A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation

Native Australian seedlings exhibit novel strategies to acclimate to repeated heatwave events

Heatwaves are becoming more intense and frequent. Plant photosystem thermal thresholds can vary with species, but also shift in response to environmental triggers. Both upper and lower thresholds can acclimate to repeated heatwaves through ecological stress memory, where prior exposure primes them for subsequent events. The extent to which acclimation to repeated heat stress events varies among environmental origin and/or species is unknown. Different acclimation strategies might reflect biome of origin, or may be species-specific. For 12 species from two contrasting biomes-extreme desert and benign coastal temperate-we investigated responses to two simulated heatwaves, via shifts in upper and lower critical temperatures of photosystem II, and the difference between these thresholds, thermal tolerance breadth (TTB). Biome of origin had no effect on thermal tolerance. Observed differences among species following heat events suggested two possible acclimatory strategies. In some cases, species increased thermal thresholds during the first heatwave, but at the cost of reduced thermal tolerance during the second heatwave, a sprinter strategy. Other species acclimated to the first heatwave and further increased thermal tolerance to a second heatwave, indicative of ecological stress memory, a marathoner strategy. Synthesis: these among-species responses to heatwaves could suggest distinct vulnerabilities and resilience to repeat heat stress events, with some species having limited capacity to tolerate consecutive heatwaves, possibly as the cost of acclimation is too great, with other species having the advantage of increased tolerance via stress memory, helping them survive future stress, at least in the short-term.

Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana

Magnesium (Mg) is a crucial element in plants, particularly for photosynthesis. Mg homeostasis is influenced by environmental and genetic factors, and our understanding of its variation in natural populations remains incomplete. We examine the variation in leaf Mg accumulation across the distribution of Arabidopsis thaliana, and we investigate the environmental and genetic factors associated with Mg levels. Using genome-wide association studies in both the widespread Eurasian population and a local-scale population in Cape Verde, we identify genetic factors associated with variation in leaf Mg. We validate our main results, including effect size estimates, using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) mutagenesis. Our findings reveal a significant association between leaf Mg and latitude of origin. In Eurasia, we find a signal at the nutrient-response regulator, RAPTOR1A, and across the species range, we find that multiple alleles of the Mg transporter, MAGNESIUM RELEASE 5 (MGR5), underlie variation in leaf Mg and contribute to the observed latitudinal cline. Overall, our results indicate that the spatial distribution of leaf Mg in A. thaliana is affected by climatic and genetic factors, resulting in a latitudinal cline. Further, they show an example of allelic heterogeneity, in which multiple alleles at a single locus contribute to a trait and the formation of a phenotypic cline.

Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequence

The evolution of gene expression responses is a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis-regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learn de novo cis-regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, approaches to predict DEGs between specific environments based only on proximate DNA sequences require further development, and additional information may be required.

In situ diversification and adaptive introgression in Taiwanese Scutellaria

Island habitats provide unique opportunities to study speciation. Recent work indicates that both ex situ origination and in situ speciation contribute to island species diversity. However, clear evidence of local adaptation of endemic plant species on islands requires in-depth studies, which are scarce. This study underscores the importance of local adaptation in maintaining species boundaries by examining how adaptive introgression, hybridization, and local adaptation contribute to genetic variation in island species. Multilocus genome scanning of 51 nuclear genes was used to investigate the evolutionary relationships of the Scutellaria species complex on Taiwan Island and assess the role of in situ diversification in generating high endemism and genetic diversity. Interspecies introgressions were detected by phylogenetic networks and ABBA-BABA-based analysis, suggesting ongoing or recent speciation processes. Coalescent-based simulation identified hybrid speciation in Scutellaria taiwanensis and Scutellaria hsiehii, with evidence of hybridization between more than two parental species. Genotype-environment association studies revealed that the influence of climate, particularly precipitation- and temperature-related factors, contributed to adaptive genetic divergence between species. Additionally, adaptive introgression related to environmental pressures that may have facilitated the colonization of new island habitats were identified. This research illustrates how hybridization, introgression, and adaptation shaped the evolutionary histories and divergence of this island-endemic plant species complex and sheds light on the multifaceted mechanisms of speciation on semi-isolated islands.

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

Fully Atomistic Molecular Dynamics Simulation of Ice Nucleation Near an Antifreeze Protein

Heterogeneous ice nucleation is a widespread phenomenon in nature. Despite extensive research on ice nucleation near biological antifreeze proteins, a probe for ice nucleation and growth processes at the atomic level is still lacking. Herein, we present simulation evidence of the heterogeneous ice nucleation process on the ice-binding surface (IBS) of the Tenebrio molitor antifreeze protein (TmAFP). Our all-atomistic molecular dynamics simulations reveal detailed steps toward precritical nucleus formation from one-dimensional (1D) channel water to a 2D ice nanolayer and, finally, a 3D ice nucleus. Compared with homogeneous ice nucleation under the same supercooling conditions, the IBS of TmAFP can markedly reduce the critical size of the ice embryo and lower the nucleation free energy barrier, thereby favoring ice nucleation. Additionally, through artificial mutation of selected functional groups on the IBS, we gain deeper insights into how the specific functional groups of the IBS affect ice nucleation. We highlight that the carbonyl groups in the backbone play a crucial role by providing fixed locations for channel water. This function is essential for ensuring alignment between the 2D ice nanolayer and the ice lattice structure.

Experimental validation of genome-environment associations in Arabidopsis

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation, but GEA are rarely followed by experimental validation. Here, we tested loci identified in three different moisture-related GEA studies on Arabidopsis. We studied 44 GEA-identified genes using t-DNA knockout lines under drought and tested for effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions on performance and fitness. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, while 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments we found wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, we found that GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA putative drought-adapted genes were validated for GxE interactions for fitness under drought, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and thus demonstrate prospects for GEA discovery of new local adaptations.

Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish ecotype of Arabidopsis thaliana on contrasting soils

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents of selection and quantifying their effects is key to understanding how populations adapt to local conditions. We performed a factorial reciprocal-transplant experiment using locally adapted ecotypes of Arabidopsis thaliana at their native sites to distinguish the contributions of adaptation to soil type and climate. Overall adaptive differentiation was strong at both sites. However, we found only very small differences in the strength of selection on local and non-local soil, and adaptation to soil type at most constituted only a few per cent of overall adaptive differentiation. These results indicate that local climatic conditions rather than soil type are the primary driver of adaptive differentiation between these ecotypes.

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding

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Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally. While ideally grown in 13-21 °C, its cultivation extends into winter in milder climates. However, occasional freezing temperatures can significantly reduce yields. Therefore, the development of freezing-tolerant lettuce varieties has become a long-term goal of lettuce breeding programs. Despite its significance, our understanding of freezing tolerance in lettuce remains limited. Plants have evolved a coping mechanism against freezing, known as cold acclimation, whereby they can increase freezing tolerance when pre-exposed to low nonfreezing temperatures. The CBF pathway is well-known for its central role in cold acclimation. Previously, we identified 14 CBF genes in lettuce and discovered that one of them, LsCBF7, had a loss-of-function mutation. In this study, we uncovered that accessions from colder regions carried the wild-type allele of LsCBF7 and this allele likely contributed to increased freezing tolerance, with 14% of the lettuce population carrying this allele. Interestingly, in wild lettuce (L. serriola) that is considered a progenitor of cultivated lettuce, this wild-type allele was much more common, with a frequency of 90%. This finding suggests that this wild-type allele may have undergone negative selection during the domestication or breeding of lettuce. Our data strongly indicate that this allele could be linked to early bolting, an undesirable trait in lettuce, which may have driven the negative selection. While this wild-type allele shows promise for improving freezing tolerance in lettuce, it is crucial to decouple it from the early bolting trait to fully harness its potential in lettuce breeding.