Five Trees Undercover: Genome-Wide SNP Identification in Fraxinus Linking Genetic Characteristics to Tolerance of Agrilus planipennis
Abstract
Ash populations in North America have been decimated by the introduced pest, emerald ash borer (Agrilus planipennis [Coleoptera: Buprestidae]), having both negative impacts on forest ecology and economic interests. The majority of trees succumb to attack by emerald ash borer, however, some trees have been found to be tolerant to infestation despite years of exposure. In this study, restriction site-associated DNA (RAD) sequencing was used in order to sequence 47 individual ash trees, 28 classified as tolerant and 19 classified as susceptible based on overall vigor and crown dieback. A reference genome was constructed and single nucleotide polymorphisms (SNPs) were called using SAMtools. After several filtering criteria were implemented, a set of 17,807 SNPs were generated. Principle component analysis (PCA) of SNPs showed that some clustering was related to geography, however, five tolerant trees clustered together despite geographic diversity. Bayesian cluster analysis using STRUCTURE confirmed that these five trees form a distinct cluster that is genetically dissimilar from all other individuals. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are candidates for the selection of host tolerance. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of emerald ash borer.
Degree
M.S.
Advisors
Marshall, Purdue University.
Subject Area
Biology|Botany|Genetics
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