Natural Plant Populations Research Articles

Long-term ungulate exclusion reduces fungal symbiont prevalence in native grasslands.

When symbionts are inherited by offspring, they can have substantial ecological and evolutionary consequences because they occur in all host life stages. Although natural frequencies of inherited symbionts are commonly <100%, few studies investigate the ecological drivers of variation in symbiont prevalence. In plants, inherited fungal endophytes can improve resistance to herbivory, growth under drought, and competitive ability. We evaluated whether native ungulate herbivory increased the prevalence of a fungal endophyte in the common, native bunchgrass, Festuca campestris (rough fescue, Poaceae). We used large-scale (1ha) and long-term (7-10year) fencing treatments to exclude native ungulates and recorded shifts in endophyte prevalence at the scale of plant populations and for individual plants. We characterized the fungal endophyte in F. campestris, Epichloë species FcaTG-1 (F. campestris taxonomic group1) for the first time. Under ungulate exclusion, endophyte prevalence was 19% lower in plant populations, 25% lower within plant individuals, and 39% lower in offspring (seeds) than in ungulate-exposed controls. Population-level endophyte frequencies were also negatively correlated with soil moisture across geographic sites. Observations of high within-plant variability in symbiont prevalence are novel for the Epichloë species, and contribute to a small, but growing, literature that documents phenotypic plasticity in plant-endophyte symbiota. Altogether, we show that native ungulates can be an important driver of symbiont prevalence in native plant populations, even in the absence of evidence for direct mechanisms of mammal deterrence. Understanding the ecological controls on symbiont prevalence could help to predict future shifts in grasslands that are dominated by Epichloë host plants.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome‐wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late‐season drought in California. These ancestor‐descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (F ST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome‐wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.

Assessment of new scientific elements supporting the prolongation of prohibition of the placing on the market of genetically modified oilseed rape GT73 for food and feed purposes in Austria

Assessment of new scientific elements supporting the prolongation of prohibition of the placing on the market of genetically modified oilseed rape GT73 for food and feed purposes in Austria

Assessment of new scientific elements supporting the prolongation of prohibition of the placing on the market of genetically modified oilseed rape Ms8, Rf3 and Ms8×Rf3 for food and feed purposes in Austria

Assessment of new scientific elements supporting the prolongation of prohibition of the placing on the market of genetically modified oilseed rape Ms8, Rf3 and Ms8×Rf3 for food and feed purposes in Austria

Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum

Fungal plant pathogens are major threats to food security worldwide. Sclerotinia sclerotiorum and Botrytis cinerea are closely related Ascomycete plant pathogens causing mold diseases on hundreds of plant species. There is no genetic source of complete plant resistance to these broad host range pathogens known to date. Instead, natural plant populations show a continuum of resistance levels controlled by multiple genes, a phenotype designated as quantitative disease resistance. Little is known about the molecular mechanisms controlling the interaction between plants and S. sclerotiorum and B. cinerea but significant advances were made on this topic in the last years. This minireview highlights a selection of nine themes that emerged in recent research reports on the molecular bases of plant-S. sclerotiorum and plant-B. cinerea interactions. On the fungal side, this includes progress on understanding the role of oxalic acid, on the study of fungal small secreted proteins. Next, we discuss the exchanges of small RNA between organisms and the control of cell death in plant and fungi during pathogenic interactions. Finally on the plant side, we highlight defense priming by mechanical signals, the characterization of plant Receptor-like proteins and the hormone abscisic acid in the response to B. cinerea and S. sclerotiorum, the role of plant general transcription machinery and plant small bioactive peptides. These represent nine trends we selected as remarkable in our understanding of fungal molecules causing disease and plant mechanisms associated with disease resistance to two devastating broad host range fungi.

A below-ground herbivore shapes root defensive chemistry in natural plant populations.

Plants display extensive intraspecific variation in secondary metabolites. However, the selective forces shaping this diversity remain often unknown, especially below ground. Using Taraxacum officinale and its major native insect root herbivore Melolontha melolontha, we tested whether below-ground herbivores drive intraspecific variation in root secondary metabolites. We found that high M. melolontha infestation levels over recent decades are associated with high concentrations of major root latex secondary metabolites across 21 central European T. officinale field populations. By cultivating offspring of these populations, we show that both heritable variation and phenotypic plasticity contribute to the observed differences. Furthermore, we demonstrate that the production of the sesquiterpene lactone taraxinic acid β-D-glucopyranosyl ester (TA-G) is costly in the absence, but beneficial in the presence of M. melolontha, resulting in divergent selection of TA-G. Our results highlight the role of soil-dwelling insects for the evolution of plant defences in nature.

Genome size and ploidy levels of creeping phlox and related germplasm of mat-forming taxa from eastern and western North America

The eastern North American creeping phlox (Phlox subulata L.) is a widely cultivated flowering groundcover with a history of breeding and selection. Little is known about genome size variation and ploidy of P. subulata and related taxa. Mean holoploid (2C) and monoploid (1Cx) genome sizes and ploidy were analyzed with flow cytometry for a germplasm collection (n=53) of 11 morphologically similar creeping phlox taxa from natural plant populations, cultivars and hybrids obtained from nursery sources, and the related Microsteris gracilis. Holoploid genome sizes of accessions from natural populations were more variable than cultivated taxa and ranged from 7.47 to 22.86pg and corresponded to diploid (2n=2x=14) tetraploid (2n=4x=28), and hexaploid (2n=6x=42) levels, but most accessions were diploid and genome size ranged from 7.60 to 8.47pg. Two tetraploid accessions were discovered, but hexaploids were limited to one population of P. subulata. Most accessions consisted of a single cytotype, but intrapopulation differences in holoploid genome size were found among P. subulata and P. nivalis. The monoploid genome size of M. gracilis differed significantly from all Phlox, supporting separation of the genera. All cultivar accessions were diploid with genome sizes similar to wild diploid P. subulata, however Phlox×procumbens had a mean genome size (8.73pg) intermediate to parental taxa, P. stolonifera×P. subulata, supporting hybrid origin. Knowledge of cytotype variation in Phlox germplasm will be useful for plant breeders, systematists, and conservationists.

Contemporary evolution of host plant range expansion in an introduced herbivorous beetle Ophraella communa.

Host range expansion of herbivorous insects is a key event in ecological speciation and insect pest management. However, the mechanistic processes are relatively unknown because it is difficult to observe the ongoing host range expansion in natural population. In this study, we focused on the ongoing host range expansion in introduced populations of the ragweed leaf beetle, Ophraella communa, to estimate the evolutionary process of host plant range expansion of a herbivorous insect. In the native range of North America, O.communa does not utilize Ambrosia trifida, as a host plant, but this plant is extensively utilized in the beetle's introduced range. Larval performance and adult preference experiments demonstrated that native O.communa beetles show better survival on host plant individuals from introduced plant populations than those from native plant populations and they also oviposit on the introduced plant, but not on the native plant. Introduced O.communa beetles showed significantly higher performance on and preference for both introduced and native A.trifida plants, when compared with native O.communa. These results indicate the contemporary evolution of host plant range expansion of introduced O.communa and suggest that the evolutionary change of both the host plant and the herbivorous insect involved in the host range expansion.

Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage.

Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after invivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages.

Can anthropogenic linear gaps increase plant abundance and diversity?

Context Seed-dispersing animals often move along “linear gaps” (linear anthropogenic features such as roads and trails that contain little vegetation), especially in densely-vegetated landscapes. As a result, linear gaps and their verges may receive more seeds than adjacent habitats. In addition, linear gap verges may provide more suitable conditions for plant establishment than neighboring habitats. In this way, linear gaps may increase plant abundance and diversity, and facilitate connectivity of native and non-native plant populations, ultimately increasing plant diversity in the landscape.

Precision of systematic and random sampling in clustered populations: habitat patches and aggregating organisms.

Natural populations of plants and animals spatially cluster because (1) suitable habitat is patchy, and (2) within suitable habitat, individuals aggregate further into clusters of higher density. We compare the precision of random and systematic field sampling survey designs under these two processes of species clustering. Second, we evaluate the performance of 13 estimators for the variance of the sample mean from a systematic survey. Replicated simulated surveys, as counts from 100 transects, allocated either randomly or systematically within the study region, were used to estimate population density in six spatial point populations including habitat patches and Matérn circular clustered aggregations of organisms, together and in combination. The standard one-start aligned systematic survey design, a uniform 10 x 10 grid of transects, was much more precise. Variances of the 10 000 replicated systematic survey mean densities were one-third to one-fifth of those from randomly allocated transects, implying transect sample sizes giving equivalent precision by random survey would need to be three to five times larger. Organisms being restricted to patches of habitat was alone sufficient to yield this precision advantage for the systematic design. But this improved precision for systematic sampling in clustered populations is underestimated by standard variance estimators used to compute confidence intervals. True variance for the survey sample mean was computed from the variance of 10 000 simulated survey mean estimates. Testing 10 published and three newly proposed variance estimators, the two variance estimators (v) that corrected for inter-transect correlation (ν₈ and ν(W)) were the most accurate and also the most precise in clustered populations. These greatly outperformed the two "post-stratification" variance estimators (ν₂ and ν₃) that are now more commonly applied in systematic surveys. Similar variance estimator performance rankings were found with a second differently generated set of spatial point populations, ν₈ and ν(W) again being the best performers in the longer-range autocorrelated populations. However, no systematic variance estimators tested were free from bias. On balance, systematic designs bring more narrow confidence intervals in clustered populations, while random designs permit unbiased estimates of (often wider) confidence interval. The search continues for better estimators of sampling variance for the systematic survey mean.

A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population.

Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.

GENETIC DIVERSITY AND STRUCTURE OF Oenocarpus mapora GERMPLASM CONSERVED AT EASTERN AMAZON

ABSTRACT The aim of this study was to evaluate the genetic diversity and structure in the germoplasm of Oenocarpus mapora conserved at Eastern Amazon. Thus, 88 individuals were genotyped with five microsatellite loci. These individuals belong to 24 accessions that were sampled in eight sample places of three Brazilian Amazon states conserved at the Active Germplasm Bank (AGB) of Embrapa Eastern Amazon. All loci were polymorphic and they generated 85 alleles with an average of 17 alleles per loci. Total genetic diversity (HE) was 0.48. Sample places were considered genetically distinct, with ?p = 0.354. The analysis of molecular variance (AMOVA) identified that the genetic portion among areas was of 36.14% and within 63.86%. The Nei distances varied from 0.091 between Abaetetuba and Santo Antônio do Tauá, both in the state of Pará (PA), to 4.18, between Parintins, AM and Rio Branco, AC. By means of Bayesian analysis, it was identified nine clusters that compose the accessions of the germplasm bank, with different distributions among individuals. The study showed high fixation rates per sample area, which indicates that there may have been significant inbreeding or crossing among parental individuals. It suggests that future samples should be made of different plants in natural populations. Even though, it was verified that there is considerable genetic variation in the germplasm of O. mapora.

Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits.

DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.

Analysis of Genetic Diversity and Population Structure for the Native Tree Viburnum rufidulum Occurring in Kentucky and Tennessee

Viburnum rufidulum is a deciduous tree native to North America that has four-season appeal, which provides commercial horticultural value. In addition, the plant has unique and attractive red pubescence on leaf buds and petioles, common to no other Viburnum species. As habitat undergoes development and subsequent fragmentation of native plant populations, it is important to have baseline genetic information for this species. Little is known about the genetic diversity within populations of V. rufidulum. In this study, seven microsatellite loci were used to measure genetic diversity, population structure, and gene flow of 235 V. rufidulum trees collected from 17 locations in Kentucky and Tennessee. The genotype data were used to infer population genetic structure using the program InStruct and to construct an unweighted pair group method with arithmetic mean dendrogram. A single population was indicated by the program InStruct and the dendrogram clustered the locations into two groups; however, little bootstrap support was evident. Observed and expected heterozygosity were 0.49 and 0.78, respectively. Low-to-moderate genetic differentiation (FST = 0.06) with evidence of gene flow (Nm = 4.82) was observed among 17 populations of V. rufidulum. A significant level of genetic diversity was evident among V. rufidulum populations with most of the genetic variations among individual trees (86.37%) rather than among populations (13.63%), and a Mantel test revealed significant correlation between genetic and geographical distance (r = 0.091, P = 0.001). The microsatellites developed herein provide an initial assessment or a baseline of genetic diversity for V. rufidulum in a limited area of the southeastern region of the United States. The markers are a genetic resource and can be of assistance in breeding programs, germplasm assessment, and future studies of V. rufidulum populations, as this is the first study to provide genetic diversity data for this native species.

High incidence of pollen theft in natural populations of a buzz-pollinated plant

More than 20,000 angiosperm species possess non-dehiscent anthers that open through small pores at the anther’s tip. These flowers are visited by bees that use vibrations to remove pollen, a phenomenon known as buzz pollination. However, some floral visitors fail to transfer pollen efficiently, either through a mismatch of flower and insect size, or because they are unable to buzz-pollinate. These visitors collect pollen, but provide little or no pollination, behaving as pollen thieves. Although pollen theft is widespread in plants, few studies have quantified the incidence of pollen thieves for buzz-pollinated plants. We use observations of natural populations and floral manipulations of Solanum rostratum (Solanaceae) to investigate the incidence of pollen theft, find morphological and behavioural differences between pollinators and thieves, measure the pollination efficiency of visitors, and characterize the reproductive ecology of this herb. We found that most visitors act as thieves, with <20 % of all bees contacting the stigma. Insect visitors that regularly failed to contact the stigma (illegitimate visitors), included buzzing and non-buzzing bees, were significantly smaller, visited fewer flowers per bout, and stayed longer in each flower than (legitimate) visitors that regularly contact the stigma. Few flowers visited solely by illegitimate visitors set fruit. Our results show that S. rostratum requires insect visitation to set seed and natural populations experience moderate pollen limitation. We conclude that insect size, relative to the flower, is the main determinant of whether a visitor acts as a pollinator or a pollen thief in S. rostratum.

Range-Wide Variation in the Ecological Niche and Floral Polymorphism of the Western Mediterranean GeophyteNarcissus dubiusGouan

Premise of research. Comparative studies of variation in the ecology and genetics of natural plant populations located at the limits and in the center of a species range provide fundamental insights into the historical formation of species distribution patterns.Methodology. In this study, we quantify variation in the ecological niche and the expression of a floral polymorphism across the range of the Mediterranean geophyte Narcissus dubius Gouan. An exhaustive data set of known locations was compiled to distinguish groups of geographically central and peripheral populations in both Spain and France. These occur across a double climatic gradient. First, there is a gradient from a hot and dry Mediterranean climatic regime in eastern Spain to a milder Mediterranean climatic regime in southern France (lower maximum temperature and shorter summer drought). Second, there is a shift to a more continental climate in peripheral populations in inland Spain. We also modeled the current climatic niche and produced hi...

Contrasting Mechanisms of Recovery from Defoliation in Two Intermountain-Native Bunchgrasses

Grazing tolerance of dominant native species may determine the fate of rangeland ecosystems, and using native plant populations with good grazing tolerance in restoration seedings may improve ecosystem resilience, especially when domestic herbivores are present. We examined interspecific and intraspecific differences in shoot biomass and defoliation tolerance for two semiarid, perennial cool-season bunchgrasses native to the Intermountain West, USA, Pseudoroegneria spicata and Elymus wawawaiensis, on the basis of four functional traits (specific leaf area [SLA], plant basal area, tiller number, and tiller mass). We applied two treatments, control and boot-defoliation, where the latter included defoliation at the early-reproductive (“boot”) stage, the phenological stage most vulnerable to herbivory, while the control treatment did not. We tested two contrasting hypotheses (i.e., that boot-defoliation tolerance is increased through either increases in SLA or through more favorable tiller demography). For shoot biomass, both grasses were less productive under the boot-defoliation treatment than for the control, but E. wawawaiensis displayed higher boot-defoliation tolerance than P. spicata. Interpopulation variation occurred in all four functional traits for P. spicata, but there were no such variation for E. wawawaiensis. The tiller demography hypothesis better explained boot-defoliation tolerance in both species, and neither SLA nor plant basal area was correlated with shoot biomass for either treatment. Of the traits measured, high tiller number served as the primary mechanism for shoot biomass and boot-defoliation tolerance in P. spicata, while tiller number and tiller mass were both important predictors of both shoot biomass and boot-defoliation tolerance.

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia.

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers in the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10–40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. The taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and tundra ecosystems.

Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley.

Alternative methods for genomic prediction of traits and trait differences are compared and recommendations made. We make recommendations for implementing methods in the context of DUS testing. High-throughput genotyping provides an opportunity to explore the application of genotypes in predicting plant phenotypes. We use a genome-wide prediction model to estimate the contribution of all loci and sum over multiple minor effects to predict traits. A potential use is in plant variety protection to discriminate among varieties on distinctness. We investigate this use with alternate scenarios in a set of 431 winter and spring barley varieties, with trait data from UK DUS trials comprising 28 characteristics, together with SNP genotype data. Firstly, each trait is predicted from genotypes by ridge regression with discrimination among varieties using predicted traits. Secondly, squared trait differences between each pair of varieties are regressed on genetic distances between each variety by ridge regression, with discrimination among varieties using the predicted squared trait differences directly. This latter approach is analogous to the use of phenotype and marker differences introduced to human genetic linkage analysis by Haseman and Elston and to the analysis of heritability in natural populations of plants by Ritland. We compare correlations between methods, both trait by trait and summarised across all traits. Our results show wide variation among correlations for each trait. However, the aggregate distances calculated from values predicted by genotypes show higher correlations with distances calculated from measured values than any previously reported. We discuss the applicability of these results to implementation of UPOV Model 2 in DUS testing and suggest 'success criteria' that should be considered by testing authorities seeking to implement UPOV Model 2.