Biology subjects

Lasky, J. R.

Publications and source records attributed to Lasky, J. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic history and ecology of local adaptation in sky-island Arabidopsis thaliana

Adaptation to local environments in isolated habitats may produce independent solutions to similar ecological challenges, yielding insight into the predictability of evolution. Alpine plants on tropical sky-islands, in particular, must cope with extreme diurnal fluctuations in temperature and radiation. These populations may undergo parallel local adaptation to high elevation, or alternatively, distinct local adaptations due to intermountain heterogeneity. For instance, abiotic stress on mountain peaks could select for stress tolerance or stress escape/bet-hedging strategies. We tested these hypotheses in experiments with 163 newly sequenced Arabidopsis thaliana genotypes from East Africa. Genomic history followed geography: Ugandan genotypes were the most divergent, and Ethiopian genotypes more closely related. Effective population size decreased towards the present on all mountains, in concert with declining climatic suitability since the end of the African Humid Period. Genotypes from the colder and seasonally drier mountains showed strong seed dormancy, rapid flowering, short/curved inflorescences. In contrast, genotypes from the milder and less seasonal mountains showed less seed dormancy, delayed flowering, and long/erect inflorescences. Elevational clines found in multiple mountains included seed dormancy-release with short (vs. long) stratification, and shorter inflorescences, at higher elevations. In a genome-wide association study (GWAS) with inflorescence length, we detected the TCP5 transcription factor, but these variants only segregated in some mountains and showed an elevational allele frequency cline at only one mountain. Allele reuse based on GWAS was greater between Ethiopian populations (QTL allele-frequency r > 0.9 for most traits), and generally lower between Uganda and the rest. Results indicate limited evidence of parallel local adaptation along elevation, suggesting that dwarf inflorescences are selected for in multiple mountain tops, while bet-hedging prevails in cold and seasonally dry sky-islands, and divergent selection along elevation in other traits can evolve in mountains with milder climates. Overall these results suggest a long history of isolation and ecological complexity limit the predictability of local adaptation.

evolutionary biology↗

bioRxiv2026

Functional genomic map of local adaptation in sorghum to guide allele mining

Genomic data from genebanks could be exploited to find alleles adapted to target environments for resilience breeding, but it can be difficult to prioritize among the thousands of accessions and millions of genomic variants. There are competing hypotheses for the molecular basis and architecture of local adaptations: e.g. whether cis-regulatory versus amino acid changing variants are more important; or whether small-effect, low pleiotropy versus large-effect, high pleiotropy variants are more important. Here, we compare a range of variant types and genomic contexts thought to influence effect size, pleiotropy, and selection for their role in local adaptation in 443 whole genome resequenced African sorghum landraces. We used genotype-environment associations (GEAs) as evidence of local adaptation. We found that GEA were particularly enriched in the vicinity of genes and depleted elsewhere. However, enrichment was strongest in likely cis-regulatory contexts: accessible chromatin, unmethylated regions, and in transposable elements close to genes. Near genes, there were clear peaks in GEAs at the transcription start site, where mutations are demonstrated to have the largest expression effects. Additionally, GEAs in accessible chromatin and unmethylated regions were better predictors of genetic variation in response to experimental drought than comparable loci. Having tested hypotheses about the variants underlying local adaptation, we can now use this knowledge of the importance of cis-regulatory variation in the search for new environmentally-adaptive alleles for plant improvement.

evolutionary biology↗

bioRxiv2026

Crop yields under simulated nuclear winter: a growth chamber experiment

A global nuclear war could inject soot into the stratosphere, blocking sunlight and causing rapid cooling. Assessments of the resulting agricultural collapse rely on crop models never validated under such conditions. We grew wheat, canola, and potato in growth chambers simulating the light and temperature of an extreme nuclear winter at tropical and temperate sites. In the tropical chamber (18-20 {degrees}C, 200 mol m-2 s-1 PAR), all three crops produced viable yields. Wheat yielded 2.1-2.3 t/ha (n=3 well-watered, n=3 water-stressed pots), 60% of the global average, and single-pot observations of canola and potato suggested biological yields comparable to global averages. In the temperate chamber simulating nuclear winter irradiance (60-360 mol m-2 s-1), wheat stems collapsed under their own weight. Although hand-harvesting recovered 0.6-2.8 t/ha of grain, mechanical field harvest of a flat canopy would recover substantially less. This failure mode was not observed in a higher-light control chamber and is not captured by existing crop models, which may therefore overestimate temperate cereal production under nuclear winter. Canola produced comparable yields under both temperate light regimes without lodging. Empirical screening of additional staples is needed to identify which remain viable under nuclear winter.

plant biology↗

bioRxiv2026

Phenotypic plasticity evolved for climate variability constrains performance under climate warming

Phenotypic plasticity allows plants to rapidly respond to changing environments without the need for evolutionary change or migration. While selection can create variation in plasticity across natural populations, these responses are not adaptive in all environments. To predict whether plasticity will be adaptive requires evaluation of its fitness effects across a range of environments, including novel ones. Here, we test how traits and their plasticity vary for genotypes collected across a natural hybrid zone between two tree species with contrasting climatic niches. Fast-growing Populus trichocarpa inhabits maritime environments with relatively warm and stable temperatures, while P. balsamifera inhabits continental environments with cold winters and large temperature variance throughout the year. We planted 44 clonally replicated genotypes into thirteen common gardens and measured vegetative phenology, leaf morphology, stomata morphology and conductance, and photochemistry. Overall, genotypes from colder, more continental environments exhibited higher plasticity. P. balsamifera ancestry was associated with increased plasticity in timing of fall phenology, stomatal conductance, and leaf mass per unit area. We assessed the effects of trait plasticity on fitness estimated as yearly growth across common gardens and found that the plasticity-fitness relationship was often garden-specific, indicating that the planting environment did not consistently mediate plasticity-fitness relationships. When the effects of trait plasticity on growth varied by garden temperature, higher plasticity generally had neutral or negative associations with growth in warmer environments. These results suggest that elevated plasticity evolved in a P. balsamifera genomic background as part of a climate generalist strategy to seasonal temperature variability, but that there is a trade-off between plasticity and growth in warmer environments. Consequently, less-plastic but warm-adapted P. trichocarpa genotypes are likely to have a fitness advantage under warming climates. These results demonstrate that plasticity may sometimes be maladaptive and will not be universally beneficial in a warming world.

evolutionary biology↗

bioRxiv2025

Persistent trade-offs balance competition and colonization across centuries

Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature--or are eroded as lineages adapt through compensatory changes--remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins--phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare--while the tailocins production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient -- historical genomes spanning two centuries show that the trade-off has been maintained for at least 10-10 generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome. SignificanceWhen a microbe colonizes a host, it must both establish infection and outcompete other organisms. Short-term experiments show that gains in competitive ability can reduce colonization, creating trade-offs, but whether microbes resolve these conflicts over long evolutionary timescales is unknown. We show that a trade-off between competitive killing and host colonization has been stably maintained for centuries in natural Pseudomonas populations infecting Arabidopsis thaliana. Tailocins--phage-derived weapons--provide strong competitive advantages, yet their production reduces colonization success, explaining why the most broadly lethal variants remain rare. Genomic surveys and historical genomes spanning two centuries reveal that the polymorphisms underlying this trade-off have persisted across 10-10 generations. Understanding such long-lived constraints can inform antimicrobial strategies that exploit evolutionary trade-offs.

evolutionary biology↗

bioRxiv2025

Population genomic structure of sorghum landraces across landscape, environment and culture

The spread of staple crops to diverse environments over time and their current genetic structure may reflect historical dispersal by humans, sustained human preference for particular traits, and adaptation to local environments. Sorghum is a drought-tolerant crop native to Africa cultivated by hundreds of millions of smallholders globally. Here we examined the ecological context of population-genomic structure of 1,806 sorghum landraces across Africa and Eurasia to infer the relative contribution of environmental and cultural factors to sorghum genetic diversity across different relative time periods. Sorghum landraces were spatially and linguistically structured at a large-scale and within subregions, following a pattern of isolation by distance. Within regions, much of genomic structure was best explained by a mechanistic model of human travel time. In our assessment of hierarchical linguistic structure, we found that language families explain 4% of genomic variation while individual languages explain 13% of genomic variation, suggesting the importance of human culture and relationships in gene flow and selection. Variance partitioning showed that travel time, language, and climate explain up to 27% of genomic variation among landraces. We also observed regional differences in the degree of genetic relatedness across space and time in our assessment of shared ancestry. East Africa showed particularly strong geographic turnover in genomic composition and haplotype sharing, while West Africa showed substantial haplotype sharing even over large distances, signifying some rapidly spreading lineages. Thus, space, travel time, and culture likely capture important forces controlling sorghum genomic variation, but these factors operate heterogeneously over space.

plant biology↗

bioRxiv2025

Legacy of warming and microbial treatments shape root exudates and rhizosphere fungal communities of a tropical tree

O_LIPlant metabolites play a pivotal role in shaping rhizosphere microbial communities, yet how plant and microbial functions respond to environmental change remains poorly understood. We combined ecometabolomics and fungal community profiling to investigate how multiple abiotic and biotic treatments influence root exudate chemistry and fungal community assemblage in a tropical tree. C_LIO_LIGuarea guidonia seedlings were grown in sterilized soil primed with inoculum from long-term experimentally warmed or ambient plots in Puerto Rico. We manipulated soil microbes, soil moisture, and plant density and tested metabolite-fungi-plant trait associations. C_LIO_LIMetabolite diversity was significantly influenced by soil microbial legacy and moisture, while antimicrobial treatments altered metabolite composition without affecting diversity. Metabolite clusters exhibited distinct treatment-specific patterns. Fungal alpha diversity increased under low moisture, community composition shifted with antimicrobial treatments, and certain families showed strong treatment-specific responses. Although fungal diversity was not correlated with metabolite diversity, fungal community structure was significantly associated with metabolite composition. We also found global and pathway-specific correlations between fungal and metabolite distances, and weak but significant associations between metabolite/fungal composition and seedling traits. C_LIO_LIThese results underscore how environmental conditions shape belowground interactions, highlighting metabolite-fungal associations as potential early indicators of plant response to disturbance. C_LI

plant biology↗

bioRxiv2025

Strigolactone effects on Sorghum bicolor ecophysiology and symbioses

Strigolactones are ecologically, developmentally, and physiologically important hormones, but much remains unknown about their evolution and role in non-model species. Sorghum is a globally important C4 cereal and exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to parasitic plants, but with evidence for potential trade-offs. We studied sorghum mutants of loci in the strigolactone biosynthetic pathway, CAROTENOID CLEAVAGE DIOXYGENASE 8 (SbCCD8b) and LOW GERMINATION STIMULANT 1 (LGS1), previously shown to be Striga resistant by stimulating little germination of the parasite. SbCCD8b CRISPR-Cas9 deletions changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and diminished the establishment and benefit of mycorrhizal symbionts. For Striga-resistant LGS1 CRISPR-Cas9 deletions, differentially expressed genes were enriched with promoter motifs for stress response and growth pathways, net carbon assimilation rate was reduced, and the colonization of mycorrhizal symbionts was delayed. We additionally restored functional LGS1 into the RTx430 genetic background, which normally has the lgs1-2 natural deletion allele. While root exudates from LGS1 insertion mutants rescued Striga susceptibility, we did not see consistent rescue of other traits impacted in LGS1 loss-of-function mutants. We hypothesize that epistasis with a neighboring strigolactone synthesis gene, which is rarely lost without concomitant loss of LGS1, may alter the phenotypic effects of LGS1 variation. Our study gives context to potential trade-offs associated with host resistance to parasitic plants and, more broadly, builds on the contribution of strigolactones in shaping sorghum physiological processes, growth, and development.

plant biology↗

bioRxiv2025

Delivering trait-enhanced varieties to African smallholders through a pangenomic breeding network

Pangenomics has been promoted to accelerate breeding of orphan crops, but smallholder farmers in developing nations have seen little benefit so far. To address this gap, we built a global pangenomic breeding network, integrating African breeding programs, U.S. land grant universities, and international nonprofit research organizations. Here we demonstrate that pangenomics, when integrated with local crop improvement knowledge and global scientific partnerships, can facilitate breeding of drought and pest resilient varieties for smallholders. To breed trait-enhanced sorghum varieties with lgs1-1 resistance to witchweed (Striga hermonthica) for smallholders in Niger, one of the worlds least developed nations, we used population genomics across local and global scales to develop lgs1-1 Striga resistance markers, and deployed them for rapid introgression of resistance into locally-preferred varieties. Genomic characterization, along with controlled experiments in laboratory, pot, field stations, and smallholder farms, confirmed lgs1-1 resistance was introgressed without loss of essential local-preference traits. New pangenomic resources, including global resequencing and graph pangenomes, further accelerated design of broadly-applicable markers. Unlocking the potential of pangenomics for stress-resilience breeding depended on stakeholder input, strong inference, South-led decision support software, and a dense collaborative network. The experience of the network provides a scalable roadmap for collaborative pangenomic breeding of trait-enhanced varieties for the worlds lowest-resourced farmers.

genomics↗

bioRxiv2025

Nonphotochemical quenching changes with abiotic stressor and developmental stages

Nonphotochemical quenching (NPQ) is a critical photoprotective mechanism in plants, safeguarding photosystem II (PSII) and PSI from photodamage under abiotic stress. However, it is unclear if different stressors lead to similar NPQ phenotypes, and the magnitude of natural variation (between and within plant species) in NPQ response to abiotic stress is unknown. Testing a semi-high-throughput leaf-disc approach for examining the NPQ kinetics parameters, we investigated NPQ under chilling, drought and low nitrogen stress across multiple species and/or genotypes. Our results show substantial variation in NPQ phenotypes across species, genotypes and treatments. In C3 crops, tobacco and soybean, multiple NPQ parameters generally increased under chilling and drought, while in C4 crops, maize and sorghum, NPQ traits were more variable including a decrease of multiple NPQ parameters. Low-N stress revealed genotype- and developmental stage-specific effects on NPQ, potentially reflecting distinct adaptive strategies and regulatory changes in NPQ stress response. A significant effect of ecotype and stress treatment was detected on most NPQ kinetics traits in Arabidopsis thaliana, however, the interaction between ecotype and treatment was stronger in drought than in chilling. Differential regulation of NPQ could be associated with a combination of changes in proton motive, ATPase synthase activity, and PSI redox state. Our findings highlight that interpreting relative changes in NPQ under abiotic stress is inherently complex and demands a broader integration of physiological data across multiple regulatory layers.

physiology↗

bioRxiv2025

It's all in the timing: vegetative phase change alters selection under drought and contributes to local adaptation

The timing of developmental transitions is critical for adaptation, aligning stress-tolerant and sensitive stages with harsh and benign periods. At the same time, tradeoffs can promote diversity in development within populations. While geographic clines in developmental timing are often documented, there are few documented genetic tradeoffs in stress tolerance across developmental stages. Here, we study the juvenile-to-adult vegetative phase change (VPC), a conserved transition marked by changes in leaf morphology and physiology. In Arabidopsis, we found strong rank-changing genotype-by-environment interactions for fitness depending on the stage of drought exposure, indicating tradeoffs and stage-specific mechanisms of drought adaptation. Adult plants significantly increased water-use efficiency under drought, while juveniles did not, indicating lower juvenile plasticity. VPC timing varied with climate in Iberia, where genotypes from warm, dry climates transitioned earlier than those from cool, moist climates. However, SNPs associated with VPC timing and drought fitness showed little global geographic variation, suggesting tradeoffs maintain diversity across the species range. Genome-wide association mapping revealed candidate loci for VPC timing and stage-specific drought responses, several validated in T-DNA lines. Our results show that VPC timing contributes to drought adaptation and that genetic tradeoffs across developmental stages help maintain natural diversity.

plant biology↗

bioRxiv2025

Local trade-offs shape flower size evolution across Arabidopsis thaliana distribution.

The diversification of flowers, largely driven by mutualistic interactions with animal pollinators, has generated remarkable variation in floral form and size and is thought to have driven the evolutionary radiation of angiosperms. Here, we investigate the geographic variation in reproductive organ growth in the self-fertilizing species Arabidopsis thaliana, where the loss of pollinator dependence is predicted to favour reduced floral investment through resource reallocation. We find extensive variation in flower size underpinned by a polygenic architecture, in which derived alleles both increase and decrease petal size and show signatures of positive selection. Nevertheless, the evolutionary direction of flower size differs across regions, reflecting environmentally mediated shifts in the relationship between flower size and seed production. Strong purifying selection at the climatic margins favours smaller flowers, whereas relaxed environmental constraints in more suitable habitats allow the emergence and persistence of both small and large-flower variants. This biogeographic pattern extends to other life-history traits, highlighting how environmental heterogeneity and resource allocation constraints shape evolutionary trajectories and maintain phenotypic diversity in selfing lineages.

evolutionary biology↗

bioRxiv2025

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, and selection (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.

evolutionary biology↗

bioRxiv2024

Tropical Forest Soil Microbiome Modulates Leaf Heat Tolerance More Strongly Under Warming than Ambient Conditions

Tropical forests are increasingly threatened by climate change. Yet, it is still unclear how tropical plants respond to increasing temperatures. Leaf heat tolerance (LHT) in tropical plants is often at its upper limit, suggesting that climate change might negatively impact tropical forests. We hypothesized that intraspecific variation in this leaf trait might be associated with changes in the soil microbiome, which might also respond to climate. Specifically, we hypothesized that warming would increase LHT through changes in the soil microbiome: this study combined an in-situ tropical warming experiment with a shade house experiment in Puerto Rico. The shade house experiment consisted of growing seedlings of Guarea guidonia, a dominant forest species, under different soil microbiome treatments (reduced arbuscular mycorrhizal fungi, reduced plant pathogens, reduced microbes, and unaltered) and soil inoculum from the field experiment. Heat tolerance was determined using chlorophyll fluorescence (FV/Fm) on individual seedlings in the field and on pooled seedlings by pot in the shade house. We sequenced soil fungal DNA to analyze the impacts of the field and shade house treatments on the soil microbiome. In the field, seedlings from ambient temperature plots showed higher FV/Fm values under high temperatures (0.648 at 46 {degrees}C and 0.067 at 52 {degrees}C) than seedlings from the warming plots (0.535 at 46 {degrees}C and 0.031 at 52 {degrees}C). In the shade house, the soil microbiome treatments, which significantly influenced the fungal community composition, significantly influenced LHT. Reduction in fungal pathogen abundance and diversity altered FV/Fm before T50 for seedlings grown with soil inoculum from the warming plots but after T50 for seedlings grown with soil inoculum from the ambient plots. Our findings emphasize that the soil microbiome might play an important role in modulating the impacts of climate change on plants. Understanding and harnessing this relationship might be vital for mitigating the effects of warming on tropical forests, emphasizing the need for further research on microbial responses to climate change.

ecology↗

bioRxiv2024

Local adaptation to climate facilitates a global invasion

Local adaptation may facilitate range expansion during invasions, but the mechanisms underlying successful invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with severe impacts in western North America. We aimed to identify mechanisms and consequences of local adaptation in the North American cheatgrass invasion. We sequenced 307 range-wide genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Nearly half of North American cheatgrass comprises a mosaic of [~]19 locally adapted, near-clonal genotypes, each seemingly very successful in a different part of North America. Additionally, ancestry, phenotype, and allele frequency-environment clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the USA Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Our results indicate that multiple introductions and migration within the invaded range fueled local adaptation and success of cheatgrass in western North America. Understanding how environment and gene flow shape adaptation and invasion is critical for managing ongoing invasions.

evolutionary biology↗

bioRxiv2024

Maladaptation in cereal crop landraces following a soot-producing climate catastrophe

Aerosol-producing global catastrophes such as nuclear war, super-volcano eruption, or asteroid strike, although rare, pose a serious threat to human survival. Light-absorbing aerosols would sharply reduce temperature and solar radiation reaching the earths surface, decreasing crop productivity including for locally adapted traditional crop varieties, i.e. landraces. Here, we test post-catastrophic climate impacts on barley, maize, rice, and sorghum, four crops with extensive landrace cultivation, under a range of nuclear war scenarios that differ in the amount of black carbon aerosol (soot) injected into the climate model. We used a crop growth model to estimate gradients of environmental stressors that drive local adaptation. We then fit genotype environment associations using high density genomic markers with gradient forest offset (GF offset) methods and predicted maladaptation through time. As a validation, we found that our GF models successfully predicted local adaptation of maize landraces in multiple common gardens across Mexico. We found strong concordance between GF offset and disruptions in climate, and landraces of all tested crop species were predicted to be the most maladapted across space and time where soot-induced climate change was the greatest. We further used our GF models to identify landrace varieties best matched to specific post-catastrophic conditions, indicating potential substitutions for agricultural resilience. We found the best landrace genotype was often far away or in another nation, though countries with more climatic diversity had better within-country substitutions. Our results highlight that a soot-producing catastrophe would result in the global maladaptation of landraces and suggest that current landrace adaptive diversity is insufficient for agricultural resilience in the case of the soot scenarios with the greatest change to climate.

evolutionary biology↗

bioRxiv2023

Bacterial assembly in the switchgrass rhizosphere is shaped by phylogeny, host genotype, and growing site.

O_LISince microbial traits are conserved at different taxonomic levels, plant hosts may influence microbiome composition differently at different levels to broadly promote or resist microbiota with traits that impact host fitness. We tested this hypothesis by assessing signals of host genetic influence on bacterial composition in the switchgrass rhizosphere using 128 genotypes in dissimilar growing sites. C_LIO_LIWe employed three common gardens, combined with host genetic mapping, 16S rRNA gene sequence analysis, hierarchical modeling, tests of phylogenetic conservation of host influence, and genome-wide association analyses to determine the contributions of host genetics in shaping rhizosphere bacterial composition at different taxonomic levels. C_LIO_LIModeling bacterial assembly showed that growing site was a strong factor shaping bacterial composition in the rhizosphere, though host genetic influence played a significant role. The heritability of bacterial abundance was strongest at the genus level. Phylogenetic signal for heritability was detected within the bacterial phylogeny but conserved clades differed between common gardens. We identified shared host genetic variants associated with bacterial abundance and host traits related to plant metabolism. C_LIO_LIOur results suggest further investigation is required regarding the genotype-by-environment-by-microbiome relationship to elucidate the factors shaping rhizosphere microbiome composition and the agroecological dynamics shaping plant phenotype. C_LI

plant biology↗

bioRxiv2022

Century-long timelines of herbarium genomes predict plant stomatal response to climate change

Dissecting plant responses to the environment is key to understanding if and how plants adapt to anthropogenic climate change. Stomata, plants pores for gas exchange, are expected to decrease in density following increased CO2 concentrations, a trend already observed in multiple plant species. However, it is unclear if such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 A. thaliana historical herbarium specimens collected over the last 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a polygenic score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the last centuries without requiring direct phenotype observation of historical samples. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes have already responded to climate change through adaptive evolution. One sentence summaryUsing a molecular-knowledge based genetic phenotype proxy, historical whole-genome A. thaliana timelines compared with contemporary data indicate a shift of stomatal density following climate-associated predictions.

plant biology↗