Biology subjects

Hämälä, T.

Publications and source records attributed to Hämälä, T..

4 recordsLinked to original sources

bioRxiv2026

Pangenome and transcriptome analyses reveal extensive diversity and breeding signatures in the oat GDSL-esterase/lipase gene family

Lipolytic enzymes play critical roles in plant development, growth, and stress responses. In oat (Avena sativa), they are of particular interest because lipid hydrolysis contributes to rancidity and reduced grain quality, yet little is known about genomic variation in oat lipolytic enzymes. Here, we investigated genomic and expression diversity of the GDSL-esterase/lipase gene family using pangenome, transcriptome, and genome-wide association analyses. Across 22 A. sativa and two A. sterilis genome assemblies, we identified 7,775 GDSL genes (~324 per assembly), revealing wide conservation of ancestral orthologs alongside extensive copy-number variation among homoeologs and paralogs. Transcriptome profiling across 20 genotypes and six tissues demonstrated preferential expression in embryo and root, with tissue-specific patterns highlighting candidates for specific functions, such as seed lipid metabolism. Associations with structural variants further uncovered candidate mutations underlying expression variation among accessions. Comparisons of cultivated and wild oat detected loci with signatures of breeding-based selection, suggesting that GDSL genes have contributed to diversification of the cultivated gene pool. Using 629 whole-genome sequenced accessions, we also identified associations between GDSL regions and agronomic traits, particularly plant height and effective tiller number. Several regions showed patterns consistent with selection, highlighting candidate loci for further investigation of agronomic variation. Together, our results reveal substantial genomic and transcriptional diversity within the oat GDSL gene family and identify candidate genes and genomic regions for improving seed quality and agronomic performance. More broadly, our study demonstrates how pangenomic resources can be used to investigate gene-family diversity and function in complex polyploid crops.

genomics↗

bioRxiv2022

Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata

Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint - the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Together, our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.

evolutionary biology↗

bioRxiv2019

Maintenance of adaptive dynamics in a bottlenecked range-edge population that retained outcrossing

During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European sub-species Arabidopsis lyrata ssp petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that non-synonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived non-synonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp petraea shows a strong resilience to the effect of range expansion.

evolutionary biology↗

bioRxiv2018

Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in Arabidopsis lyrata

Short-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory, but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modelling indicates that populations within the gradients diverged less than 2000 years ago and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high divergence and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

evolutionary biology↗