Biology subjects

Whittet, R.

Publications and source records attributed to Whittet, R..

3 recordsLinked to original sources

bioRxiv2025

European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility

European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by ash dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples, with particular focus on individuals showing low ADB susceptibility. We identified 362,965 structural variants (SVs) present in more than three individuals, including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this reduced the fraction of the genome estimated as dispensable from 35.9% to 8.7%, identifying 3,412 high-confidence dispensable genes, including 141 annotated with gene ontology terms associated with defence response. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This revealed 220 single nucleotide polymorphisms (SNPs) showing allele frequency shifts between healthy and highly damaged pools of individuals that are broadly consistent across the mainly UK seed sources sampled, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

genomics↗

bioRxiv2025

Genetic and plastic effects on trait variability in two major tree species: insights from common garden experiments across Europe

Phenotypic plasticity and genetic adaptation are key mechanisms that enable species to respond to changing environments. Tree traits do not vary independently but rather in coordination. However, our understanding of whether functional traits are governed by the same mechanism is far from complete. Thus, we aim at assessing the drivers of trait variability of sessile oak and European beech provenances across their distribution ranges. We estimated growth-related and leaf morphological traits from 9 and 11 provenances of oak and beech, respectively, grown in four different common gardens distributed across their respective distribution areas. Overall, phenotypic plasticity played a dominant role in explaining individual trait variability. For most oak traits, variation among provenances and genetically based plasticity were correlated with the climate of origin, whereas fewer significant associations were found for beech. In oak, climate-transfer distance analyses revealed that traits such as DBH, height, specific leaf area, and long-term growth responses to summer temperature decreased when provenances were moved away from their local precipitation regime. In beech, significant climate-transfer distances were fewer and primarily related to temperature-related parameters. These results suggest that natural selection and local adaptation may play a secondary but notable role. The pattern of multi-trait phenotypes indicates that resource-use strategies among provenances covary with the temperatures of origin in both species. The limited genetic responses in beech could hinder its survival if it reaches the boundaries of trait plasticity, while oak may better adjust through adaptation. Our study contributes to a better understanding of the interplay between genetic adaptation and phenotypic plasticity in long-lived forest trees.

ecology↗

bioRxiv2025

Genetic basis of traits and local adaptation in UK silver birch

Knowledge of the genomic basis of phenotypes in forest trees lags that of other economically important organisms. We sequenced the genomes of 2054 silver birch trees from 20-year-old field trials at three locations in Britain. Each trial site contains trees from the same 29 source populations, and one trial site (Drummond) is outside the climate envelope of the source sites. We discovered many single nucleotide polymorphisms (SNP), and a structural polymorphism, associated with several growth traits. Using models trained with genome-wide SNPs we estimate the genomic breeding values of 148 plus trees. We discover 117 SNPs significantly associated with source-site environmental variables, but genetic offset estimates using these SNPs provide poor predictions of tree growth rates (Drummond excluded). They are outperformed in this task by offset estimates using thousands of non-significant SNPs. Such estimates for Drummond in current climates are higher than for source sites under a future worst case climate scenario.

genomics↗