Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)

Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.

An evolutionary look into the history of lentil reveals unexpected diversity

The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold‐season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty‐three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were “enzymes,” “Cell Wall Organization,” and “external stimuli response.” All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.

Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea

Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.

Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea (Cicer arietinum) Landraces from Pakistan

Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience. Here we use 8113 single nucleotide polymorphism markers to determine genetic variation and compare population structure within a previously uncharacterized collection of 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal Desert of the Punjab. Despite low levels of variation across the collection and limited genetic structure, we found some differentiation between accessions from arid, semiarid, irrigated, and coastal areas. In a subset of 232 markers, we found evidence of differentiation along gradients of elevation and isothermality. Our results highlight the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes, and the use of such data to nominate germplasm accessions with the potential to improve crop drought tolerance and other environmental traits.

Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance

Soil DNA profiling has potential as a forensic tool to establish a link between soil collected at a crime scene and soil recovered from a suspect. However, a quantitative measure is needed to investigate the spatial/temporal variability across multiple scales prior to their application in forensic science. In this study, soil DNA profiles across Miami-Dade, FL, were generated using length heterogeneity PCR to target four taxa. The objectives of this study were to (i) assess the biogeographical patterns of soils to determine whether soil biota is spatially correlated with geographic location and (ii) evaluate five machine learning algorithms for their predictive ability to recognize biotic patterns which could accurately classify soils at different spatial scales regardless of seasonal collection. Results demonstrate that soil communities have unique patterns and are spatially autocorrelated. Bioinformatic algorithms could accurately classify soils across all scales with Random Forest significantly outperforming all other algorithms regardless of spatial level.

Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers

To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past.

Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae)

PREMISE OF THE STUDY

Seedling establishment and survival are highly sensitive to soil salinity and plants that evolved in saline environments are likely to express traits that increase fitness in those environments. Such traits are of ecological interest and they may have practical value for improving salt tolerance in cultivated species. We examined responses to soil salinity and tested potential mechanisms of salt tolerance in Medicago truncatula, using genotypes that originated from natural populations occurring on saline and nonsaline soils.

METHODS

Germination and seedling responses were quantified and compared between saline and nonsaline origin genotypes. Germination treatments included a range of sodium chloride (NaCl) concentrations in both offspring and parental environments. Seedling treatments included NaCl, abscisic acid (ABA), and potassium chloride (KCl).

KEY RESULTS

Saline origin genotypes displayed greater salinity tolerance for germination and seedling traits relative to nonsaline origin genotypes. We observed population specific differences for the effects of salinity on time to germination and for the impact of parental environment on germination rates. ABA and NaCl treatments had similar negative effects on root growth, although relative sensitivities differed, with saline population less sensitive to NaCl and more sensitive to ABA compared to their nonsaline counterparts.

CONCLUSIONS

We report population differentiation for germination and seedling growth traits under saline conditions among populations derived from saline and nonsaline environments. These observations are consistent with a syndrome of adaptations for salinity tolerance during early plant development, including traits that are common among saline environments and those that are idiosyncratic to local populations.

More cells, bigger cells or simply reorganization? Alternative mechanisms leading to changed internode architecture under contrasting stress regimes

Shading and mechanical stress (MS) modulate plant architecture by inducing different developmental pathways. Shading results in increased stem elongation, often reducing whole-plant mechanical stability, while MS inhibits elongation, with a concomitant increase in stability. Here, we examined how these organ-level responses are related to patterns and processes at the cellular level by exposing Impatiens capensis to shading and MS. Shading led to the production of narrower cells along the vertical axis. By contrast, MS led to the production of fewer, smaller and broader cells. These responses to treatments were largely in line with genetic differences found among plants from open and closed canopy sites. Shading- and MS-induced plastic responses in cellular characteristics were negatively correlated: genotypes that were more responsive to shading were less responsive to MS and vice versa. This negative correlation, however, did not scale to mechanical and architectural traits. Our data show how environmental conditions elicit distinctly different associations between characteristics at the cellular level, plant morphology and biomechanics. The evolution of optimal response to different environmental cues may be limited by negative correlations of stress-induced responses at the cellular level.

Testing mechanisms and context dependence of costs of plastic shade avoidance responses in Impatiens capensis (Balsaminaceae)

PREMISE OF THE STUDY

Many plant species elongate their shoots in response to neighbor proximity and neighbor height. Although these plastic responses may be beneficial in terms of enhancing light interception, they also may have costs in terms of increased risk of mechanical failure (i.e., lodging or breaking) because of thinner stems. This trade-off between light acquisition and stability may shape the evolution of plastic elongation responses to foliage shade.

METHODS

In a field experiment manipulating elongation phenotypes and densities, we tested two hypotheses. We predicted that the risks of mechanical failure depend on plastic elongation and/or on characteristics of the immediate neighborhood, such as density and neighbor height. Further, we predicted that plants that fail mechanically would have reduced fitness.

KEY RESULTS

Mechanical failure was earlier and more frequent at high density and showed a complex interaction with neighborhood characteristics such as relative height of the neighbors and the expression of early plasticity. Plants that broke earlier had shorter lifespan and lower reproductive output.

CONCLUSIONS

Our results show that depending on the height and density of the group, plastic elongation responses can remain advantageous despite costs of increased risk of mechanical failure of the taller stems, as mechanical failure was not associated with strong costs in terms of reduced lifespan or seed production. The overall benefits of elongation outweigh the costs resulting in selection for elongation at the population level.

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.

Adapting genomics to study the evolution and ecology of agricultural systems

In the face of global change, agriculture increasingly requires germplasm with high yields on marginal lands. Identifying pathways that are adaptive under marginal conditions is increasingly possible with advances at the intersection of evolutionary ecology, population genetics, and functional genomics. Trait-based (reverse ecology) approaches have connected flowering time in Arabidopsis thaliana to single alleles with environment-specific effects. Similarly, genetic dissection of rice flooding tolerance enabled the production of near-isogenic lines exhibiting tolerance and high yields. An alternative gene-forward (forward ecology) approach identified candidate genes for local adaptation of Arabidopsis lyrata to heavy-metal rich soils. A global perspective on plant adaptation and trait correlations provides a foundation for breeding tolerant crops and suggests populations adapted to marginal habitats be conservation priorities.

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 Ca∶Mg ratio in A. lyrata.

Partitioning adaptive differentiation across a patchy landscape: shade avoidance traits in impatiens capensis

Adaptation to different habitat types across a patchy landscape may either arise independently in each patch or occur due to repeated colonization of each patch by the same specialized genotype. We tested whether open- and closed-canopy forms of Impatiens capensis, an herbaceous annual plant of eastern North America, have evolved repeatedly by comparing hierarchical measures of F(ST) estimated from AFLPs to morphological differentiation measured by Q(ST) for five pairs of populations found in open and closed habitats in five New England regions. Morphological differentiation between habitats (Q(HT)) in elongation traits was greater than marker divergence (F(HT)), suggesting adaptive differentiation. Genotypes from open- and closed-canopy habitats differed in shade avoidance traits in several population pairs, whereas patterns of AFLP differentiation suggest this differentiation does not have a single origin. These results suggest that open- and closed-canopy habitats present different selective pressures, but that the outcome of diversifying selection may differ depending on specific closed- and open-canopy habitats and on starting genetic variation. Hierarchical partitioning of F(ST) and Q(ST) makes it possible to distinguish global stabilizing selection on traits across a landscape from diversifying selection between habitat types within regions.

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.

Frequency and Microenvironmental Pattern of Selection on Plastic Shade‐Avoidance Traits in a Natural Population ofImpatiens capensis

The frequency and predictability of different selective environments are important parameters in models for the evolution of plasticity but have rarely been measured empirically in natural populations. We used an experimental phytometer approach to examine the frequency, predictability, and environmental determinants of heterogeneous selection on phytochrome-mediated shade-avoidance responses in a natural population of the annual plant Impatiens capensis. The strength and direction of selection on shade-avoidance traits varied substantially on a fine spatial scale. The shade-avoidance phenotype had high relative fecundity in some microsites but was disadvantageous in other microsites. Local seedling density proved to be a surprisingly poor predictor of microenvironmental variation in the strength and direction of selection on stem elongation in this study population. At least some of this unpredictability resulted from microenvironmental variation in water availability; the shade-avoidance phenotype was more costly in dry microsites. Thus, environmental heterogeneity in resource availability can affect the relative costs and benefits of expressing shade-avoidance traits independent of local seedling density, the inductive environmental cue. Theory predicts that these conditions may promote local genetic differentiation in reaction norms in structured populations, as observed in I. capensis.

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.

A novel social polymorphism in a primitively eusocial bee

Halictine sweat bees (Hymenoptera, Halictidae) are model organisms for the evolution of altruism, reproductive castes, and eusocial colony organization. Halictine social behavior is not only extremely variable, but also ecologically and evolutionarily labile. Among social species, colony social organization ranges from communal societies of egalitarian females to eusocial and semisocial ones with reproductive queens and more or less sterile workers. A striking aspect of halictine social variation is the mutual exclusivity of communal and eusocial types of colony social organization within the same species, these two types of social behavior being characteristic of different genera and subgenera. We report a recently discovered exception to this rule in a population of Halictus sexcinctus (Fabricius) at Daimonia-Pyla in southern Greece, that contained both communal and eusocial colonies. Moreover, communal and eusocial females exhibit morphological differences that imply a preimaginal developmental switch, which could also underlie the two types of social behavior. That the communal and eusocial forms are not merely cryptic sister species with different social behavior is indicated by the comparison of mitochondrial DNA sequences of two sections of cytochrome oxidase I, which indicate that Greek specimens of both social types are more similar than they are to conspecifics from elsewhere in Europe. The phylogenetic position of Halictus sexcinctus suggests that this unusual communal/eusocial polymorphism may represent an unstable intermediate step in an evolutionary reversal from eusocial to solitary behavior.