Biology subjects

Kirisits, T.

Publications and source records attributed to Kirisits, T..

2 recordsLinked to original sources

bioRxiv2024

Limitations of ad hoc genotyping in detecting ash dieback tolerance in Fraxinus excelsior

Ash dieback (ADB), caused by the invasive alien fungal pathogen Hymenoscyphus fraxineus, is an emerging disease that poses major threats to the survival of common ash (Fraxinus excelsior) in Europe. Here, we report on a field trial aiming at the identification of ADB tolerant genotypes while encompassing the genetic diversity of common ash in Austria. Over 35,000 progenies from more than 600 putative tolerant mother trees were assessed for ADB symptoms over a period of three years. One tolerant and one susceptible progeny from a subset of the mother tree range (570 trees) were genotyped using the 4TREE array, a genotyping tool developed specifically to screen common ash provenances for their tolerance to ash dieback. We aimed to (1) better characterize the genetic structure of common ash in Austria, (2) identify hybrids between common ash and F. angustifolia (narrow-leaved ash), (3) detect genetic loci associated with tolerance to ADB, and (4) identify genetic variation associated with abiotic factors such as temperature and precipitation influencing the severity of ADB. We identify ash individuals from Eastern Austria matching putative hybrids with F. angustifolia showing varying degrees of F. angustifolia ancestry in structure analyses. The non-hybrid gene pool is characterized by shallow genetic structure following a west to east geographic pattern. In contrast to our expectations, genotype-damage association analyses overall fail to detect SNPs associated with tolerance to ADB. Our findings underscore that the polygenic architecture governing tolerance and the rapid decay of genomic linkage disequilibrium (LD) (within approximately 10 kb) significantly limit the ability to identify association outliers using the 4TREE SNP array. This highlights the constrained utility of chip genotyping approaches for this specific purpose. In contrast, the array proves successful in detecting hybrids between common ash and narrow-leaved ash, as well as outlier SNPs associated with abiotic predictors (such as annual precipitation and temperature) known to influence the severity of ADB damage.

genetics↗

bioRxiv2023

Multiple, single trait GWAS and supervised machine learning reveal the genetic architecture of Fraxinus excelsior tolerance to ash dieback in Europe

Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among clones in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior remains poorly understood. Here, we integrate quantitative genetics and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and its relationship to phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). We use whole-genome sequencing of 486 F. excelsior genotypes to confirm the genotypic correlation between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Although, our results suggest that the examined traits are polygenic, a relatively small number of single nucleotide polymorphisms (SNPs) explained a large proportion of the variation in both disease tolerance and autumn leaf yellowing. We could explain up to 63% (based on 9155 unlinked SNPs) of variation in individual response to ash dieback crown damage and up to 72% (based on 3740 unlinked SNPs) of variation in autumn yellowing. We identified eight SNPs encoding non-synonymous substitutions, of which those with the highest predictive power were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). Overall, our results provide insights of a multifaceted defence response, according to which a combination of direct defence mechanisms and phenological avoidance of pathogen spread constitute tolerance to ash dieback.

plant biology↗