SSRs identify limited genetic diversity across pathogen populations responsible for the global emergence of boxwood blight

Authors: LEBLANC, NICHOLAS - Orise Fellow; GEHESQUIÈRE, BJÖRN - Institute For Agricultural And Fisheries Research (ILVO); SALGADO-SALAZAR, CATALINA - Orise Fellow; HEUNGENS, KURT - Institute For Agricultural And Fisheries Research (ILVO); Crouch, Jo Anne

Submitted to: Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2019
Publication Date: 2/14/2019
Citation: Leblanc, N., Gehesquière, B., Salgado-Salazar, C., Heungens, K., Crouch, J.A. 2019. SSRs identify limited genetic diversity across pathogen populations responsible for the global emergence of boxwood blight. Plant Pathology. 68(5):861-868. https://doi.org/10.1111/ppa.13003.
DOI: https://doi.org/10.1111/ppa.13003

Interpretive Summary: Boxwood plants worldwide are threatened by a deadly fungal disease known as boxwood blight. Currently the disease is spreading rapidly across the U.S. and parts of Asia, but has been present in Europe since the late 1990s. This research was conducted to learn about the distribution of different DNA types of the blight fungus, and understand how the fungus has been able to multiply worldwide. A new set of custom DNA tools called SSRs were developed, and used to screen 306 samples of the fungus collected worldwide since the disease was first observed in boxwood in 1998. There were 16 different SSR DNA types, but only two of the SSR DNA types have global distributions. Only two SSR DNA types are present in the U.S. and Asia; the remaining SSR DNA types are limited to Europe. All SSR DNA types were very similar and closely related to one another. This shows that these fungi have primarily multiplied by making clones of themselves that have spread throughout the world. This research is important because it shows how spread of the blight fungus has occurred and suggests how it will continue to move in the U.S. This research will be used by plant pathologists, plant breeders extension personnel and quarantine officials to minimize the transmission and impact of boxwood blight.

Technical Abstract: Boxwood blight is an emerging disease of ornamental and non-cultivated boxwood. The disease became widely established in Europe at the beginning of the 21st century, prior to its more recent discovery in North America and Asia. Two sister-species of fungi cause the disease, Calonectria pseudonaviculata (Cps) and C. henricotiae (Ch). Prior efforts to quantify intraspecific genetic polymorphisms of Cps and Ch have yielded little information, limiting our ability to understand the evolution and migration of these pathogens. Here we describe the development and implementation of simple sequence repeat (SSR) markers to analyze genetic diversity from a global collection of Cps and Ch isolates, representing major blight outbreaks since the disease was first identified from the U.K. in the late 1990s. Analysis of the Cps CB002 genome sequence identified 180 single copy SSR loci using stringent search criteria, 11 of which were found to be polymorphic and used to screen a global sample of 306 isolates. Fourteen multilocus genotypes of Cps and two multilocus genotypes of Ch were identified. Twelve of the 14 Cps genotypes differed from each other by a single allele. The most common Cps genotype was found on all continents where boxwood blight is confirmed. Based on measurement of linkage disequilibrium, Cps showed no evidence of sexual recombination. Further in silico analysis identified 1,594 SSRs using relaxed SSR definition criteria. Comparison of these SSR-containing loci with Cps and Ch genome sequences representing three different genotypes demonstrated that single nucleotide polymorphisms might serve as informative genetic markers for future studies.