Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

Irina Čalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John Edward Carlson, David B. Neale

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. Methods: In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1.5 K - 50 K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher's exact test and logistic regression tests were performed to test associations between SNPs and phenotypes. Results: Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes a mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. Metallothioneins represent Cys-rich metal chelators able to coordinate metal atoms and may play an important role in the resistance mechanisms against beech scale insect. Conclusion: The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs.

Original languageEnglish (US)
Article number547
JournalBMC genomics
Volume18
Issue number1
DOIs
StatePublished - Jul 20 2017

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Fagus
Disease Resistance
Genome-Wide Association Study
Genes
Single Nucleotide Polymorphism
Hemiptera
Metallothionein
Metals
North America
Cryptococcus
Chromosomes, Human, Pair 5
Genetic Loci
Chelating Agents
Breeding
Fungi
Logistic Models
Genotype
Ions
Phenotype
Messenger RNA

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Čalić, Irina ; Koch, Jennifer ; Carey, David ; Addo-Quaye, Charles ; Carlson, John Edward ; Neale, David B. / Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). In: BMC genomics. 2017 ; Vol. 18, No. 1.
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abstract = "Background: The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. Methods: In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1.5 K - 50 K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher's exact test and logistic regression tests were performed to test associations between SNPs and phenotypes. Results: Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes a mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. Metallothioneins represent Cys-rich metal chelators able to coordinate metal atoms and may play an important role in the resistance mechanisms against beech scale insect. Conclusion: The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs.",
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Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). / Čalić, Irina; Koch, Jennifer; Carey, David; Addo-Quaye, Charles; Carlson, John Edward; Neale, David B.

In: BMC genomics, Vol. 18, No. 1, 547, 20.07.2017.

Research output: Contribution to journalArticle

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AU - Čalić, Irina

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AU - Neale, David B.

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