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RAD-seq of Ash individuals

Citation

Marshall, Jordan (2022), RAD-seq of Ash individuals, Dryad, Dataset, https://doi.org/10.5061/dryad.7pvmcvdtd

Abstract

Ash (Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis, but some trees have been found to be tolerant to infestation despite years of exposure.

Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines.

Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. We were successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of A. planipennis. This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis.

Methods

RAD-seq was used to assemble a de novo reference genome of green (Fraxinus pennsylvanica) and white (F. americana) ash individuals to idenitfy SNPs that are associated with tolerance to emerald ash borer (Agrilus planipennis) infestation.

Usage Notes

AshSNPmetadata.csv includes full field assessments for all Fraxinus individuals included in this study (10.1002/ece3.8163). SSR Run IDs associated with files in AshSNPdata.zip. Field assessments include location (included in study 10.1002/ece3.8163) and species identification (G = F. pennsylvanica; W = F. americana), diameter at breast height (DBH; cm), vigor rating, percent crown dieback, and presence or absence of bark splits (BS), exit holes (EH), woodpecker damage (WP), and epicormics sprouts. Overall classification of tolerant or susceptible was determine using criteria from both vigor and dieback.