Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback

TY - JOUR

T1 - Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback

AU - Franco Ortega, Sara

AU - Bedford, James

AU - James, Sally

AU - Newling, Katherine

AU - Ashton, Peter D

AU - Boshier, David

AU - Clark, Jo

AU - Hartley, Susan E

AU - Harper, Andrea Louise

N1 - This is an author-produced version of the published paper. Uploaded in accordance with the University’s Research Publications and Open Access policy.

PY - 2025/3/25

Y1 - 2025/3/25

N2 - Ash dieback caused by the fungus Hymenoscyphus fraxineus has devastated the European ash tree population since it arrived in Europe in 1992. Great effort has been put into breeding programmes to increase the genetic diversity of ash trees and find heritable genetic markers associated with resistance, or tolerance mechanisms, to ash dieback. To facilitate identification of molecular markers, we used Oxford Nanopore Technologies combined with Illumina sequencing to obtain an accurate and contiguous ash genome. We used this genome to reanalyse transcriptome data from a Danish ash panel of 182 tree accessions. Using associative transcriptomics, we identified 175 gene expression markers (GEMs), including 11 genes annotated as dormancy MADS-box transcription factors which are associated with ash bud dormancy, flowering and senescence. We hypothesize that tolerant trees both break dormancy earlier in the year by increasing the expression of flowering-related SOC1 MADS-box and reducing the expression of SVP-like MADS-box, whilst also accelerating senescence by increasing the expression of JOINTLESS MADS-box genes. DNA methylation differences in the promoters of MADS-box genes between one tolerant and one susceptible tree indicate potential epigenetic regulation of these traits.

AB - Ash dieback caused by the fungus Hymenoscyphus fraxineus has devastated the European ash tree population since it arrived in Europe in 1992. Great effort has been put into breeding programmes to increase the genetic diversity of ash trees and find heritable genetic markers associated with resistance, or tolerance mechanisms, to ash dieback. To facilitate identification of molecular markers, we used Oxford Nanopore Technologies combined with Illumina sequencing to obtain an accurate and contiguous ash genome. We used this genome to reanalyse transcriptome data from a Danish ash panel of 182 tree accessions. Using associative transcriptomics, we identified 175 gene expression markers (GEMs), including 11 genes annotated as dormancy MADS-box transcription factors which are associated with ash bud dormancy, flowering and senescence. We hypothesize that tolerant trees both break dormancy earlier in the year by increasing the expression of flowering-related SOC1 MADS-box and reducing the expression of SVP-like MADS-box, whilst also accelerating senescence by increasing the expression of JOINTLESS MADS-box genes. DNA methylation differences in the promoters of MADS-box genes between one tolerant and one susceptible tree indicate potential epigenetic regulation of these traits.

U2 - 10.1093/g3journal/jkaf053

DO - 10.1093/g3journal/jkaf053

M3 - Article

SN - 2160-1836

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

ER -