A latitudinal cline and response to vernalization in leaf angle and morphology in Arabidopsis thaliana (Brassicaceae)

Adaptation to latitudinal patterns of environmental variation is predicted to result in clinal variation in leaf traits. Therefore, this study tested for geographic differentiation and plastic responses to vernalization in leaf angle and leaf morphology in Arabidopsis thaliana. Twenty-one European ecotypes were grown in a common growth chamber environment. Replicates of each ecotype were exposed to one of four treatments: 0, 10, 20 or 30 d of vernalization. Ecotypes from lower latitudes had more erect leaves, as predicted from functional arguments about selection to maximize photosynthesis. Lower-latitude ecotypes also had more elongated petioles as predicted by a biomechanical constraint hypothesis. In addition, extended vernalization resulted in shorter and more erect leaves. As predicted by functional and adaptive hypotheses, our results show genetically based clinal variation as well as environmentally induced variation in leaf traits.     

Coarse- versus fine-grained water stress in Arabidopsis thaliana (Brassicaceae)

The effects of coarse vs. fine-grained variation in water regime on 13 accessions of Arabidopsis thaliana were compared and it was found that the scale of environmental variation can lead to differences in which traits are affected and in the magnitude and direction of effect. Coarse-grained (between individual) variation was studied by comparing plants that received high or low amounts of water on a daily basis. Fine-grained (within individual) variation was distributed across the coarse-grained treatments; plants in the fine-grained treatment received the same amount of water per week as the corresponding high and low coarse-grained treatments; however, in the fine-grained treatments, plants received their entire weekly water allotment over 2 days. The number of leaves produced, days to bolting, length of bolt, number of basal and lateral branches, and survival to 30 days after bolting were measured and analyzed by ANOVA. Plants grown in high water generally produced more leaves, taller main axes, more branches and had increased survival, relative to those in low water. Bolting date showed a significant genotype specific effect of water level. Plants grown under fine-grained variation in watering had taller main axes relative to constant water. There were significant interactions between both types of variation for bolting date, main axis height, and survival. Principal components for all traits were loaded such that the components themselves were also independently affected by genotype, water level, variability of water level (grain), and level-by-grain interactions in ways that were largely predicted by their component traits. Overall, the effects of fine-grained variation were subtler than those of coarse-grained variation: fewer traits responded, and the magnitude of the responses was smaller. Nevertheless, the responses to fine-grained variation are distinct from those of coarse-gained variation, differing with respect to which traits respond and in the direction of response, and must therefore be treated as independent sources of environmental variation.     

Phenotypic plasticity and integration in response to flooded conditions in natural accessions of Arabidopsis thaliana (L.) Heynh (Brassicaceae)

Flood response is a crucial component of the life strategy of many plants, but it is seldom studied in non-flooded tolerant species, even though they may be subjected to stressful environmental conditions. Phenotypic plasticity in reaction to environmental stress affects the whole plant phenotype and can alter the character correlations that constitute the phenotypic architecture of the individual, yet few studies have investigated the lability of phenotypic integration to water regime. Moreover, little has been done to date to quantify the sort of selective pressures that different components of a plant's phenotype may be experiencing under contrasting water regimes. Genetic differentiation and phenotypic plasticity at the single-trait and multivariate levels were investigated in 47 accessions of the weedy plant Arabidopsis thaliana, and the relationship of plastic characters to reproductive fitness was quantified. Results indicate that these plants tend to be highly genetically differentiated for all traits, in agreement with predictions made on the basis of environmental variation and mating system. Varied patterns of apparent selection under flooded and non-flooded conditions were also uncovered, suggesting trade-offs in allocation between roots and above-ground biomass, as well as between leaves and reproductive structures. While the major components of the plants' multivariate phenotypic architecture were not significantly affected by environmental changes, many of the details were different under flooded and non-flooded conditions.     

Correlative controls of senescence and plant death in Arabidopsis thaliana (Brassicaceae)

Like most monocarpic plants, longevity of Arabidopsis thaliana plants is controlled by the reproductive structures; however, they appear to work differently from most dicots studied. Neither male- and female-sterility mutations (ms1-1 and bell1, respectively) nor surgical removal of the stems with inflorescences (bolts) at various stages significantly increased the longevity of individual rosette leaves, yet the mutants and treated plants lived 20-50 d longer, measured by the death of the last rosette and/or the last cauline leaf. A series of growth mutations (clv2-4, clv3-2, det3, vam1 enh, and dark green) also increased plant longevity by 20-30 d but did not delay the overall development of the plants. The mutations prolonged plant life through the production of new leaves and stems with inflorescences (bolts) rather than by extending leaf longevity. In growing stems, the newly-formed leaves may induce senescence in the older leaves; however, removal of the younger leaves did not significantly increase the life of the older leaves on the compressed stems of Arabidopsis. Since plants that produce more bolts also live longer, the reproductive load (dry weight) of the bolts did not seem to drive leaf or whole plant senescence here. The developing reproductive structures caused the death of the plant by preventing regeneration of leaves and bolts, which are green and presumably photosynthetic. They also exerted a correlative control (repression) on the development of additional reproductive structures.     

The efficiency of Arabidopsis thaliana (Brassicaceae) root hairs in phosphorus acquisition

Arabidopsis thaliana root hairs grow longer and denser in response to low-phosphorus availability. In addition, plants with the root hair response acquire more phosphorus than mutants that have root hairs that do not respond to phosphorus limiting conditions. The purpose of this experiment was to determine the efficiency of root hairs in phosphorus acquisition at high- and low-phosphorus availability. Root hair growth, root growth, root respiration, plant phosphorus uptake, and plant phosphorus content of 3-wk-old wild-type Arabidopsis (WS) were compared to two root hair mutants (rhd6 and rhd2) under high (54 mmol/m) and low (0.4 mmol/m) phosphorus availability. A cost-benefit analysis was constructed from the measurements to determine root hair efficiency. Under high-phosphorus availability, root hairs did not have an effect on any of the parameters measured. Under low-phosphorus availability, wild-type Arabidopsis had greater total root surface area, shoot biomass, phosphorus per root length, and specific phosphorus uptake. The cost-benefit analysis shows that under low phosphorus, wild-type roots acquire more phosphorus for every unit of carbon respired or unit of phosphorus invested into the roots than the mutants. We conclude that the response of root hairs to low-phosphorus availability is an efficient strategy for phosphorus acquisition.     

Inflorescences contribute more than rosettes to lifetime carbon gain in Arabidopsis thaliana (Brassicaceae)

A metamorphosis from rosette to inflorescence in many annuals shifts photosynthetic tissue from a two-dimensional array in the soil boundary layer during cool months to a three-dimensional structure in the troposphere as spring progresses. We propose that this shift allows escape from both self-shading and an increasingly stressful boundary layer microclimate, permitting continued increases in growth. As a first step in exploring this hypothesis, we compared the lifetime C gain, water loss, and instantaneous water use efficiency (WUE) of five Arabidopsis thaliana genotypes by measuring gas exchange across the life cycle. On average, the inflorescence contributed 55% (± 5% SE) of lifetime C gain, but only 25% of lifetime water loss. Mean inflorescence WUE was nearly fourfold that of the rosette. The inflorescence continued to fix C after rosette senescence. The percentage inflorescence: total C gain varied among genotypes, from 36% to 93%. Genotypes differed in WUE for both structures. We suggest that local climates may have selected for divergence in these traits. For many annuals and winter annuals, understanding C and water budgets and their evolution must include measures of both rosette and inflorescence gas exchange.     

Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)

Background

The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.

Methodology/Principal Findings

In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.

Conclusions/Significance

The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.     

Ontogenetic phenotypic plasticity during the reproductive phase in Arabidopsis thaliana (Brassicaceae)

While phenotypic plasticity has been the focus of much research and debate in the recent ecological and evolutionary literature, the developmental nature of the phenomenon has been mostly overlooked. A developmental perspective must ultimately be an integral part of our understanding of how organisms cope with heterogeneous environments. In this paper I use the rapid cycling Arabidopsis thaliana to address the following questions concerning developmental plasticity. (1) Are there genetic and/or environmental differences in parameters describing ontogenetic trajectories? (2) Is ontogenetic variation produced by differences in genotypes and/or environments for two crucial traits of the reproductive phase of the life cycle, stem elongation and flower production? (3) Is there ontogenetic variability for the correlation between the two characters? I found genetic variation, plasticity, and variation for plasticity affecting at least some of the growth parameters, indicating potential for evolution via heterochronic shifts in ontogenetic trajectories. Within-population differences among families are determined before the onset of the reproductive phase, while among-population variation is the result of divergence during the reproductive phase of the ontogeny. Finally, the ontogenetic profiles of character correlations are very distinct between the ecologically meaningful categories of early- and late-flowering “ecotypes” in this species, and show susceptibility to environmental change.     

Parental environmental effects on life history traits in Arabidopsis thaliana (Brassicaceae)

Environmentally induced maternal effects on offspring phenotype are well known in plants. When genotypes or maternal lineages are replicated and raised in different environmental conditions, the phenotype of their offspring often depends on the environment in which the parents developed. However, the degree to which such maternal effects are maintained over subsequent generations has not been documented in many taxa. Here we report the results of a study designed to assess the effects of parental environment on vegetative and reproductive traits, using glasshouse-raised maternal lines sampled from natural populations of Arabidopsis thaliana . Replicates of five highly selfed lines from each of four wild populations were cultivated in two abiotic environments in the glasshouse, and the quality and performance of seeds derived from these two environments were examined over two generations. We found that offspring phenotype was strongly influenced by parental environment, but because the parental environments differed with respect to the time of seed harvest, it was not possible to distinguish clearly between parental environmental effects and the possible (but unlikely) effects of seed age on offspring phenotype. We observed a rapid decline in the expression of ancestral environmental effects, and no main environmental effects on progeny phenotype persisted in the second generation. The mechanism of transmission of environmental effects did not appear to be associated with the quantity or quality of reserves in the seeds, suggesting that environmental effects may be transmitted across subsequent generations via some mechanism that generates environment-specific gene expression.     

Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae)

? Premise of the study: Plant populations that face new environments adapt and diverge simultaneously, and both processes leave footprints in their genetic diversity. Arabidopsis lyrata is an excellent species for studying these processes. Pairs of populations and subspecies of A. lyrata represent different stages of divergence. These populations are also known to be locally adapted and display various stages of emerging reproductive isolation. ? Methods: We used nucleotide diversity data from 19 loci to estimate divergence times and levels of diversity among nine A. lyrata populations. Traditional distance-based methods and model-based clustering analysis were used to supplement pairwise coalescence-based analysis of divergence. ? Key results: Estimated divergence times varied from 130000 generations between North American and European subspecies to 39000 generations between central European and Scandinavian populations. In concordance with previous studies, the highest level of diversity was found in Central Europe and the lowest in North America and a diverged Russian Karhum?ki population. Local adaptation among Northern and central European populations has emerged during the last 39000 generations. Populations that are reproductively isolated by prezygotic mechanisms have been separated for a longer time period of ～70000 generations but still have shared nucleotide polymorphism. ? Conclusions: In A. lyrata, reproductively isolated populations started to diverge ～70000 generations ago and more closely related, locally adapted populations have been separate lineages for ～39000 generations. However, based on the posterior distribution of divergence times, the processes leading to reproductive isolation and local adaptation are likely to temporally coincide.     

Correlation between time of flowering and phenotypic plasticity in Arabidopsis thaliana (Brassicaceae)

We observed substantial variation in the time of flowering among 13 populations of Arabidopsis thaliana (Brassicaceae) from an extensive latitudinal range when grown under uniform experimental conditions. The later the onset of flowering, the greater was potential reproduction. Later flowering plants also had greater plasticity in a host of morphological and physiological traits measured in nutrient-rich vs. nutrient-poor test environments. This relationship between flowering time and overall plasticity was only apparent for traits measured at the time of seed production, not at the time of flowering or earlier. At the time of seed production in this short-lived annual, the regression of a multivariate measure of overall plasticity on the time of flowering was linear and highly significant (r² = 0.90, P < 0.0001). These correlations among time of flowering, reproductive fitness, and plasticity support the idea that selection for late-flowering genotypes would select concomitantly for greater plasticity.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

Genetic diversity of the natural populations of Arabidopsis thaliana in China

Although extensive studies have been conducted on the genetic structure of Arabidopsis thaliana (A. thaliana) populations worldwide, the populations from China have never been studied. In this study, we collected 560 individuals from 19 natural populations of A. thaliana distributed in East China along the lower reaches of the Yangtze River, and two populations from northwest China (Xinjiang Province). We adopted two kinds of molecular marker, inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPDs) to investigate the genetic diversity within and among populations, and the correlation between the genetic and geographic distances. Thirteen ISSR primers produced 165 polymorphic bands (PPB) (96%) and 11 RAPD primers produced 162 polymorphic bands (98%) in about 560 individuals. The two marker systems generated similar patterns of genetic diversity in these natural populations. The AMOVA analysis indicated about 42-45% of the total genetic variation existed within populations, and found possible geographic structure. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. A close genetic relationship was found among four populations in the Jiangxi Province, and these always appeared clustered together as a monophyletic group in unweighted pair-group method with arithmetic averages dendrograms based on both ISSR and RAPD data sets. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity.     

Sinapate esters provide greater UV-B attenuation than flavonoids in Arabidopsis thaliana (Brassicaceae)

Mutants affected in flavonoid (tt4) or sinapate ester (fah1) biosynthesis were used to assess the relative importance of these phenolic UV photoprotectants in Arabidopsis. Flavonoid and sinapate ester absorption was more specific for UV-B than major nonphenolic chromophores in crude extracts. A new method of evaluating phenolic UV-B attenuation was developed using fluorescence analysis. When excited by UV-B, sinapate ester containing leaves and cotyledons had enhanced sinapate ester fluorescence and reduced chlorophyll fluorescence relative to those without sinapate esters. Although fluorescence analysis gave no evidence of UV-B attenuation by flavonoids, enhanced chlorophyll and protein loss were observed upon UV-B exposure in flavonoid-deficient leaves, suggesting they have another mechanism of UV-B protection. The hydroxycinnamates have been largely ignored as UV-B attenuating pigments, and the results indicate that greater attention should be paid to their role in attenuating UV-B.     

The contribution of spontaneous mutation to variation in environmental responses of Arabidopsis thaliana: responses to light

It has been hypothesized that new, spontaneous mutations tend to reduce fitness more severely in more stressful environments. To address this hypothesis, we grew plants representing 20 Arabidopsis thaliana mutation-accumulation (M-A) lines, advanced to generation 17, and their progenitor, in differing light conditions. The experiment was conducted in a greenhouse, and two treatments were used: full sun and shade, in which influx of red light was reduced relative to far-red. The shade treatment was considered the more stressful because mean absolute fitness was lower in that treatment, though not significantly so. Plants from generation 17 of M-A developed significantly faster than those from generation 0 in both treatments. A significant interaction between generation and treatment revealed that, counter to the hypothesis, M-A lines tended to have higher fitness on average relative to the progenitor in the shaded conditions, whereas, in full sun, the two generations were similar in fitness. A secondary objective of this experiment was to characterize the contribution of new mutations to genotype x environment interaction. We did not, however, detect a significant interaction between M-A line and treatment. Plots of the line-specific environmental responses indicate no tendency of new mutations to contribute to fitness trade-offs, between environments. They also do not support a model of conditionally deleterious mutation, in which a mutant reduces fitness only in a particular environment. These results suggest that interactions between genotype and light environment previously documented for A. thaliana are not explicable primarily as a consequence of steady input of spontaneous mutations having environment-specific effects.     

Pleiotropic effects of flowering time genes in the annual crucifer Arabidopsis thaliana (Brassicaceae)

Variation in flowering time of Arabidopsis thaliana was studied in an experiment with mutant lines. The pleiotropic effects of flowering time genes on morphology and reproductive yield were assessed under three levels of nutrient supply. At all nutrient levels flowering time and number of rosette leaves at flowering varied among mutant lines. The relationship between these two traits depended strongly on nutrient supply. A lower nutrient supply first led to an extension of the vegetative phase, while the mean number of leaves at flowering was hardly affected. A further reduction resulted in no further extension of the vegetative phase and, on average, plants started flowering with a lower leaf number. At low nutrients, early flowering affected the timing of production of siliques rather than the total output, whereas late flowering was favorable at high nutrients. This may explain the fact that many plant species flower at a relatively small size under poor conditions. Flowering time genes had pleiotropic effects on the leaf length, number of rosette and cauline leaves, and number of axillary flowering shoots of the main inflorescence. Silique production was positively correlated with the number of axillary shoots of the main inflorescence; the number of axillary primordia appeared to have a large impact on reproductive yield.     

Transcriptional responses of Arabidopsis thaliana plants to As (V) stress

Background

Plants encode a large number of leucine-rich repeat receptor-like kinases. Legumes encode several LRR-RLK linked to the process of root nodule formation, the ligands of which are unknown. To identify ligands for these receptors, we used a combination of profile hidden Markov models and position-specific iterative BLAST, allowing us to detect new members of the CLV3/ESR (CLE) protein family from publicly available sequence databases.

Results

We identified 114 new members of the CLE protein family from various plant species, as well as five protein sequences containing multiple CLE domains. We were able to cluster the CLE domain proteins into 13 distinct groups based on their pairwise similarities in the primary CLE motif. In addition, we identified secondary motifs that coincide with our sequence clusters. The groupings based on the CLE motifs correlate with known biological functions of CLE signaling peptides and are analogous to groupings based on phylogenetic analysis and ectopic overexpression studies. We tested the biological function of two of the predicted CLE signaling peptides in the legume Medicago truncatula. These peptides inhibit the activity of the root apical and lateral root meristems in a manner consistent with our functional predictions based on other CLE signaling peptides clustering in the same groups.

Conclusion

Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides. The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.     

Genetic diversity of natural populations of Arabidopsis thaliana (L.) Heynh. in Karelia

The genetic structure of ten natural populations of Arabidopsis thaliana (L.) Heynh. at eight isozyme loci was studied. The populations were located in the northern part of the species range, 200 km from the north to the south along the Onega Lake coast in Karelia. Considerable genetic diversity (P99% = 43.7, Hobs = 0.003) was revealed that is not typical of populations of self-pollinating plant species. A direct correlation between the proportion of polymorphic loci and geographical latitude was shown (r = 0.68; P < 0.05). It is suggested that a high polymorphism level in Karelian Arabidopsis thaliana (L.) populations increasing from the south to the north is due to extreme environmental conditions in the northern part of the species range. The distribution of genetic diversity within and between populations is typical of self-pollinating species: the larger part of the total diversity resides among populations (GST = 0.583).     

Discordant longitudinal clines in flowering time and phytochrome C in Arabidopsis thaliana

Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.