Biology subjects

Doonan, J. M.

Publications and source records attributed to Doonan, J. M..

3 recordsLinked to original sources

bioRxiv2025

Genomic selection for accelerated heartwood formation in Pedunculate oak (Quercus robur L.) using whole-genome sequencing

Heartwood traits in trees are critical for timber quality but are notoriously difficult to phenotype due to their late expression and the need for destructive sampling. In this proof-of-concept study, we demonstrate that combining genome-wide association studies (GWAS) with Bayesian genomic prediction models provides an effective strategy to overcome these challenges. By using GWAS to preselect trait associated SNPs and integrating them into predictive models, we substantially improve the accuracy of genomic predictions for heartwood related traits in oaks. Our approach allows for reliable selection of superior genotypes at the seedling stage, long before heartwood traits can be directly measured, thus enabling early and cost-effective breeding decisions. We also identify the number of rings in sapwood as a genetically controlled, easily measured proxy trait that enhances selection strategies for heartwood content. Together, these findings provide a scalable framework for integrating genomics into operational tree breeding programs and demonstrate how combining GWAS and genomic prediction can accelerate the improvement of complex wood traits in long lived forest tree species.

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↗

bioRxiv2023

Chemical cues from beetle larvae trigger proliferation and virulence of a plant pathogen

Agricultural crop productivity and global forest biomes are coming under increasing threat from insect pests and microbial pathogens. This impact is worsened by inter- kingdom insect-microbe interactions that can increase transmission and disease severity in affected plants. Whilst bacterial chemical cues have been shown to directly influence insect behaviour, the impact of insect-derived compounds on phytopathogens is poorly understood. Here, we investigated the chemical basis for interactions between beetle larvae and bacteria in acute oak decline (AOD), a disease characterised by inner bark necrosis and involving a polymicrobial consortium including Brenneria goodwinii and larval galleries of Agrilus biguttatus. We found that A. biguttatus larval extracts contain chemical elicitors that increase bacterial growth rate and final cell density during in vitro culture, and stimulate the differential expression of [~]600 genes, including the Type III Secretion System and its effectors, which are major virulence factors in plant pathogens. Chemical compounds from closely related insect species did not have this effect. These findings highlight the importance of inter-kingdom interactions in plant disease and suggests a novel mode-of-action for insect-derived chemical elicitors in facilitating the virulence of phytopathogens.

ecology↗