RNA sequence reads from each cDNA library mapped to the full-length copy of the candidate gene transcript sequence from contig 03321, representing the expression of the candidate Mt gene after the challenge by the insect vector. (DOCX 161Â kb

Charles Addo-Quaye (119385)

David Carey (2936301)

David Neale (2836163)

Irina ÄaliÄ (4262899)

Jennifer Koch (238315)

John Carlson (4491)

BMC Genomics

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Additional file 9: of Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

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

Irina Ćalić

Jennifer Koch

David Carey

Charles Addo-Quaye

John E. Carlson

David B. Neale

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

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BackgroundThe 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.MethodsIn this case-control genome-wide association study (GWAS), we tested 16&nbsp;K high quality SNPs using the Affymetrix Axiom 1.5&nbsp;K - 50&nbsp;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.ResultsAssociation 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.ConclusionThe 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

Ćalić, Irina

Koch, Jennifer

Carey, David

Addo-Quaye, Charles

Carlson, John E

Neale, David B

eScholarship - University of California

English

https://figshare.com/articles/Additional_file_9_of_Genome-wide_association_study_identifies_a_major_gene_for_beech_bark_disease_resistance_in_American_beech_Fagus_grandifolia_Ehrh_/5230141

Additional file 9: of Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

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eScholarship - University of California