Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system

Abstract

Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack‐associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.

Differential Introgression Between the Northern and Southern Extents of the Lodgepole x Jack Pine Hybrid Zone Suggests Environmentally-driven Selection and Local Adaptation.

“…. Samples were collected as previously published data (Burns et al, 2019;Cullingham et al, 2020;Peery et al, (submitted)) as well as 258 individuals unique to this study.…”

“…Genomic DNA was isolated from pine needles as described in Burns et al (2019) and Peery et al (2020). Briefly, frozen needle samples were chopped and ground using a Retsch MM301 mixer mill or Geno Grinder (Thermo Fisher Scientific, Waltham, MA, USA).…”

“…Samples with a concentration ≥20ng•L -1 and 260/280 ratio values of 1.7-2.1 were genotyped. Additionally, samples from Peery et al (2020) were amplified using a PCR control as an additional quality control measure.…”

“…In addition to lodgepole and jack pine being key timber resources, they also provide wildlife habitat, watershed management, carbon sequestering, and recreational opportunities. Genetic information is an important consideration in forestry management as the relationship between environment, genotype and phenotype has been well established in many tree species (Cullingham et al, 2020;Romagosa & Fox, 1993). This realization has increased genetic research in forest trees given their combined important economic and ecological status (Isabel et al 2020).…”

“…Temperature increases, drought frequency and severity and precipitation variability associated with climate change all threaten ecosystem function (Brooks et al, 1998). With warmer temperatures, invasive pests, such as mountain pine beetle, are able to survive the warmer winters and expand their ranges, posing an enormous threat to stand health and survival as we have seen in lodgepole pine in previous years (Adams et al, 2013;Cullingham et al, 2020;Erbilgin, 2019).…”