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The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.

Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively, microbial assemblages could change simply as a consequence of time and the opportunity for microbial succession. Previous studies suggest that rhizosphere microbial assemblages shift across plant developmental stages, but time since germination is confounded with developmental stage. We asked how elapsed time and potential microbial succession relative to host development affected microbial diversity in the rhizosphere using monogenic flowering-time mutants of Arabidopsis thaliana. Under our experimental design, different developmental stages were present among host genotypes after the same amount of time following germination, e.g. at 76 days following germination some host genotypes were flowering while others were fruiting or senescing. We found that elapsed time was a strong predictor of microbial diversity whereas there were few differences among developmental stages. Our results support the idea that time and, likely, microbial succession more strongly affect microbial community assembly than host developmental stage. [ABSTRACT FROM AUTHOR]

The circadian clock regulates many aspects of leaf gas supply and biochemical demand for CO2, and is hypothesized to improve plant performance. Yet the extent to which the clock may regulate the efficiency of photosystem II (PSII) and photoprotective mechanisms such as heat dissipation is less explored. Based on measurements of chlorophyll a fluorescence, we estimated the maximum efficiency of PSII in light (Fv′/Fm′) and heat dissipation by nonphotochemical quenching (NPQ). We further dissected total NPQ into its main components, qE (pH‐dependent quenching), qT (state‐transition quenching), and qI (quenching related to photoinhibition), in clock mutant genotypes of Arabidopsis thaliana, the cognate wild‐type genotypes, and a panel of recombinant inbred lines expressing quantitative variation in clock period. Compared with mutants with altered clock function, we observed that wild‐type genotypes with clock period lengths of approximately 24 hr had both higher levels of Fv′/Fm′, indicative of improved PSII function, and reduced NPQ, suggestive of lower stress on PSII light harvesting complexes. In the recombinant inbred lines, genetic variances were significant for Fv′/Fm′ and all 3 components of NPQ, with qE explaining the greatest proportion of NPQ. Bivariate tests of association and structural equation models of hierarchical trait relationships showed that quantitative clock variation was empirically associated with Fv′/Fm′ and NPQ, with qE mediating the relationship with gas exchange. The results demonstrate significant segregating variation for all photoprotective components, and suggest the adaptive significance of the clock may partly derive from its regulation of the light reactions of photosynthesis and of photoprotective mechanisms. This manuscript provides novel insights on circadian regulation of PSII efficiency and photoprotective mechanisms in the model plant system, Arabidopsis thaliana. This research article reports significant differences in the efficiency of PSII and in thermal dissipation of excess light energy (i.e., nonphotochemical quenching, NPQ) between wild‐type plants and mutants with altered clock function. Further, we report segregating variation for all photoprotective components in RILs of A. thaliana, and significant associations between quantitative clock variation and PSII function, NPQ, and components of NPQ. The study has implications for better understanding photoprotective mechanisms and the role of the clock in adaptation to varying light availability and light stress. [ABSTRACT FROM AUTHOR]

Summary: Circadian rhythms are key regulators of diverse biological processes under controlled settings. Yet, the phenotypic and fitness consequences of quantitative variation in circadian rhythms remain largely unexplored in the field. As with other pathways, phenotypic characterization of circadian outputs in the field may reveal novel clock functions. Across consecutive growing seasons, we test for associations between clock variation and flowering phenology, plant size, shoot architecture, and fruit set in clock mutants and segregating progenies of Arabidopsis thaliana expressing quantitative variation in circadian rhythms. Using structural equation modeling, we find that genotypic variation in circadian rhythms within a growing season is associated directly with branching, which in turn affects fruit production. Consistent with direct associations between the clock and branching in segregating progenies, cauline branch number is lower and rosette branch number higher in a short‐period mutant relative to wild‐type and long‐period genotypes, independent of flowering time. Differences in branching arise from variation in meristem fate as well as leaf production rate before flowering and attendant increases in meristem number. Our results suggest that clock variation directly affects shoot architecture in the field, suggesting a novel clock function and means by which the clock affects performance. [ABSTRACT FROM AUTHOR]

Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity. Subtler adjustments via genomic introgression of naturally occurring alleles indicated that clock periods slightly >24 hr were adaptive, consistent with prior models describing how well the timing of biological processes is adjusted within a diurnal cycle (referred to as phase). In segregating recombinant inbred lines ( RILs), circadian phase varied up to 2 hr across months of the growing season, and both period and phase expressed significant genetic variances. Performance metrics including developmental rate, size and fruit set were described by principal components ( PC) analyses and circadian parameters correlated with the first PC, such that period lengths slightly >24 hr were associated with improved performance in multiple RIL sets. These experiments translate functional analyses of clock behaviour performed in controlled settings to natural ones, demonstrating that quantitative variation in circadian phase is highly responsive to seasonally variable abiotic factors. The results expand upon prior studies in controlled settings, showing that discrete and quantitative variation in clock phenotypes correlates with performance in nature. [ABSTRACT FROM AUTHOR]

Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, the influences of epistasis × environment interactions on adaptive trait evolution remain largely uncharacterized., Across three field trials, we quantified aliphatic glucosinolate ( GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation., We found that aliphatic GSL accumulation was primarily influenced by additive and epistatic genetic variation, leaf damage was primarily influenced by environmental variation and relative fitness was primarily influenced by epistasis and epistasis × environment interactions. Epistasis × environment interactions accounted for up to 48% of the relative fitness variation in the field. At a single field site, the impact of epistasis on relative fitness varied significantly over 2 yr, showing that epistasis × environment interactions within a location can be temporally dynamic., These results suggest that the environmental dependency of epistasis can profoundly influence the response to selection, shaping the adaptive trajectories of natural populations in complex ways, and deserves further consideration in future evolutionary studies. [ABSTRACT FROM AUTHOR]

The article talks about the contribution of environmental heterogeneity in the maintenance of glucosinolates (GSL) variations in Arabidopsis thaliana. Heterogeneous selective forces are generated with shifting biotic pressures, which can maintain standing natural variation within a species. It was observed that variation in naturally polymorphic GSL genes, affected the fitness in each of our environments.

The genetic architecture of floral traits is evolutionarily important due to the fitness consequences of quantitative variation in floral morphology. Yet, little is known about the genes underlying these traits in natural populations. Using Arabidopsis thaliana, we examine molecular variation at GIBBERELLIC ACID REQUIRING 1 ( GA1) and test for associations with floral morphology., We examined full-length sequence in 32 accessions and describe two haplotypes (comprising four nonsynonymous polymorphisms) in GA1 that segregate at intermediate frequencies. In 133 A. thaliana accessions, we test for genotype-phenotype associations and corroborate these findings in segregating progenies., The two common GA1 haplotypes were associated with the length of petals, stamens, and to a lesser extent style-stigma length. Associations were confirmed in a segregating progeny developed from 19 accessions. We find analogous results in recombinant inbred lines of the Bayreuth × Shahdara cross, which differ only at one of 4 SNPs, suggesting that this SNP may contribute to the observed association., Assuming GA1 causally affects floral organ size, it is interesting that adjacent petal and stamen whorls are most strongly affected. This pattern suggests that GA1 could contribute to the greater strength of petal-stamen correlations relative to other floral-length correlations observed in some Brassicaceous species. [ABSTRACT FROM AUTHOR]

Association studies utilize the action of recombination over numerous generations to identify loci that underlie quantitative traits. We use a candidate-gene association approach, segregation analyses and analyses of local linkage disequilibrium (LD) to evaluate the potentially causal effects of molecular variation at PIF4 ( PHYTOCROME INTERACTING FACTOR 4) on ecologically important traits in Arabidopsis thaliana. A preliminary analysis of sequence diversity in 14 natural genotypes revealed one intermediate-frequency replacement polymorphism at PIF4. A sample of 161 natural accessions was genotyped at PIF4 and screened for average length of early internodes, inflorescence length, days to flowering and flowering interval (days between bolting and flowering) under high- and low-density environments to test for genotype-phenotype associations. PIF4 was associated with early internode lengths, while the PIF4× treatment interaction was associated with flowering interval in the panel of 161 accessions. Further, in a set of recombinant inbred lines that segregate for the PIF4 polymorphism, nucleotide substitutions at PIF4 co-segregated with early internode lengths, days to flowering and fruit set, suggesting that cryptic population structure in the association-mapping panel and attendant LD with a physically distant locus do not account for the observed association. Finally, in a panel of pseudochromosomes from 20 re-sequenced genotypes, LD appeared to decay rapidly in the immediate vicinity of PIF4, suggesting that flanking loci contribute little to the observed association. In sum, the results suggest that PIF4 causally affects early internode lengths on the primary inflorescence, potentially via effects on reproductive timing and that these traits in turn affect fitness. [ABSTRACT FROM AUTHOR]

The ratio of red to far-red light (R : FR) experienced by seeds during maturation affects germination, but the genetic regulation of this effect is poorly understood. In Arabidopsis thaliana, responses to R : FR are governed by five phytochrome photoreceptors, PHYA–PHYE. PHYA, PHYB and PHYE mediate germination, but their roles in germination response to the seed maturation environment are largely unknown. Seeds of A. thaliana phytochrome mutants and natural accessions were matured in a factorial combination of cold (16 °C) and warm (24 °C) temperatures and high (R : FR = 1) and low (R : FR = 0.6) R : FR environments, resembling sunlight and foliar shade, respectively. Germination was observed in resulting seeds. All five phytochromes mediated germination responses to seed maturation temperature and/or R : FR environment. PHYA suppressed germination in seeds matured under cold temperature, and PHYB promoted germination under the same conditions. PHYD and PHYE promoted germination of seeds matured under warm temperature, but this effect diminished when seeds matured under reduced R : FR. The A. thaliana natural accessions exhibited interesting variation in germination responses to the experimental conditions. Our results suggest that the role of individual PHY loci in regulating plant responses to R : FR varies depending on temperature and provide novel insights into the genetic basis of maternal effects. [ABSTRACT FROM AUTHOR]

The importance of genes of major effect for evolutionary trajectories within and among natural populations has long been the subject of intense debate. For example, if allelic variation at a major-effect locus fundamentally alters the structure of quantitative trait variation, then fixation of a single locus can have rapid and profound effects on the rate or direction of subsequent evolutionary change. Using an Arabidopsis thaliana RIL mapping population, we compare G-matrix structure between lines possessing different alleles at ERECTA, a locus known to affect ecologically relevant variation in plant architecture. We find that the allele present at ERECTA significantly alters G-matrix structure-in particular the genetic correlations between branch number and flowering time traits-and may also modulate the strength of natural selection on these traits. Despite these differences, however, when we extend our analysis to determine how evolution might differ depending on the ERECTA allele, we find that predicted responses to selection are similar. To compare responses to selection between allele classes, we developed a resampling strategy that incorporates uncertainty in estimates of selection that can also be used for statistical comparisons of G matrices. [ABSTRACT FROM AUTHOR]

• Phenotypic plasticity, the ability of a genotype to express different phenotypes across environments, is an adaptive strategy expected to evolve in heterogeneous environments. One widely held hypothesis is that the evolutionary benefits of plasticity are reduced by its costs, but when compared with the number of traits tested, the evidence for costs is limited. • Selection gradients were calculated for traits and trait plasticities to test for costs of plasticity to density in a field study using recombinant inbred lines (RILs) of Brassica rapa. • Significant costs of putatively adaptive plasticity were found in three out of six measured traits. For one trait, petiole length, a cost of plasticity was detected in both environments tested; such global costs are expected to more strongly constrain the evolution of plasticity than local costs expressed in a single environment. • These results, in combination with evidence from studies in segregating progenies of Arabidopsis thaliana, suggest that the potential for genetic costs of plasticity exists in natural populations. Detection of costs in previous studies may have been limited because historical selection has purged genotypes with costly plasticity, and experimental conditions often lack environmental stresses. [ABSTRACT FROM AUTHOR]

Identifying the molecular genetic basis of intraspecific variation in quantitative traits promises to provide novel insight into their evolutionary history as well as genetic mechanisms of adaptation. In an attempt to identify genes responsible for natural variation in competitive responses in Arabidopsis thaliana, we examined DNA sequence diversity at seven loci previously identified as members of the phytochrome B signalling network. For one gene, GIGANTEA ( GI), we detected significant haplotype structure. To test for GI haplogroup–phenotype associations, we genotyped 161 A. thaliana accessions at GI and censused the same accessions for total fruit set and the expression of three phenotypic traits (days to flowering, petiole length, and inflorescence height) in a greenhouse experiment where plants were grown in crowded and uncrowded environments. We detected a significant association between GI and total fruit set that resulted in a 14% difference in average fruit set among GI haplogroups. Given that fruit set is an important component of fitness in this species and given the magnitude of the effect, the question arises as to how variation at this locus is maintained. Our observation of frequent and significant epistasis between GI and background single nucleotide polymorphisms (SNP), where the fitness ranking of the GI allele either reverses or does not differ depending on the allele at the interacting SNP, suggests that epistatic selection may actively maintain or at least slow the loss of variation at GI. This result is particularly noteworthy in the light of the ongoing debate regarding the genetic underpinnings of phenotypic evolution and recent observations that epistasis for phenotypic traits and components of fitness is common in A. thaliana. [ABSTRACT FROM AUTHOR]

In natural populations of the annual plant Arabidopsis thaliana, season of germination determines life history. Spring annuals overwinter as seeds and germinate and flower in spring. Winter annuals germinate in fall, overwinter as rosettes, and flower in spring. In many plant species, germination is affected by the maternal phenotype during seed production. In those that produce seeds on branches from the main stem and branches from basal nodes, like A. thaliana, there may be positional effects on germination. This study examines the effects of maternal branch type on germination in artificial seasonal spring and fall environments. Seeds from apical and basal branches of 41 accessions of A. thaliana were weighed and divided between spring (low temperature for 21 d) and fall (ambient temperature) germination environments. Maternal branch type had significant effects on germination fraction and seed mass, but the direction of the effect differed among accessions. The genetic correlation between seed mass and germination fraction was positive for seeds in the spring germination environment and negative in the fall germination environment. There was a positive longitudinal cline for seed mass, a negative longitudinal cline for germination fraction, and a latitudinal cline for germination fraction that depended on the germination environment. These results show that there is geographic variation in germination traits and suggest that genetic variation in mass can lead to variation in season of germination for A. thaliana. [ABSTRACT FROM AUTHOR]

As a rosette plant, Arabidopsis thaliana forms leaves near to the ground, which causes the plant to be vulnerable to shading by neighbours. One mechanism to avoid such shading is the regulation of leaf inclination, such that leaves can be raised to more vertical orientations to prevent neighbouring leaves from overtopping them. Throughout Arabidopsis rosette development, rosette leaves move to more vertical orientations when shaded by neighbouring leaves, exposed to low light levels or placed in the dark. After dark-induced reorientation of leaves, returning them to white light causes the leaves to reorient to more horizontal inclinations. These light-dependent leaf movements are more robust than, and distinct from, the diurnal movements of rosette leaves. However, the movements are gated by the circadian clock. The light-dependent leaf orientation response is mediated primarily through phytochromes A, B and E, with the orientation varying with the ratio of red light to far-red light, consistent with other shade-avoidance responses. However, even plants lacking these phytochromes were able to alter leaf inclination in response to white light, suggesting a role for other photoreceptors. In particular, we found significant changes in leaf inclination for plants exposed to green light. This green light response may be caused, in part, by light-dependent regulation of abscisic acid (ABA) biosynthesis. [ABSTRACT FROM AUTHOR]

Reports that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. Suggestion that the allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus; Indication that both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.

Abstract Quantitative-genetic approaches have offered significant insights into phenotypic evolution. However, quantitative-genetic analyses fail to provide information about the evolutionary relevance of specific loci. One complex and ecologically relevant trait for plants is their resistance to herbivory because natural enemies can impose significant damage. To illustrate the insights of combined molecular and ecological research, we present the results of a field study mapping quantitative trait loci (QTL) for resistance and tolerance to natural rabbit herbivory in the genetic model, Arabidopsis thaliana . Replicates of the Ler × Col recombinant inbred lines were planted into field sites simulating natural autumn and spring seasonal germination cohorts. Shortly after flowering, herbivores removed the main flowering inflorescence (apical meristem). We found several main-effect QTL for resistance within each seasonal cohort and significant QTL–season interactions, demonstrating that the loci underlying resistance to a single herbivore differ across seasonal environments. The presence of QTL × environment also shows that variation at specific loci is only available to selection in some environments. Despite significant among-line variance components, no QTL for tolerance were detected. The combined results of the quantitative-genetic and QTL analyses demonstrate that many loci of small effect underlie tolerance to damage by rabbits, and counter the hypothesis of locus-specific tradeoffs between resistance and tolerance. The results also provide insights as to the locus-specific nature of evolutionary constraints, i.e. some loci influence flowering time and resistance in both seasonal cohorts. Our results show how linking molecular-genetic tools with field studies in ecologically relevant settings can clarify the role of specific loci in the evolution of quantitative traits. [ABSTRACT FROM AUTHOR]

Reports the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compares the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population. [ABSTRACT FROM AUTHOR]

The circadian clock facilitates coordination of the internal rhythms of an organism to daily environmental conditions, such as the light-dark cycle of one day. Circadian period length (the duration of one endogenous cycle) and phase (the timing of peak activity) exhibit quantitative variation in natural populations. Here, we measured circadian period and phase in June, July and September in three Arabidopsis thaliana recombinant inbred line populations. Circadian period and phase were estimated from bioluminescence of a genetic construct between a native circadian clock gene (COLD CIRCADIAN RHYTHM RNA BINDING 2) and the reporter gene (LUCIFERASE) after lines were entrained under field settings. Using a Bayesian mapping approach, we estimated the median number and effect size of genomic regions (Quantitative Trait Loci, QTL) underlying circadian parameters and the degree to which these regions overlap across months of the growing season. We also tested for QTL associations between the circadian clock and plant morphology. The genetic architecture of circadian phase was largely independent across months, as evidenced by the fact that QTL determining phase values in one month of the growing season were different from those determining phase in a second month. QTL for circadian parameters were shared with both cauline and rosette branching in at least one mapping population. The results provide insights into the QTL architecture of the clock under field settings, and suggest that the circadian clock is highly responsive to changing environments and that selection can act on clock phase in a nuanced manner. [ABSTRACT FROM AUTHOR]

Plant phenotyping is central to understand causal effects of genotypes and environments on trait expression and is a critical factor in expediting plant breeding. Previously, plant phenotypic traits were quantified using invasive, time-consuming, labor-intensive, cost-inefficient, and often destructive manual sampling methods that were also prone to observer error. In recent years, photogrammetry and image processing techniques have been introduced to plant phenotyping, but cost efficiency issues remain when combining these two techniques within large-scale plant phenotyping studies. Using these high-throughput techniques in basic plant biology research and agriculture are still in the developmental stages but show great promise for rapid phenotyping, which will materially aid both science and crop improvement efforts. In this study, we introduce an automated high-throughput phenotyping pipeline using affordable imaging systems and image processing algorithms to build 2D mosaicked orthophotos. Chamber-based and ground-level field implementations are used to measure phenotypic traits such as leaf length and rosette area in 2D images. Our automated pipeline has cross-platform capabilities and a degree of instrument independence, making it suitable for various situations. [ABSTRACT FROM AUTHOR]