Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

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 ecos...

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Autores principales:	Cecelia E. Hale, Mark A. Jordan, Gloria Iriarte, Kirk Broders, Andrew J. Storer, Vamsi J. Nalam, Jordan M. Marshall
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	ash emerald ash borer RAD‐seq survival tolerance Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/dea4b96a86dd45ed99b3b2c5afe1cd30
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spelling	oai:doaj.org-article:dea4b96a86dd45ed99b3b2c5afe1cd302021-11-08T17:10:40ZGenome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis2045-775810.1002/ece3.8163https://doaj.org/article/dea4b96a86dd45ed99b3b2c5afe1cd302021-11-01T00:00:00Zhttps://doi.org/10.1002/ece3.8163https://doaj.org/toc/2045-7758Abstract 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. de novo SNPs were called using SAMtools and, after filtering criteria were implemented, a set of 17,807 SNPs were generated. Principal component analysis (PCA) of SNPs aligned individual trees into clusters related to geography; however, five tolerant trees clustered together despite geographic location. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are potential candidates for the selection of host tolerance. 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. This study was 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. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack.Cecelia E. HaleMark A. JordanGloria IriarteKirk BrodersAndrew J. StorerVamsi J. NalamJordan M. MarshallWileyarticleashemerald ash borerRAD‐seqsurvivaltoleranceEcologyQH540-549.5ENEcology and Evolution, Vol 11, Iss 21, Pp 14775-14788 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	ash emerald ash borer RAD‐seq survival tolerance Ecology QH540-549.5
spellingShingle	ash emerald ash borer RAD‐seq survival tolerance Ecology QH540-549.5 Cecelia E. Hale Mark A. Jordan Gloria Iriarte Kirk Broders Andrew J. Storer Vamsi J. Nalam Jordan M. Marshall Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
description	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. de novo SNPs were called using SAMtools and, after filtering criteria were implemented, a set of 17,807 SNPs were generated. Principal component analysis (PCA) of SNPs aligned individual trees into clusters related to geography; however, five tolerant trees clustered together despite geographic location. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are potential candidates for the selection of host tolerance. 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. This study was 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. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack.
format	article
author	Cecelia E. Hale Mark A. Jordan Gloria Iriarte Kirk Broders Andrew J. Storer Vamsi J. Nalam Jordan M. Marshall
author_facet	Cecelia E. Hale Mark A. Jordan Gloria Iriarte Kirk Broders Andrew J. Storer Vamsi J. Nalam Jordan M. Marshall
author_sort	Cecelia E. Hale
title	Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
title_short	Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
title_full	Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
title_fullStr	Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
title_full_unstemmed	Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
title_sort	genome‐wide snp identification in fraxinus linking genetic characteristics to tolerance of agrilus planipennis
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/dea4b96a86dd45ed99b3b2c5afe1cd30
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Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

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