Genotyping-by-sequencing reveals fine-scale population differentiation in populations of Pseudoperonospora humuli

Authors: Gent, David - Dave; Adair, Nanci; Knaus, Brian; Grunwald, Niklaus - Nik

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2019
Publication Date: 6/14/2019
Citation: Gent, D.H., Adair, N.L., Knaus, B.J., Grunwald, N.J. 2019. Genotyping-by-sequencing reveals fine-scale population differentiation in populations of Pseudoperonospora humuli. Phytopathology. https://doi.org/10.1094/PHYTO-12-18-0485-R.
DOI: https://doi.org/10.1094/PHYTO-12-18-0485-R

Interpretive Summary: Downy mildew of hop is one of the most important diseases of this plant and a limiting factor for production of susceptible cultivars in certain environments. This research was conducted to understand if and how populations of the pathogen are related genetically within and between fields. This is important because it provide insights into how the pathogen may be spread and informs efforts to breed new cultivars resistant to the disease. We found that the pathogen population appears to be dominated by one clonal genetic group, although there is some indication of small genetic differences at the field and even plant level. This suggests that infections of the pathogen are persistent and possibly associated with the source of the planting material.

Technical Abstract: Pseudoperonospora humuli is the causal agent of downy mildew of hop, one of the most important diseases of this plant and a limiting factor for production of susceptible cultivars in certain environments. The degree of genetic diversity and population differentiation within and among P. humuli populations at multiple spatial scales. Hierarchical sampling was conducted to collect isolates from three hop yards in Oregon, plants within these yards, and infected shoots within heavily diseased plants. Additional isolates also were collected broadly from other geographic regions and from the two clades of the sister species, P. cubensis. Genotyping of these 240 isolates produced a final quality-filtered data set of 216 isolates possessing 25,227 variants. Plots of G’ST values indicated that the majority of variants had G’ST values near 0 and were scattered randomly across chromosomal positions. However, there were 15 variants that were highly differentiated (G’ST > 0.3) and reproducible when genotyped independently. Within P. humuli, there was evidence of genetic differentiation at the level of hop yards and plants within yards; 19.8% of the genetic variance was associated with differences among yards and 20.3% of the variance was associated with plants within the yard. Isolates of P. humuli were well differentiated from the two clades of P. cubensis. Mantel tests found evidence that the genetic distance between isolates collected from heavily diseased plants within a hop yard was associated with physical distance of the plants the isolates were collected from. The sum of the data presented here indicates that populations of P. humuli are consistent with an overall clonal genetic structure with a small, yet significant differentiation of populations among yards and plants within yards. Fine-scale genetic differentiation at the yard and plant scales may point to persistence of founder genotypes associated with planting due to chronic, systemic infection of hop plants by P. humuli.