Research Progress HIGHLIGHTS

Activity 3 – Pathogenicity Zones

Activity 3.1 Genomic variability in tree pathogens

Dothistroma

We established a reference collection of Dothistroma spp. for North America which currently includes more than 300 isolates. In addition, we could source isolates from collaborators in Europe (M. Mullett) and South Africa (I. Barnes) who have extensive Dothistroma spp. collections covering major parts of the currently known distribution range of Dothistroma spp.

Pilot study (Completed 2018)

We have conducted preliminary genotyping by sequencing on our BC and Alberta isolates. The Smithers and Prince George are both locations of severe pine needle blight since the end of the 1990’s, while the Alberta populations were related to a more recent outbreak in 2013. The pilot analysis of these isolates with the Genotyping By Sequencing technique (GBS) resulted in ~3,500 Single Nucleotide Polymorphims (SNPs). STRUCTURE analysis supported the separation of the isolates in geographical clusters that correspond to the three areas sampled. The samples from the Prince-George area shows a deeper structure, with the clear differentiation of several subpopulations. Populations of the Alberta area have a large majority of admixed genotypes, which could be the result of the introduction of few individuals from the more diverse BC populations. This scenario will be challenged to alternative ones by using population history modeling approaches.

Structure of Dothistroma septosporum populations (133 isolates) collected in BC and Alberta.

For more information, contact Nicholas Feau and Richard Hamelin.

 

Genomic variability (Updated March 2020) 

Analyses of the population structure of D. septosporum at the global scale (~300 genomes) show that the populations in western North America are genetically different from the populations in the other parts of the world. Within western North America we find several geographically and genetically distinct D. septosporum populations. However, we also find some genotype groups with a wide geographic distribution and in some areas different genetic groups are coexisting.

Population structure of Dothistroma septosporum in western North America. A) Neighbor joining tree based on 147,012 SNPs being variable within the D. septosporum population in western North America. The tree includes 206 genomes and is rooted with a European D. septosporum genome. Genetically distinct groups are color-coded (vertical bar). B) Map location of the genetic groups distinguished in A).

 

Guided by the genetics data, select isolates representative of the different genetic groups were grown at different temperature to investigate possible difference in temperature preference. The experiment revealed significant differences in growth speed and temperature effect for the genetic groups tested.

Boxplots showing the growth per day of the different isolates tested at three temperatures (15°C, 20°C and 25°C). Results were grouped by using the same genetic clusters identified in the population structure study.

 

For more information, contact Renate Heinzelmann and Richard Hamelin.


Swiss needle cast (Phaeocryptopus gaeumannii) (Updated January 2020)

Our extensive reference collection of Swiss needle cast (SNC) has been built and contains over 800 strains. We have generated more than 550 strains from new field collections from BC, Alaska, and Oregon and have also acquired ~280 strains from Oregon State University’s collection (Dr. Jeff Stone).

We have sequenced the genome of a worldwide collection of ~250 SNC isolates. Structure analysis of this global collection indicated that the SNC global population is subdivided in three main genetic lineages : Lineage 1c and Lineage2 on coastal Douglas fir and Lineage 1i on interior Douglas fir.

 

Genetic structure of the global population of the Swiss needle cast (SNC).
A. PCA based on 134,403 SNPs; the three putative SNC lineages are indicated with different colors.
B. geographical distribution of the genomes sequenced.
C. Split-tree network based on pairwise identities between individuals.

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For more information, contact Nicholas Feau and Richard Hamelin.


Activity 3.3 Climate models of outbreak risks

Activity 3.3.1/3.3.2 Dothistroma

Occurrence records of Dothistroma spp. are being cumulated from several different sources such as Forest Insect and Disease Survey (FIDS) of the Canadian Forest Service, provinces, scientific publications, and online databases. To date, we have assembled 410 observations of Dothistroma spp. occurrence points from Canada and USA. More observations will be added to this dataset by spring/summer 2018. These data will eventually be used in climate-based modeling.

For more information, contact Barbara Wong and Kishan Sambaraju.

Activity 3.3.3/3.3.4 Swiss Needle Cast (Updated January 2020)

Swiss needle cast (SNC), a foliar disease of the Douglas-fir, has been increasing in severity in recent decades. Nothophaeocryptopus gaeumannii, the causal agent of SNC, is native to the Pacific Northwest and occurs across Douglas-fir’s natural and planted range, but severity levels of the pathogen vary with climate and other site conditions. The BC Ministry of Forests, Lands, Natural Resource Operations and Rural Development (BCMoF) sampled Douglas-fir trees with SNC symptoms from 36 monitoring sites in the summer of 2017 and 2018. The 2017 sites are located near Chilliwack, while the 2018 sites are primarily located on Vancouver Island and the Sunshine Coast (Figure 1). Technicians at the Hamelin lab then assessed SNC severity, which was measured in terms of pseudothecial presence and density on sampled needles. We also collected 334 records of presence of SNC in Canada from a number of sources such as government herbaria, online databases and scientific publications (Figure 2).

Figure 1. BCMoF 2017 and 2018 monitoring sites with associated severity levels.

 

Figure 2 BCMoF monitoring sites (points in red) and historical SNC presence records (points in blue) in British Columbia.

 

In this project we are using predictive modelling to further our understanding of fine-scale SNC disease epidemiology, test the effects of different management regimes, site characteristics and climate on disease severity, and finally use spatial modelling to forecast the patterns of the disease’s severity in British Columbia (BC) in several climate change scenarios. Our data has already revealed differences between the fine-scale patterns of disease severity in BC and those reported in Washington and Oregon; we are hence looking for possible climatic and/or genetic explanations for these.

We have tree and site-level data from 36 BCMoF monitoring sites including disease prevalence and severity, site productivity index, slope, aspect, tree species richness, site management system and summarized them appropriately to provide information that is biologically relevant to biotic disturbance patterns. We have obtained climate data for the different sites/year from ClimateBC and selected variables that are biologically relevant to N. gaeumannii life cycle. We are currently developing multi-level mixed-effects models that include site and climate variables.

Next steps:

We plan to incorporate information on the different N. gaeumannii lineages detected at the BCMoF monitoring sites into our analysis. We intend to test whether lineage is related to SNC severity, as well as whether the presence of different lineages is determined by climate. We also plan to collect more severity data from other locations in BC in order to improve our model predictions. We aim to develop a severity map by interpolating the predictions to known Swiss needle cast occurrence locations throughout BC (Figure 2). We then will apply this procedure to map disease severity patterns under several climate change scenarios.

For more information, contact Naomie Herpin-Saunier and Kishan Sambaraju.