The Search for Agroislands in the Chickpea Genome

Biophysics - The concentration of genes that control domestication traits in so-called “agroislands” complicates breeding. Therefore, information about where such islands are located in...     

Dispersal biology of Liatris scariosa var. novae-angliae (Asteraceae), a rare New England grassland perennial

Propagule dispersal biology is a crucial avenue of research for rare plant species, especially those adapted to disturbance, such as northern blazing star (Liatris scariosa var. novae-angliae), a rare, early-successional New England grassland perennial. We examined the dispersal ability of northern blazing star propagules collected from 14 populations covering the entire latitudinal range of the taxon. Multiple regression demonstrated that dispersal ability, as measured by drop time in still air and flight distance in a low-speed wind tunnel, decreased significantly with propagule size and achene length, and increased with achene width and (for flight distance) pappus length. We used this multiple regression model to test for differences in predicted dispersal capability among maternal families, populations, and inland, coastal, and island habitats. Dispersal capability differed significantly among families and populations but not regions, and allometric relationships between morphological measurements were consistent across populations. Overall, dispersal capability was negatively correlated with germination success in a common greenhouse environment. However, germination success for a given dispersal ability, as well as achene shape, differed among populations. These results suggest specific populations to be targeted for management efforts promoting dispersal and establishment.     

Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata

Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.     

Larger Triticum aestivum plants do not preempt nutrient-rich patches in a glasshouse experiment

Plant competition belowground generally appears to be size-symmetric, i.e. larger plants only obtain a share of belowground resources proportional to their size, and therefore do not suppress smaller individuals. The experimental evidence for size-symmetric belowground competition comes primarily from experiments with homogenous soil conditions. It has been hypothesized that the presence of high nutrient patches that can be pre-empted by larger plants can make competition belowground size-asymmetric. We tested this hypothesis by growing Triticum aestivum individuals singly and in pairs in containers with aboveground dividers so that competition occurred only belowground. Plants grew in either a homogenous soil mixture, or in the same mixture with a band of enriched soil between them. Initial size differences were generated by a seven day difference in sowing date. There was no evidence of size-asymmetric competition with or without soil heterogeneity. Large plants did not have a disproportionate effect on smaller plants, nor did they perform disproportionately better when paired with a small neighbor. Our results suggest that in heterogeneous soil conditions, roots of larger plants that reach nutrient patches first are not able to prevent roots of smaller plants that arrive later from obtaining resources from the patch. This revised version was published online in August 2006 with corrections to the Cover Date.     

Conclusions about niche expansion in introduced Impatiens walleriana populations depend on method of analysis

Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas.     

Physiological mechanism of population differentiation in shade-avoidance responses between woodland and clearing genotypes of Impatiens capensis

Forest understory plants often respond less intensely to reduced ratios of red to far red (R : FR) light, an important signal of foliage shade, than conspecific or congeneric plants from open-canopy sites. Reduced responsiveness to low R : FR in plants from closed-canopy sites could be caused by two physiological mechanisms. First, closed-canopy plants could have less sensitive shade-avoidance responses to low R : FR. Second, the high irradiance response to FR (FR-HIR), which allows seedling de-etiolation under low R : FR, might be stronger or persist longer after de-etiolation in closed-canopy plants, thus counteracting shade-avoidance responses to low R : FR. These hypotheses were tested using diodes that emit red and far-red light to distinguish the responses to altered R : FR of genotypes of Impatiens capensis collected from a pair of open- and closed-canopy populations that have previously been shown to differ in sensitivity to R : FR. Genotypes from the open-canopy environment exhibited typical shade-avoidance responses, elongating in response to supplemental FR. However, genotypes from the closed-canopy environment responded to supplemental FR by elongating less than under ambient control conditions, indicating a persistent FR-HIR. Thus, the observed population differentiation in response to low R : FR may be linked to population differences in FR-HIR.     

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors

Background

Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles.

Results

We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R²=0.97.

Conclusions

We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited.

     

Nutrient enrichment enhances hidden differences in phenotype to drive a cryptic plant invasion

Many mechanisms of invasive species success have been elucidated, but those driving cryptic invasions of non‐native genotypes remain least understood. In one of the most successful cryptic plant invasions in North America, we investigate the mechanisms underlying the displacement of native Phragmites australis by its Eurasian counterpart. Since invasive Phragmites’ populations have been especially prolific along eutrophic shorelines, we conducted a two‐year field experiment involving native and invasive genotypes that manipulated nutrient level and competitor identity (inter‐ and intra‐genotypic competition) to assess their relative importance in driving the loss of native Phragmites. Inter‐genotypic competition suppressed aboveground biomass of both native and invasive plants regardless of nutrient treatment (～ 27%), while nutrient addition disproportionately enhanced the aboveground biomass (by 67%) and lateral expansion (by > 3 × farther) of invasive Phragmites. Excavation of experimental plots indicated that nutrient addition generates these differences in aboveground growth by differentially affecting rhizome production in invasive vs native plants; invasive rhizome biomass and rhizome length increased by 595% and 32% with nutrient addition, respectively, while natives increased by only 278% and 15%. Regardless of nutrient level, native rhizomes produced twice as many roots compared to invasives, which field surveys revealed are heavily infected with mycorrhizal symbionts. These results suggest that native Phragmites competes well under nutrient‐limited conditions because its rhizomes are laden with nutrient‐harvesting roots and mycorrhizae. Invasive Phragmites’ vigorous aboveground response to nutrients and scarcity of lateral roots, in contrast, may reflect its historic distribution in eutrophic Eurasian wetlands and correspond to its prevalence in New England marshes characterized by elevated nutrient availability and relaxed nutrient competition. These findings reveal that discrete differences in phenotype can interact with anthropogenic modification of environmental conditions to help explain the success of cryptic invaders.     

The Park Grass Experiment and next‐generation approaches: local adaptation of sweet vernal grass revisited

Long‐term ecological experiments provide unique opportunities to observe the effects of natural selection. The Park Grass Experiment at Rothamsted Experiment Station in Hertfordshire, UK, is the longest running ecological experiment that incorporates fertilization treatments and has been ongoing since 1856. In the 1970s, local adaptation was observed in the grass Anthoxanthum odoratum to the elevated soil aluminium levels of the fertilized plots. Gould et al. ( 2014 ) have utilized this system to reevaluate the extent of local adaptation, first documented nearly 45 years ago (Snaydon 1970 ), and to use emerging molecular approaches to identify candidate genes for the adaptation. From their work, they identify several plausible candidate loci for aluminium tolerance. This work shows the power of long‐term field‐based trials in a scientific age concentrated on rapidly emerging molecular techniques often utilized in short, narrowly focused laboratory or controlled environment experiments. The current study clearly illustrates the benefits gained by combining these molecular approaches within long‐term monitoring experiments that can be regularly revisited in a changing world and used to address questions on evolutionary scales.