291 RXLR effectors that show transcript evidence across all isolates with RPKM values >0. RNA-seq analysis of OR502AA-infected hop leaf samples at different time points after infection revealed highly expressed effectors that may be important in pathogenicity. Quantitative RT-PCR analysis confirmed the differential expression of selected effectors. The P. humuli core effectors that show transcript evidence in all tested isolates and elevated expression during infection constitute candidates for functional analysis and effector-assisted breeding to develop downy mildew resistant hop cultivars.