Evolutionary genetics of plant adaptation

Looking back to look ahead: the temporal dimension of conservation seed bank collections

A wealth of plant material and data is stored globally in conservation seed banks. This material represents not only a repository of plant genetic resources but also an asset for nature-based solutions (NbS), such as ecological restoration and reforestation, and research in plant science. Here, we explore the temporal and spatial dimensions of seed collections and the challenges limiting their use in NbS and research, while highlighting how they could be a source of material for adaptation and evolution studies. However, existing seed lots originally collected for conservation purposes will not be sufficient to support NbS and research on their own. We propose a long-term experimental approach that, together with new targeted collecting programmes, can leverage the temporal dimension of seed collections by carrying out repeated sampling from the same population. At the same time, we stress how these approaches will benefit from new dedicated collections holding seeds from each maternal line separately. By moving towards a bidimensional (space and time) collecting approach, conservation seed banks can go beyond long-term conservation per se and transform their collections into dynamic repositories capable of addressing pressing ecological, evolutionary, and conservation questions and help to understand and shape plant communities of the future.

Systems genomics of salinity stress response in rice

Populations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under balancing and purifying selection, respectively, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.

Among- and within-population variation in germination response shapes ecological resilience in the Mediterranean cliff species Brassica incana

BACKGROUND AND AIMS

Understanding how plant species respond to extreme conditions is crucial for predicting their ecological resilience under climate change. Here, we aimed to forecast the ecological resilience of the Mediterranean cliff species Brassica incana (Brassicaceae) by estimating population variation in germination response under novel extreme environmental conditions.

METHODS

We investigated the thermal germination responses in 14 populations of B. incana by exposing seeds to temperatures within and outside conditions experienced in their local environment. Then, we quantified among- and within-population variation in germination response to extreme temperatures, estimated genotype-by-environment interactions (G × E) and tested if population performance at extreme temperatures is explained by local climate.

KEY RESULTS

We found significant among-population differences in germination response, a different level of within-population variability and different mechanisms underlying G × E patterns. Also, populations experiencing higher temperatures in their local environment showed a better performance at both cold and hot extremes while populations experiencing lower temperatures showed a limited ability to germinate under extreme conditions.

CONCLUSIONS

Our results suggest that populations experiencing higher temperatures in their local environment have a greater potential to face future thermal extreme conditions and their role is thus crucial to promote species ecological resilience.

Phenotypic plasticity vs. local genetic adaptation: essential oil diversity of natural immortelle (Helichrysum italicum (Roth.) G.Don) populations along eastern Adriatic coast

The essential oil of Helichrysum italicum (Roth) G.Don, commonly known as immortelle, is produced in Mediterranean countries to meet the increasing demand of the cosmetic and pharmaceutical industries. This study focused on the analysis of secondary metabolites, specifically essential oils, extracted from plants grown from the seeds of natural immortelle populations collected along the eastern Adriatic coast and cultivated ex situ under uniform conditions. Field trials were conducted to determine whether the observed variability was due to phenotypic plasticity or local genetic adaptation. Eighteen natural immortelle populations were sampled, hydrodistilled and their essential oil composition determined by gas chromatography-mass spectrometry. A total of 84 compounds were identified. Eighteen essential oil compounds were present in concentrations greater than 5% in at least one sample of 18 populations. The populations differed significantly in nine essential oil compounds: Limonene, linalool, nerol, neryl acetate, trans-caryophyllene, neryl propionate, ar-curcumene, β-selinene and δ-selinene and the differences were attributed to genetic adaptation to the native environment. Three chemotypes were identified within which the populations were grouped. Results showed a significant and strong correlation between biochemical and bioclimatic distance, with 22.4% of biochemical differentiation between populations explained by bioclimatic distance. Correlations between the 18 main compounds and the bioclimatic variables of the populations' native environment revealed that BIO14 Precipitation of driest month and BIO15 Precipitation seasonality, were the most informative. These results can serve as a first step for future selection of immortelle populations with desirable adaptations to obtain commercial cultivars that ensure high quality immortelle essential oil.

Phenological and morphological variations of Oryza rufipogon and O. nivara in Sri Lanka and their evolutionary implications

Phenological and morphological variation are widely viewed as a pivotal driver of ecological adaptation and speciation. Here, we investigate variation patterns of flowering phenology and morphological traits within and between O. rufipogon and O. nivara populations in Sri Lanka by incorporating the in situ observation in natural habitats and manipulative experiments in the common gardens. First, we observed varying degrees of phenological variation under different temporal and spatial conditions, suggesting that flowering phenology of two Oryza species varied depending on both environments and management practices. Particularly, the Sri Lankan O. nivara exhibits high plasticity in flowering phenology, implying that O. nivara might not be an annual in the strict sense. Second, the observation that flowering time of the two species overlapped suggests that the primary factor to maintain the species divergence in Sri Lanka may not be flowering time but rather environments. Third, our selection analysis suggests that interspecific divergence in the traits related to reproduction and habitat preference is adaptive and most likely driven by natural selection. Together, our case study on the Sri Lankan O. rufipogon and O. nivara enhances the understanding of the roles of phenotypic plasticity and environmental factors in the processes of adaptation and speciation.

Systems genomics of salinity stress response in rice

Populations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under balancing and purifying selection, respectively, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.

Climatic variation allows montane willows to escape an adaptive trade-off

Adaptive responses to climate change, based on heritable variation in stress tolerance, may be important for plant population persistence. It is unclear which populations will mount the strongest future adaptive responses. It may be fruitful to identify populations that have escaped trade-offs among performance traits, which can hinder adaptation. Barring strong genetic constraints, the extent of trade-offs may depend on spatial relationships among climate variables shaping different traits. Here, we test for climate-driven ecotypic variation and trade-offs among drought and freezing sensitivity, and growth, for Lemmon's willow (Salix lemmonii) in a common garden study of 90 genotypes from 38 sites in the Sierra Nevada, USA. Salix lemmonii exhibits ecotypic variation in leaf turgor loss point, a measure of drought sensitivity, from -0.95 to -0.74 MPa along a gradient of spring snowpack. We also find variation in spring freezing sensitivity with minimum May temperature. However, we find no trade-off, as the climatic gradients shaping these traits are spatially uncorrelated in our study region, despite being negatively correlated across the Sierra Nevada. Species may escape adaptive trade-offs in geographic regions where climate variables are spatially decoupled. These regions may represent valuable reservoirs of heritable adaptive phenotypic variation.

Short-term fluctuating and long-term divergent selection on sympatric Monkeyflowers: insights from decade-spanning reciprocal transplants

Sympatric species are often locally adapted to distinct microhabitats. However, temporal variation may cause local maladaptation and species boundary breakdown, especially during extreme climatic events leading to episodic selection. Repeated reciprocal transplants can reveal the interplay between short and long-term patterns of natural selection. To examine evolutionary trajectories of sympatric Monkeyflowers adapted to different niches, Mimulus guttatus and M. laciniatus, we performed three replicated transplants and combined them with previous experiments to leverage a dataset of five transplants spanning 10 years. We performed phenotypic selection analyses on parents and hybrids in parental habitats in Yosemite NP, CA during years of drastically differing snowpack. If there is ecological isolation, then we predicted divergent phenotypic selection between habitats in line with species' differences and local adaptation. We found interannual fluctuations in phenotypic selection, often in unpredicted directions. However, a combined-year analysis detected longer-term divergent selection on flowering time, a key temporally isolating and adaptative trait, suggesting that selection may reinforce species boundaries despite short-term fluctuations. Finally, we found temporal variation in local adaptation with M. laciniatus locally adapted in low snowpack years, while an extremely high snowpack year contributed to average local maladaptation of M. guttatus.

Transgenerational plasticity in salinity tolerance of rice: unraveling non-genetic phenotypic modifications and environmental influences

Transgenerational plasticity in plants enables rapid adaptation to environmental changes, allowing organisms and their offspring to adapt to the environment without altering their underlying DNA. In this study, we investigated the transgenerational plasticity in salinity tolerance of rice plants using a reciprocal transplant experimental strategy. Our aim was to assess whether non-genetic environment-induced phenotypic modifications and transgenerational salinity affect the salinity tolerance of progeny while excluding nuclear genomic factors for two generations. Using salt-tolerant and salt-sensitive rice genotypes, we observed that the parentally salt-stressed salt-sensitive genotype displayed greater growth performance, photosynthetic activity, yield performance, and transcriptional responses than the parentally non-stressed salt-sensitive plants under salt stress conditions. Surprisingly, salt stress-exposed salt-tolerant progeny did not exhibit as much salinity tolerance as salt stress-exposed salt-sensitive progeny under salt stress. Our findings indicate that the phenotypes of offspring plants differed based on the environment experienced by their ancestors, resulting in heritable transgenerational phenotypic modifications in salt-sensitive genotypes via maternal effects. These results elucidated the mechanisms underlying transgenerational plasticity in salinity tolerance, providing valuable insights into how plants respond to changing environmental conditions.

High-intensity light promotes adaptive divergence of photosynthetic traits between sun-exposed and shaded populations in Saxifraga fortunei

PREMISE

Light is essential for plants, and local populations exhibit adaptive photosynthetic traits depending on their habitats. Although plastic responses in morphological and/or physiological characteristics to different light intensities are well known, adaptive divergence with genetic variation remains to be explored. This study focused on Saxifraga fortunei (Saxifragaceae) growing in sun-exposed and shaded habitats.

METHODS

We measured the leaf anatomical structure and photosynthetic rate of plants grown in their natural habitats and in a common greenhouse (high- and low-intensity light experimental sites). To assess differences in ecophysiological tolerance to high-intensity light between the sun and shade types, we evaluated the level of photoinhibition of photosystem II and the leaf mortality rate under high-intensity light conditions. In addition, population genetic analysis was conducted to investigate phylogenetic origins.

RESULTS

Clear phenotypic differences were found between the sun and shade types despite their recent phylogenetic origin. The leaf anatomical structure and photosynthetic rate showed plastic changes in response to growing conditions. Moreover, the sun type had a well-developed palisade parenchyma and a higher photosynthetic rate, which were genetically fixed, and a lower level of photoinhibition under high-intensity light.

CONCLUSIONS

Our findings demonstrate that light intensity is a selective pressure that can rapidly promote phenotypic divergence between the sun and shade types. While phenotypic changes in multiple photosynthetic traits were plastic, genetic divergence in specific traits related to adaptation to high-intensity light would be fundamental for ecotypic divergence to different light regimes.

Salt tolerance in a neotropical orchid in the absence of local adaptation to salt spray

PREMISE

Salt tolerance has rarely been investigated regionally in the neotropics and even more rarely in Orchidaceae, one of the largest families. Therefore, investigating local adaptation to salt spray and its physiological basis in Epidendrum fulgens, a neotropical orchid species, brings important new insights.

METHODS

We assessed the degree of salt tolerance in E. fulgens by testing whether coastal populations are more tolerant to salt, which could point to local adaptation. To understand the physiological basis of such salt tolerance, we exposed wild-collected individuals to salt spray for 60 days, then measured leaf expansion, osmotic potential, sodium leaf concentration, chlorophyll leaf index, chlorophyll fluorescence, relative growth rate, and pressure-volume curves.

RESULTS

There is no local adaptation to salt spray since both inland and coastal plants have a high tolerance to salt stress. This tolerance is explained by the ability to tolerate high concentrations of salt in leaf tissues, which is related to the high succulence displayed by this species.

CONCLUSIONS

We showed an unprecedented salt tolerance level for an orchid species, highlighting our limited knowledge of that trait beyond the traditional studied groups. Another interesting finding is that salt tolerance in E. fulgens is linked to succulence, is widespread, and is not the result of local adaptation. We suggest that E. fulgens and its allied species could be an interesting group to explore the evolution of important traits related to tolerance to salt stress, like succulence.

Physiological Responses of C4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints

C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.

Biotic interactions promote local adaptation to soil in plants

Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the "number of open flowers", a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.

Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

MicroRNAs (miRNAs) are pivotal regulators of gene expression, playing crucial roles in plant developmental processes and environmental responses. However, the function of miRNAs in influencing deciduous traits has been little explored. Here, we utilized sRNA-seq on two deciduous species, Ilex polyneura (Hand.-Mazz.) S. Y. Hu and Ilex asprella Champ. ex Benth., along with an evergreen species, Ilex latifolia Thunb., to identify and annotate miRNAs within these species. Our analysis revealed 162 species-specific miRNAs (termed SS-miRNAs) from 120 families, underscoring the fundamental roles and potential influence of SS-miRNAs on plant phenotypic diversity and adaptation. Notably, three SS-miRNAs in I. latifolia were found to target crucial genes within the abscission signaling pathway. Analysis of cis-regulatory elements suggested a novel regulatory relationship that may contribute to the evergreen phenotype of I. latifolia by modulating the abscission process in a light-independent manner. These findings propose a potential mechanism by which SS-miRNAs can influence the conserved abscission pathway, contributing to the phenotypic divergence between deciduous and evergreen species within the genus Ilex.

Climate of origin shapes variations in wood anatomical properties of 17 Picea species

BACKGROUND

Variations in hydraulic conductivity may arise from species-specific differences in the anatomical structure and function of the xylem, reflecting a spectrum of plant strategies along a slow-fast resource economy continuum. Spruce (Picea spp.), a widely distributed and highly adaptable tree species, is crucial in preventing soil erosion and enabling climate regulation. However, a comprehensive understanding of the variability in anatomical traits of stems and their underlying drivers in the Picea genus is currently lacking especially in a common garden.

RESULTS

We assessed 19 stem economic properties and hydraulic characteristics of 17 Picea species grown in a common garden in Tianshui, Gansu Province, China. Significant interspecific differences in growth and anatomical characteristics were observed among the species. Specifically, xylem hydraulic conductivity (Ks) and hydraulic diameter exhibited a significant negative correlation with the thickness to span ratio (TSR), cell wall ratio, and tracheid density and a significant positive correlation with fiber length, and size of the radial tracheid. PCA revealed that the first two axes accounted for 64.40% of the variance, with PC1 reflecting the trade-off between hydraulic efficiency and mechanical support and PC2 representing the trade-off between high embolism resistance and strong pit flexibility. Regression analysis and structural equation modelling further confirmed that tracheid size positively influenced Ks, whereas the traits DWT, D_r, and TSR have influenced Ks indirectly. All traits failed to show significant phylogenetic associations. Pearson's correlation analysis demonstrated strong correlations between most traits and longitude, with the notable influence of the mean temperature during the driest quarter, annual precipitation, precipitation during the wettest quarter, and aridity index.

CONCLUSIONS

Our results showed that xylem anatomical traits demonstrated considerable variability across phylogenies, consistent with the pattern of parallel sympatric radiation evolution and global diversity in spruce. By integrating the anatomical structure of the stem xylem as well as environmental factors of origin and evolutionary relationships, our findings provide novel insights into the ecological adaptations of the Picea genus.

Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence

Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.

Selective sweep and GWAS provide insights into adaptive variation of Populus cathayana leaves

Leaf morphology plays a crucial role in predicting the productivity and environmental adaptability of forest trees, making it essential to understand the genetic mechanisms behind leaf variation. In natural populations of Populus cathayana, leaf morphology exhibits rich intraspecific variation due to long-term selection. However, there have been no studies that systematically reveal the genetic mechanisms of leaf variation in P. cathayana. To fill this gap and enhance our understanding of leaf variation in P. cathayana, we collected nine leaf traits from the P. cathayana natural population, consisting of 416 accessions, and conducted the preliminary classification of leaf types with four categories. Subsequently, we conducted an analysis of selective sweep and genome-wide association studies (GWAS) to uncover the genetic basis of leaf traits variation. Most of the leaf traits displayed significant correlations, with broad-sense trait heritability ranging from 0.38 to 0.74. In total, three selective sweep methods ultimately identified 278 positively selected candidate regions and 493 genes associated with leaf size. Single-trait and multi-trait GWAS methods detected 13 and 59 genes, respectively. By integrating the results of selective sweep and GWAS, we further identified a total of nine overlapping genes. These genes may play a role in the leaf development process and are closely associated with leaf size. In particular, the gene CBSCBSPB3 (Pca07G009100) located on chromosome 7, was associated with the response to light stimulation. This study will deepen our understanding of the genetic mechanism of leaf adaptive variation in P. cathayana and provide valuable gene resources.

Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies?

Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.

Natural variation in Brachypodium distachyon responses to combined abiotic stresses

The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated with B. distachyon responses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone.

Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.

Comparison of Growth and Physiological Effects of Soil Moisture Regime on Plantago maritima Plants from Geographically Isolated Sites on the Eastern Coast of the Baltic Sea

The aim of the present study was to evaluate the morphological and physiological responses of P. maritima plants from five geographically isolated sites growing in habitats with different conditions to different substrate moisture levels in controlled conditions. Plants were produced from seed and cultivated in a greenhouse at four relatively constant soil moisture regimes: at 25, 50, and 75% soil water content and in soil flooded 3 cm above the surface (80% F). The two morphological traits that varied most strikingly among P. maritima accessions were the number of flower stalks and the number of leaves. Only plants from two accessions uniformly produced generative structures, and allocation to flowering was suppressed by both low moisture and flooding. Optimum shoot biomass accumulation for all accessions was at 50 and 75% soil moisture. The Performance Index Total was the most sensitive among the measured photosynthesis-related parameters, and it tended to decrease with an increase in soil water content for all P. maritima accessions. The initial hypothesis-that plants from relatively dry habitats will have a higher tolerance against low soil water levels, but plants from relatively wet habitats will have a higher tolerance against waterlogged or flooded soil-was not proven. The existence of three ecotypes of P. maritima within the five accessions from geographically isolated subpopulations on the eastern coast of the Baltic Sea at the level of morphological responses to soil water content can be proposed. P. maritima plants can be characterized as extremely tolerant to soil waterlogging and highly tolerant to soil flooding and low soil water content.

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

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.

Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis

Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.

Plant physical defenses contribute to a latitudinal gradient in resistance to insect herbivory within a widespread perennial grass

PREMISE

Herbivore pressure can vary across the range of a species, resulting in different defensive strategies. If herbivory is greater at lower latitudes, plants may be better defended there, potentially driving a latitudinal gradient in defense. However, relationships that manifest across the entire range of a species may be confounded by differences within genetic subpopulations, which may obscure the drivers of these latitudinal gradients.

METHODS

We grew plants of the widespread perennial grass Panicum virgatum in a common garden that included genotypes from three genetic subpopulations spanning an 18.5° latitudinal gradient. We then assessed defensive strategies of these plants by measuring two physical resistance traits-leaf mass per area (LMA) and leaf ash, a proxy for silica-and multiple measures of herbivory by caterpillars of the generalist herbivore fall armyworm (Spodoptera frugiperda).

RESULTS

Across all genetic subpopulations, low-latitude plants experienced less herbivory than high-latitude plants. Within genetic subpopulations, however, this relationship was inconsistent-the most widely distributed and phenotypically variable subpopulation (Atlantic) exhibited more consistent latitudinal trends than either of the other two subpopulations. The two physical resistance traits, LMA and leaf ash, were both highly heritable and positively associated with resistance to different measures of herbivory across all subpopulations, indicating their importance in defense against herbivores. Again, however, these relationships were inconsistent within subpopulations.

CONCLUSIONS

Defensive gradients that occur across the entire species range may not arise within localized subpopulations. Thus, identifying the drivers of latitudinal gradients in herbivory defense may depend on adequately sampling the diversity within a species.

Non-stressful temperature changes affect transgenerational phenotypic plasticity across the life cycle of Arabidopsis thaliana plants

BACKGROUND AND AIMS

Plants respond in a plastic manner to seasonal changes, often resulting in adaptation to environmental variation. Although much is known about how seasonality regulates developmental transitions within generations, transgenerational effects of non-stressful environmental changes are only beginning to be unveiled. This study aimed to evaluate the effects of ambient temperature changes on the expression of transgenerational plasticity in key developmental traits of Arabidopsis thaliana plants.

METHODS

We grew Columbia-0 plants in two contrasting temperature environments (18 and 24 °C) during their whole life cycles, or the combination of those temperatures before and after bolting (18-24 and 24-18 °C) across two generations. We recorded seed germination, flowering time and reproductive biomass production for the second generation, and seed size of the third generation.

KEY RESULTS

The environment during the whole life cycle of the first generation of plants, even that experienced before flowering, influenced the germination response and flowering time of the second generation. These effects showed opposing directions in a pattern dependent on the life stage experiencing the cue in the first generation. In contrast, the production of reproductive biomass depended on the immediate environment of the progeny generation. Finally, the seed area of the third generation was influenced positively by correlated environments across generations.

CONCLUSIONS

Our results suggest that non-stressful environmental changes affect the expression of key developmental traits across generations, although those changes can have contrasting effects depending on the parental and grandparental life stage that perceives the cue. Thus, transgenerational effects in response to non-stressful cues might influence the expression of life-history traits and potential adaptation of future generations.

Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria

Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.

Unlocking Nature's Clock: CRISPR Technology in Flowering Time Engineering

Flowering is a crucial process in the life cycle of most plants as it is essential for the reproductive success and genetic diversity of the species. There are situations in which breeders want to expedite, delay, or prevent flowering, for example, to shorten or prolong vegetative growth, to prevent unwanted pollination, to reduce the risk of diseases or pests, or to modify the plant's phenotypes. This review aims to provide an overview of the current state of knowledge to use CRISPR/Cas9, a powerful genome-editing technology to modify specific DNA sequences related to flowering induction. We discuss the underlying molecular mechanisms governing the regulation of the photoperiod, autonomous, vernalization, hormonal, sugar, aging, and temperature signal pathways regulating the flowering time. In addition, we are investigating the most effective strategies for nominating target genes. Furthermore, we have collected a dataset showing successful applications of CRISPR technology to accelerate flowering in several plant species from 2015 up to date. Finally, we explore the opportunities and challenges of using the potential of CRISPR technology in flowering time engineering.

Adaptation of perennial flowering phenology across the European range of Arabis alpina

Flowering phenology is important in the adaptation of many plants to their local environment, but its adaptive value has not been extensively studied in herbaceous perennials. We used Arabis alpina as a model system to determine the importance of flowering phenology to fitness of a herbaceous perennial with a wide geographical range. Individual plants representative of local genetic diversity (accessions) were collected across Europe, including in Spain, the Alps and Scandinavia. The flowering behaviour of these accessions was documented in controlled conditions, in common-garden experiments at native sites and in situ in natural populations. Accessions from the Alps and Scandinavia varied in whether they required exposure to cold (vernalization) to induce flowering, and in the timing and duration of flowering. By contrast, all Spanish accessions obligately required vernalization and had a short duration of flowering. Using experimental gardens at native sites, we show that an obligate requirement for vernalization increases survival in Spain. Based on our analyses of genetic diversity and flowering behaviour across Europe, we propose that in the model herbaceous perennial A. alpina, an obligate requirement for vernalization, which is correlated with short duration of flowering, is favoured by selection in Spain where the plants experience a long growing season.

Genomic signals of local adaptation in Picea crassifolia

BACKGROUND

Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere.

RESULTS

Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding.

CONCLUSIONS

Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.

The Impact of Increased Homozygosity on Human Fertility: A Comprehensive Review

This comprehensive review explores the multifaceted relationship between increased homozygosity and human fertility, delving into the genetic, ethical, cultural, and public health dimensions of this complex phenomenon. Homozygosity, characterized by identical alleles at specific gene loci, can result from consanguineous marriages, genetic drift, and population isolation. The review highlights key findings, including the heightened risk of recessive genetic disorders, the implications for immune system diversity, and the influence on complex traits and diseases. It underscores the critical role of genetic counseling in addressing these consequences, considering the ethical implications, and respecting cultural practices. The delicate balance between genetic diversity and cultural norms is emphasized, calling for increased awareness and community engagement. Looking ahead, the review suggests emerging technologies, longitudinal studies, and interdisciplinary research as crucial avenues for further exploration, with the ultimate goal of informing effective public health policies and interventions that safeguard genetic diversity and cultural traditions for future generations.

Predicting the Potential Geographical Distribution of Rhodiola L. in China under Climate Change Scenarios

Rhodiola L. has high nutritional and medicinal value. Little is known about the properties of its habitat distribution and the important eco-environmental factors shaping its suitability. Rhodiola coccinea (Royle) Boriss., Rhodiola gelida Schrenk, Rhodiola kirilowii (Regel) Maxim., and Rhodiola quadrifida (Pall.) Fisch. et Mey., which are National Grade II Protected Plants, were selected for this research. Based on high-resolution environmental data for the past, current, and future climate scenarios, we modeled the suitable habitat for four species by MaxEnt, evaluated the importance of environmental factors in shaping their distribution, and identified distribution shifts under climate change scenarios. The results indicate that the growth distribution of R. coccinea, R. kirilowii, and R. quadrifida is most affected by bio10 (mean temperature of warmest quarter), bio3 (isothermality), and bio12 (annual precipitation), whereas that of R. gelida is most affected by bio8 (mean temperature of wettest quarter), bio13 (precipitation of wettest month), and bio16 (precipitation of wettest quarter). Under the current climate scenario, R. coccinea and R. quadrifida are primarily distributed in Tibet, eastern Qinghai, Sichuan, northern Yunnan, and southern Gansu in China, and according to the 2070 climate scenario, the suitable habitats for both species are expected to expand. On the other hand, the suitable habitats for R. gelida and R. kirilowii, which are primarily concentrated in southwestern Xinjiang, Tibet, eastern Qinghai, Sichuan, northern Yunnan, and southern Gansu in China, are projected to decrease under the 2070 climate scenario. Given these results, the four species included in our study urgently need to be subjected to targeted observation management to ensure the renewal of Rhodiola communities. In particular, R. gelida and R. kirilowii should be given more attention. This study provides a useful reference with valuable insights for developing effective management and conservation strategies for these four nationally protected plant species.

Temporal Variation in Selection Influences Microgeographic Local Adaptation

AbstractEcological heterogeneity can lead to local adaptation when populations exhibit fitness trade-offs among habitats. However, the degree to which local adaptation is affected by the spatial and temporal scale of environmental variation is poorly understood. A multiyear reciprocal transplant experiment was performed with populations of the annual plant Leptosiphon parviflorus living on adjacent serpentine and nonserpentine soil. Local adaptation over this small geographic scale was observed, but there were differences in the temporal variability of selection across habitats. On serpentine soil, the local population had a consistently large survival advantage, presumably as a result of the temporal stability in selection imposed by soil cation content. In contrast, a fecundity advantage was observed for the sandstone population on its native soil type but only in the two study years with the highest rainfall. A manipulative greenhouse experiment demonstrated that the fitness advantage of the sandstone population in its native soil type depends critically on water availability. The temporal variability in local adaptation driven by variation in precipitation suggests that continued drought conditions have the potential to erode local adaptation in these populations. These results show how different selective factors can influence spatial and temporal patterns of variation in fitness trade-offs.

Revisiting the Role of Genetic Variation in Adaptation

AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.

Genome-wide identification and analysis of MIKC-type MADS-box genes expression in Chimonanthus salicifolius

BACKGROUND

MIKC type MADS-box transcription factors are one of the largest gene families and play a pivotal role in flowering time and flower development. Chimonanthus salicifolius belongs to the family Calycanthaceae and has a unique flowering time and flowering morphology compared to other Chimonanthus species, but the research on MIKC type MADS-box gene family of C. salicifolius has not been reported.

OBJECTIVE

Identification, comprehensive bioinformatic analysis, the expression pattern of MIKC-type MADS-box gene family from different tissues of C. salicifolius.

METHODS

Genome-wide investigation and expression pattern under different tissues of the MIKC-type MADS-box gene family in C. salicifolius, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element were performed.

RESULTS

A total of 29 MIKC-type MADS-box genes were identified from the whole genome sequencing. Interspecies synteny analysis revealed more significant collinearity between C. salicifolius and the magnoliids species compared to eudicots and monocots. MIKC-type MADS-box genes from the same subfamily share similar distribution patterns, gene structure, and expression patterns. Compared with Arabidopsis thaliana, Nymphaea colorata, and Chimonanthus praecox, the FLC genes were absent in C. salicifolius, while the AGL6 subfamily was expanded in C. salicifolius. The selectively expanded promoter (AGL6) and lack of repressor (FLC) genes may explain the earlier flowering in C. salicifolius. The loss of the AP3 homologous gene in C. salicifolius is probably the primary cause of the morphological distinction between C. salicifolius and C. praecox. The csAGL6a gene is specifically expressed in the flowering process and indicates the potential function of promoting flowering.

CONCLUSION

This study offers a genome-wide identification and expression profiling of the MIKC-types MADS-box genes in the C. salicifolius, and establishes the foundation for screening flowering development genes and understanding the potential function of the MIKC-types MADS-box genes in the C. salicifolius.

Intraspecific trait variation and adaptability of Stipa krylovii: Insight from a common garden experiment with two soil moisture treatments

Understanding patterns of intraspecific trait variation can help us understand plant adaptability to environmental changes. To explore the underlying adaptation mechanisms of zonal plant species, we selected seven populations of Stipa krylovii, a dominant species in the Inner Mongolia Steppe of China, and evaluated the effects of phenotypic plasticity and genetic differentiation, the effects of climate variables on population trait differentiation, and traits coordinated patterns under each soil moisture treatment. We selected seeds from seven populations of S. krylovii in the Inner Mongolia Steppe, China, and carried out a soil moisture (2) × population origin (7) common garden experiment at Tianjin City, China, and measured ten plant traits of S. krylovii. General linear analyses were used to analyze how soil moisture and population origin affected each trait variation, Mantel tests were used to analyze population trait differentiation-geographic distance (or climatic difference) relationships, regression analyses were used to evaluate trait-climatic variable relationships, and plant trait networks (PTNs) were used to evaluate traits coordinated patterns. Both soil moisture and population origin showed significant effects on most of traits. Aboveground biomass, root-shoot ratio, leaf width, specific leaf area, and leaf nitrogen (N) content were significantly correlated with climate variables under the control condition. Specific leaf area and leaf N content were significantly correlated with climate variables under the drought condition. By PTNs, the hub trait(s) was plant height under the control condition and were aboveground biomass, root length, and specific leaf area under the drought condition. This study indicates that both phenotypic plasticity and genetic differentiation can significantly affect the adaptability of S. krylovii. In addition, soil moisture treatments show significant effects on trait-climate relationships and traits coordinated patterns. These findings provide new insights into the adaptive mechanisms of zonal species in the semiarid grassland region.

A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane

Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.

Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment

There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.

Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis

Quantitative traits may be controlled by many loci, many alleles at each locus, and subject to genotype-by-environment interactions, making them difficult to map. One example of such a complex trait is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate. Here, we use artificial selection under contrasting nitrate supplies to dissect the genetic architecture of this complex trait, where loci identified by association mapping failed to explain heritability estimates. We found a consistent response to selection for high branching, with correlated responses in other traits such as plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tens of loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. While signals of selection could be detected in the populations selected for high branching on low nitrate, there was very little overlap in the regions selected in three independent populations. Thus the regulatory network controlling shoot branching can be tuned in different ways to give similar phenotypes.

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Glasshouse plants are species that trap warmth via specialized morphology and physiology, mimicking a human glasshouse. In the Himalayan alpine region, the highly specialized glasshouse morphology has independently evolved in distinct lineages to adapt to intensive UV radiation and low temperature. Here we demonstrate that the glasshouse structure - specialized cauline leaves - is highly effective in absorbing UV light but transmitting visible and infrared light, creating an optimal microclimate for the development of reproductive organs. We reveal that this glasshouse syndrome has evolved at least three times independently in the rhubarb genus Rheum. We report the genome sequence of the flagship glasshouse plant Rheum nobile and identify key genetic network modules in association with the morphological transition to specialized glasshouse leaves, including active secondary cell wall biogenesis, upregulated cuticular cutin biosynthesis, and suppression of photosynthesis and terpenoid biosynthesis. The distinct cell wall organization and cuticle development might be important for the specialized optical property of glasshouse leaves. We also find that the expansion of LTRs has likely played an important role in noble rhubarb adaptation to high elevation environments. Our study will enable additional comparative analyses to identify the genetic basis underlying the convergent occurrence of glasshouse syndrome.

Germination temperature sensitivity differs between co-occurring tree species and climate origins resulting in contrasting vulnerability to global warming

Climate change is shifting temperatures from historical patterns, globally impacting forest composition and resilience. Seed germination is temperature-sensitive, making the persistence of populations and colonization of available habitats vulnerable to warming. This study assessed germination response to temperature in foundation trees in south-western Australia's Mediterranean-type climate forests (Eucalyptus marginata (jarrah) and Corymbia calophylla (marri)) to estimate the thermal niche and vulnerability among populations. Seeds from the species' entire distribution were collected from 12 co-occurring populations. Germination thermal niche was investigated using a thermal gradient plate (5-40°C). Five constant temperatures between 9 and 33°C were used to test how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to the climate of origin. Germination response differed among species; jarrah had a lower optimal temperature and thermal limit than marri (T o 15.3°C, 21.2°C; ED50 23.4°C, 31°C, respectively). The thermal limit for germination differed among populations within both species, yet only marri showed evidence for adaptation to thermal origins. While marri has the capacity for germination at higher thermal temperatures, jarrah is more vulnerable to global warming exceeding safety margins. This discrepancy is predicted to alter species distributions and forest composition in the future.

An evolutionarily conserved bimodular domain anchors ZC3HC1 and its yeast homologue Pml39p to the nuclear basket

The proteins ZC3HC1 and TPR are structural components of the nuclear basket (NB), a fibrillar structure attached to the nucleoplasmic side of the nuclear pore complex (NPC). ZC3HC1 initially binds to the NB in a TPR-dependent manner and can subsequently recruit additional TPR polypeptides to this structure. Here, we examined the molecular properties of ZC3HC1 that enable its initial binding to the NB and TPR. We report the identification and definition of a nuclear basket-interaction domain (NuBaID) of HsZC3HC1 that comprises two similarly built modules, both essential for binding the NB-resident TPR. We show that such a bimodular construction is evolutionarily conserved, which we further investigated in Dictyostelium discoideum and Saccharomyces cerevisiae. Presenting ScPml39p as the ZC3HC1 homologue in budding yeast, we show that the bimodular NuBaID of Pml39p is essential for binding to the yeast NB and its TPR homologues ScMlp1p and ScMlp2p, and we further demonstrate that Pml39p enables linkage between subpopulations of Mlp1p. We eventually delineate the common NuBaID of the human, amoebic, and yeast homologue as the defining structural entity of a unique protein not found in all but likely present in most taxa of the eukaryotic realm.

Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes' Selective Footprints in the Genes Network Regulating Flowering Time

Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.

Variation in gene expression along an elevation gradient of Rhododendron sanguineum var. haemaleum assessed in a comparative transcriptomic analysis

Selection along environmental gradients may play a vital role in driving adaptive evolution. Nevertheless, genomic variation and genetic adaptation along environmental clines remains largely unknown in plants in alpine ecosystems. To close this knowledge gap, we assayed transcriptomic profiles of late flower bud and early leaf bud of Rhododendron sanguineum var. haemaleum from four different elevational belts between 3,000 m and 3,800 m in the Gaoligong Mountains. By comparing differences in gene expression of these samples, a gene co-expression network (WGCNA) was constructed to identify candidate genes related to elevation. We found that the overall gene expression patterns are organ-specific for the flower and leaf. Differentially expressed unigenes were identified in these organs. In flowers, these were mainly related to terpenoid metabolism (RsHMGR, RsTPS), while in leaves mainly related to anthocyanin biosynthesis (RsCHS, RsF3'5'H). Terpenoids are the main components of flower scent (fragrance) likely attracting insects for pollination. In response to fewer pollinators at higher elevation zone, it seems relatively less scent is produced in flower organs to reduce energy consumption. Secondary metabolites in leaves such as anthocyanins determine the plants' alternative adaptive strategy to extreme environments, such as selective pressures of insect herbivory from environmental changes and substrate competition in biosynthesis pathways at high elevations. Our findings indicated that the gene expression profiles generated from flower and leaf organs showed parallel expression shifts but with different functionality, suggesting the existence of flexibility in response strategies of plants exposed to heterogeneous environments across elevational gradients. The genes identified here are likely to be involved in the adaptation of the plants to these varying mountainous environments. This study thus contributes to our understanding of the molecular mechanisms of adaptation in response to environmental change.

From common gardens to candidate genes: exploring local adaptation to climate in red spruce

Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.

Neutral and adaptive genetic diversity in plants: An overview

Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.

Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity

Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Genotype-environment associations to reveal the molecular basis of environmental adaptation

A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.

Cooperation of arbuscular mycorrhizal fungi and bacteria to facilitate the host plant growth dependent on soil pH

Almost all plants grow well in their native soils. We hypothesized that soil microbes promote the growth of their hosts in native soils by the example of soil pH. Here, bahiagrass (Paspalum notatum Flugge) indigenous to subtropical soils was grown in the native soil (the original pH = 4.85) or in pH-adjusted soils with sulfur (pH = 3.14 or 3.34) or calcium hydroxide (pH = 6.85, 8.34, 8.52 or 8.59). Plant growth, soil chemical property, and microbial community composition were characterized to reveal the microbial taxa promoting plant growth in the native soil. Results showed that shoot biomass was the highest in the native soil, while both the decrease and increase in the soil pH reduced the biomass. Compared with other soil chemical properties, soil pH was the top edaphic factor contributing to the differentiation in arbuscular mycorrhizal (AM) fungal and bacterial communities. The top 3 most abundant AM fungal OTUs belonged to Glomus, Claroideoglomus, and Gigaspora, while the top 3 most abundant bacterial OTUs belonged to Clostridiales, Sphingomonas, and Acidothermus, respectively. Regression analyses between microbial abundances and shoot biomass revealed that the most abundant Gigaspora sp. and Sphingomonas sp. were the most promotive fungal and bacterial OTUs, respectively. The application of these two isolates to bahiagrass solely or in combination indicated that Gigaspora sp. was more promotive than Sphingomonas sp. across the soil pH gradient, and they positively interacted to enhance biomass only in the native soil. We demonstrate that microbes cooperate to facilitate host plants to grow well in their native soils with the original pH. Meanwhile, a high-throughput sequencing-guided pipeline to efficiently screen for beneficial microbes is established.

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F _ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.