Distinct geographic parthenogenesis in spite of niche conservatism and a single ploidy level: A case of Rubus ser. Glandulosi (Rosaceae).

Asexual organisms often differ in their geographic distributions from their sexual relatives. This phenomenon, termed geographic parthenogenesis, has long been known, but the underlying factors behind its diverse patterns have been under dispute. Particularly problematic is an association between asexuality and polyploidy in most taxa. Here, we present a new system of geographic parthenogenesis on the tetraploid level, promising new insights into this complex topic. We used flow cytometric seed screen and microsatellite genotyping to characterise the patterns of distribution of sexuals and apomicts and genotypic distributions in Rubus ser. Glandulosi across its range. Ecological modelling and local-scale vegetation and soil analyses were used to test for niche differentiation between the reproductive groups. Apomicts were detected only in North-western Europe, sexuals in the rest of the range in Europe and West Asia, with a sharp borderline stretched across Central Europe. Despite that, we found no significant differences in ecological niches. Genotypic richness distributions suggested independence of the reproductive groups and a secondary contact. We argue that unless a niche differentiation (resulting from polyploidy and/or hybridity) evolves, the main factors behind the patterns of geographic parthenogenesis in plants are phylogeographic history and neutral microevolutionary processes, such as clonal turnover.

Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles.

BACKGROUND AND AIMS: Rubus ser. Glandulosi provides a unique model of geographical parthenogenesis on a homoploid (2n = 4x) level. We aim to characterize evolutionary and phylogeographical patterns in this taxon and shed light on the geographical differentiation of apomicts and sexuals. Ultimately, we aim to evaluate the importance of phylogeography in the formation of geographical parthenogenesis. METHODS: Rubus ser. Glandulosi was sampled across its Eurasian range together with other co-occurring Rubus taxa (587 individuals in total). Double-digest restriction site-associated DNA sequencing (ddRADseq) and modelling of suitable climate were used for evolutionary inferences. KEY RESULTS: Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. Sexuals were introgressed from Rubus dolichocarpus and Rubus moschus in West Asia and from Rubus ulmifolius agg., Rubus canescens and Rubus incanescens in Europe, whereas apomicts were characterized by alleles of Rubus subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as was occasional hybridization with other taxa. CONCLUSIONS: We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France, whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographical parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts, and maladaptive population genetic processes probably did not shape the geographical patterns.

Both male and female meiosis contribute to non-Mendelian inheritance of parental chromosomes in interspecific plant hybrids (Lolium × Festuca).

Some interspecific plant hybrids show unequal transmission of chromosomes from parental genomes to the successive generations. It has been suggested that this is due to a differential behavior of parental chromosomes during meiosis. However, underlying mechanism is unknown. We analyzed chromosome composition of the F2 generation of Festuca × Lolium hybrids and reciprocal backcrosses to elucidate effects of male and female meiosis on the shift in parental genome composition. We studied male meiosis, including the attachment of chromosomes to the karyokinetic spindle and gene expression profiling of the kinetochore genes. We found that Lolium and Festuca homoeologues were transmitted differently to the F2 generation. Female meiosis led to the replacement of Festuca chromosomes by their Lolium counterparts. In male meiosis, Festuca univalents were attached less frequently to microtubules than Lolium univalents, lagged in divisions and formed micronuclei, which were subsequently eliminated. Genome sequence analysis revealed a number of non-synonymous mutations between copies of the kinetochore genes from Festuca and Lolium genomes. Furthermore, we found that outer kinetochore proteins NDC80 and NNF1 were exclusively expressed from the Lolium allele. We hypothesize that silencing of Festuca alleles results in improper attachment of Festuca chromosomes to karyokinetic spindle and subsequently their gradual elimination.

Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance.

Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.

Stoichiometry versus ecology: the relationships between genome size and guanine-cytosine content, and tissue nitrogen and phosphorus in grassland herbs.

BACKGROUND AND AIMS: Plant tissue nitrogen (N) and phosphorus (P) and genome traits, such as genome size and guanine-cytosine (GC) content, scale with growth or metabolic rates and are linked to plant ecological strategy spectra. Tissue NP stoichiometry and genome traits are reported to affect plant growth, metabolic rates or ecological strategies in contrasting ways, although the elemental costs for building and maintaining DNA are typically overlooked. METHODS: We formulated stoichiometry- and ecology-based predictions on the relationship between genome size and GC content to tissue N, P and N : P and tested them on a set of 130 herbaceous species from a temperate grassland using ordinary, phylogenetic and quantile regression. KEY RESULTS: Genome size was only negatively linked to plant N and N : P in species with very small genomes. We found no link between genome size and plant P. GC content was negatively linked to plant N and P but we found these significant links consistently in both GC-rich and GC-poor species. Finally, GC content correlated positively with plant N : P but only in species with GC-rich genomes. CONCLUSIONS: Our results provide stronger support for the ecology-based predictions than the stoichiometry-based predictions, and for the links between GC content and plant N and P stoichiometry than for genome size. We argue that the theories of plant metabolic rates and ecological strategies (resource-acquisitive vs. conservative or ruderal vs. stress-tolerator spectra) better explain interspecific genome-NP stoichiometry relationships at the tissue level (although relatively weakly) than the stoichiometric theory based on the elemental costs for building and maintaining DNA.

Variability in mycorrhizal status of plant species is much larger within than between plots in grassland and coastal habitats.

Community-level studies linking plant mycorrhizal status to environment usually do not account for within-plot mycorrhizal status variability; thus, patterns of plant mycorrhizal status diversity are largely unknown. Here, we assessed the relative importance of within- and between-plot variability components in mycorrhizal status and examined how plant mycorrhizal status diversity is related to soil nutrient availability. We hypothesised larger between-plot variability in mycorrhizal status and higher plant mycorrhizal status diversity in P-poor soils. To test these hypotheses, we used plant phylogenies, vegetation, soil and plant mycorrhizal status data from Czech semi-natural grasslands and Scottish coastal habitats. We divided plant mycorrhizal status diversity into divergence and evenness and tested their relations to soil P, K, Ca and Mg. Within-plot variability component of mycorrhizal status was always, on average, at least 2.2 times larger than between-plot variability in our datasets. Plant mycorrhizal status divergence was positively related to Ca (in both datasets) and Mg (only in grasslands and when accounting for phylogeny). In grasslands, the relationship between Mg and plant mycorrhizal status evenness was negative when accounting for phylogeny, while it was positive when not accounting for phylogeny. Plant mycorrhizal status diversity was not linked to P and its relation to K was inconsistent. Our results suggest that high Ca in the soil can promote coexistence of mycorrhizal, facultatively mycorrhizal and non-mycorrhizal plant species. We encourage future studies to also focus on within-plot variability in mycorrhizal status, because it appears to be highly relevant in herbaceous systems.

Direct evidence for crossover and chromatid interference in meiosis of two plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei).

Crossing over, in addition to its strictly genetic role, also performs a critical mechanical function, by bonding homologues in meiosis. Hence, it is responsible for an orderly reduction of the chromosome number. As such, it is strictly controlled in frequency and distribution. The well-known crossover control is positive crossover interference which reduces the probability of a crossover in the vicinity of an already formed crossover. A poorly studied aspect of the control is chromatid interference. Such analyses are possible in very few organisms as they require observation of all four products of a single meiosis. Here, we provide direct evidence of chromatid interference. Using in situ probing in two interspecific plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei) during anaphase I, we demonstrate that the involvement of four chromatids in double crossovers is significantly more frequent than expected (64% versus 25%). We also provide a physical measure of the crossover interference distance, covering ~30-40% of the relative chromosome arm length, and show that the centromere acts as a barrier for crossover interference. The two arms of a chromosome appear to act as independent units in the process of crossing over. Chromatid interference has to be seriously addressed in genetic mapping approaches and further studies.

Mycorrhizal status is a poor predictor of the distribution of herbaceous species along the gradient of soil nutrient availability in coastal and grassland habitats.

Plant mycorrhizal status (a trait indicating the ability to form mycorrhizas) can be a useful plant trait for predicting changes in vegetation influenced by increased fertility. Mycorrhizal fungi enhance nutrient uptake and are expected to provide a competitive advantage for plants growing in nutrient-poor soils; while in nutrient-rich soils, mycorrhizal symbiosis may be disadvantageous. Some studies in natural systems have shown that mycorrhizal plants can be more frequent in P and N-poor soils (low nutrient availability) or Ca and Mg-high (high pH) soils, but empirical support is still not clear. Using vegetation and soil data from Scottish coastal habitats, and Latvian and Czech grasslands, we examined whether there is a link between plant mycorrhizal status and plant-available P, N, Ca and Mg. We performed the max test analysis (to examine the central tendency) and a combination of quantile regression and meta-analysis (to examine tendencies in different quantiles) on both community and plant species data combined with plant phylogenies. We consistently found no changes in mycorrhizal status at the community and species levels along the gradients of plant-available P, N, Ca and Mg in the central tendency and in almost all quantiles across all datasets. Thus, we found no support for the hypotheses that herbaceous species which are able to form mycorrhizas are more frequent in nutrient-poor and high pH environments. Obligatory, facultatively and non-mycorrhizal herbaceous species appear to assemble randomly along the gradients of nutrient availability in several European herbaceous habitats, suggesting that all these strategies perform similarly under non-extreme soil nutrient conditions.

Instability of Alien Chromosome Introgressions in Wheat Associated with Improper Positioning in the Nucleus.

Alien introgressions introduce beneficial alleles into existing crops and hence, are widely used in plant breeding. Generally, introgressed alien chromosomes show reduced meiotic pairing relative to the host genome, and may be eliminated over generations. Reduced pairing appears to result from a failure of some telomeres of alien chromosomes to incorporate into the leptotene bouquet at the onset of meiosis, thereby preventing chiasmate pairing. In this study, we analysed somatic nuclei of rye introgressions in wheat using 3D-FISH and found that while introgressed rye chromosomes or chromosome arms occupied discrete positions in the Rabl's orientation similar to chromosomes of the wheat host, their telomeres frequently occupied positions away from the nuclear periphery. The frequencies of such abnormal telomere positioning were similar to the frequencies of out-of-bouquet telomere positioning at leptotene, and of pairing failure at metaphase I. This study indicates that improper positioning of alien chromosomes that leads to reduced pairing is not a strictly meiotic event but rather a consequence of a more systemic problem. Improper positioning in the nuclei probably impacts the ability of introgressed chromosomes to migrate into the telomere bouquet at the onset of meiosis, preventing synapsis and chiasma establishment, and leading to their gradual elimination over generations.

Nuclear Disposition of Alien Chromosome Introgressions into Wheat and Rye Using 3D-FISH.

During interphase, the chromosomes of eukaryotes decondense and they occupy distinct regions of the nucleus, called chromosome domains or chromosome territories (CTs). In plants, the Rabl's configuration, with telomeres at one pole of nucleus and centromeres at the other, appears to be common, at least in plants with large genomes. It is unclear whether individual chromosomes of plants adopt defined, genetically determined addresses within the nucleus, as is the case in mammals. In this study, the nuclear disposition of alien rye and barley chromosomes and chromosome arm introgressions into wheat while using 3D-FISH in various somatic tissues was analyzed. All of the introgressed chromosomes showed Rabl's orientation, but their relative positions in the nuclei were less clear. While in most cases pairs of introgressed chromosomes occupied discrete positions, their association (proximity) along their entire lengths was rare, and partial association only marginally more frequent. This arrangement is relatively stable in various tissues and during various stages of the cell cycle. On the other hand, the length of a chromosome arm appears to play a role in its positioning in a nucleus: shorter chromosomes or chromosome arms tend to be located closer to the centre of the nucleus, while longer arms are more often positioned at the nuclear periphery.

Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale.

BACKGROUND AND AIMS: Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x-8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation. METHODS: The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables. KEY RESULTS: The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group. CONCLUSIONS: Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different evolutionary origins of cytotypes via hybridization of parental combinations with different genome sizes in the south-western and south-eastern part of Europe, introgression between cytotypes, and antropic dispersal. The role of broad-scale and fine-scale environmental variables in shaping genome size is probably of minor importance in A. oleraceum.

Morphological, ecological and geographic differences between diploids and tetraploids of Symphytum officinale (Boraginaceae) justify both cytotypes as separate species.

Polyploidization is generally considered to be an important evolutionary driver affecting the genetic diversity, that can alter the morphology, phenology, physiology or ecology of plants, which in turn may make the taxonomy of polyploids more difficult. One such example is the Symphytum officinale complex, a polyploid species group represented by three major cytotypes: tetraploids (2n = 48), less common, geographically restricted diploids (2n = 24) and hypotetraploids (2n = 40). In most European floras only one polymorphic species, S. officinale, is widely recognized, while the particular cytotypes are usually considered conspecific. Our study provided a thorough evaluation of the ploidy level diversity, morphological and ecological variation, with a special attempt to clarify the status of 'white-flowered' diploids. Using flow cytometry, we identified three cytotypes: widespread tetraploids (76.1 %); less frequent diploids (23.6 %) with scattered distribution across the range of tetraploids and confined only to several areas of Europe; and extremely rare triploids (0.3 %). Diploids and tetraploids showed diffuse parapatric pattern of distribution, with only four mixed-cytotype populations (2.7 %) found, but almost entirely without triploids, suggesting reproductive isolation between di- and tetraploids. Niche of diploids falls nearly completely within the niche of tetraploids that showed niche expansion. Tetraploids also showed a shift in niche optimum towards a less continental and colder climate, coupled with expansion to more disturbance-prone sites with higher nutrient availability. Diploids were clearly distinguishable morphologically from tetraploids. The morphological differentiation of studied cytotypes appears to be taxonomically significant, especially in combination with ecological differences and the apparent presence of hybridization barriers. Both cytotypes should be treated as separate species (i.e. S. bohemicum and S. officinale s. str.).

Genome Dominance in Allium Hybrids (A. cepa × A. roylei).

Genome dominance is a phenomenon in wide hybrids when one of the parental genomes becomes "dominant," while the other genome turns to be "submissive." This dominance may express itself in several ways including homoeologous gene expression bias and modified epigenetic regulation. Moreover, some wide hybrids display unequal retention of parental chromosomes in successive generations. This may hamper employment of wide hybridization in practical breeding due to the potential elimination of introgressed segments from progeny. In onion breeding, Allium roylei (A. roylei) Stearn has been frequently used as a source of resistance to downy mildew for cultivars of bulb onion, Allium cepa (A. cepa) L. This study demonstrates that in A. cepa × A. roylei hybrids, chromosomes of A. cepa are frequently substituted by those of A. roylei and in just one generation, the genomic constitution shifts from 8 A. cepa + 8 A. roylei chromosomes in the F1 generation to the average of 6.7 A. cepa + 9.3 A. roylei chromosomes in the F2 generation. Screening of the backcross generation A. cepa × (A. cepa × A. roylei) revealed that this shift does not appear during male meiosis, which is perfectly regular and results with balanced segregation of parental chromosomes, which are equally transmitted to the next generation. This indicates that female meiotic drive is the key factor underlying A. roylei genome dominance. Single nucleotide polymorphism (SNP) genotyping further suggested that the drive has different strength across the genome, with some chromosome segments displaying Mendelian segregation, while others exhibiting statistically significant deviation from it.

Complex distribution patterns, ecology and coexistence of ploidy levels of Allium oleraceum (Alliaceae) in the Czech Republic.

BACKGROUND AND AIMS: Despite extensive study of polyploidy, its origin, and ecogeographical differences between polyploids and their diploid progenitors, few studies have addressed ploidy-level structure and patterns of ecogeographical differentiation at various spatial scales using detailed sampling procedures. The pattern of coexistence of polyploids in the geophyte Allium oleraceum at the landscape and locality scale and their ecology were studied. METHODS: Flow cytometry and root-tip squashes were used to identify the ploidy level of 4347 plants from 325 populations sampled from the Czech Republic using a stratified random sampling procedure. Ecological differentiation among ploidy levels was tested by comparing sets of environmental variables recorded at each locality. KEY RESULTS: Across the entire sampling area, pentaploids (2n = 5x = 40) predominated, while hexaploids (2n = 6x = 48) and tetraploids (2n = 4x = 32) were less frequent. The distribution of tetra- and hexaploids was partially sympatric (in the eastern part) to parapatric (in the western part of the Czech Republic) whereas pentaploids were sympatric with other cytotypes. Plants of different ploidy levels were found to be ecologically differentiated and the ruderal character of cytotypes increased in the direction 4x --> 5x --> 6x with the largest realized niche differences between tetra- and hexaploids. Most populations contained only one ploidy level (77 %), 22 % had two (all possible combinations) and 1 % were composed of three ploidy levels. The majority of 4x + 5x and 5x + 6x mixed populations occurred in sympatry with uniform populations of the participating cytotypes in sites with ecologically heterogeneous or marginal environment, suggesting secondary contact between cytotypes. Some mixed 4x + 6x populations dominated by tetraploids being sympatric and intermixed with uniform 4x populations might represent primary zones of cytotype contact. Almost no mixed accessions were observed on the fine spatial scale in mixed populations. CONCLUSIONS: The results provide evidence for adaptive differences among ploidy levels, which may contribute to their complex distribution pattern. The prevalence of asexual reproduction, limited dispersal and equilibrium-disrupting processes may support local coexistence of cytotypes.

Clade composition of a plant community indicates its phylogenetic diversity.

Phylogenetic diversity quantification is based on indices computed from phylogenetic distances among species, which are derived from phylogenetic trees. This approach requires phylogenetic expertise and available molecular data, or a fully sampled synthesis-based phylogeny. Here, we propose and evaluate a simpler alternative approach based on taxonomic coding. We developed metrics, the clade indices, based on information about clade proportions in communities and species richness of a community or a clade, which do not require phylogenies. Using vegetation records from herbaceous plots from Central Europe and simulated vegetation plots based on a megaphylogeny of vascular plants, we examined fit accuracy of our proposed indices for all dimensions of phylogenetic diversity (richness, divergence, and regularity). For real vegetation data, the clade indices fitted phylogeny-based metrics very accurately (explanatory power was usually higher than 80% for phylogenetic richness, almost always higher than 90% for phylogenetic divergence, and often higher than 70% for phylogenetic regularity). For phylogenetic regularity, fit accuracy was habitat and species richness dependent. For phylogenetic richness and divergence, the clade indices performed consistently. In simulated datasets, fit accuracy of all clade indices increased with increasing species richness, suggesting better precision in species-rich habitats and at larger spatial scales. Fit accuracy for phylogenetic divergence and regularity was unreliable at large phylogenetic scales, suggesting inadvisability of our method in habitats including many distantly related lineages. The clade indices are promising alternative measures for all projects with a phylogenetic framework, which can trade-off a little precision for a significant speed-up and simplification, such as macroecological analyses or where phylogenetic data is incomplete.

Intricate Distribution Patterns of Six Cytotypes of Allium oleraceum at a Continental Scale: Niche Expansion and Innovation Followed by Niche Contraction With Increasing Ploidy Level.

The establishment and success of polyploids are thought to often be facilitated by ecological niche differentiation from diploids. Unfortunately, most studies compared diploids and polyploids, ignoring variation in ploidy level in polyploids. To fill this gap, we performed a large-scale study of 11,163 samples from 1,283 populations of the polyploid perennial geophyte Allium oleraceum with reported mixed-ploidy populations, revealed distribution ranges of cytotypes, assessed their niches and explored the pattern of niche change with increasing ploidy level. Altogether, six ploidy levels (3x-8x) were identified. The most common were pentaploids (53.6%) followed by hexaploids (22.7%) and tetraploids (21.6%). Higher cytotype diversity was found at lower latitudes than at higher latitudes (>52° N), where only tetraploids and pentaploids occurred. We detected 17.4% of mixed-ploidy populations, usually as a combination of two, rarely of three, cytotypes. The majority of mixed-ploidy populations were found in zones of sympatry of the participating cytotypes, suggesting they have arisen through migration (secondary contact zone). Using coarse-grained variables (climate, soil), we found evidence of both niche expansion and innovation in tetraploids related to triploids, whereas higher ploidy levels showed almost zero niche expansion, but a trend of increased niche unfilling of tetraploids. Niche unfilling in higher ploidy levels was caused by a contraction of niche envelopes toward lower continentality of the climate and resulted in a gradual decrease of niche breadth and a gradual shift in niche optima. Field-recorded data indicated wide habitat breadth of tetraploids and pentaploids, but also a pattern of increasing synanthropy in higher ploidy levels. Wide niche breadth of tetra- and pentaploids might be related to their multiple origins from different environmental conditions, higher "age", and retained sexuality, which likely preserve their adaptive potential. In contrast, other cytotypes with narrower niches are mostly asexual, probably originating from a limited range of contrasting environments. Persistence of local ploidy mixtures could be enabled by the perenniality of A. oleraceum and its prevalence of vegetative reproduction, facilitating the establishment and decreasing exclusion of minority cytotype due to its reproductive costs. Vegetative reproduction might also significantly accelerate colonization of new areas, including recolonization of previously glaciated areas.

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations.

Seed dormancy and timing of its release is an important developmental transition determining the survival of individuals, populations, and species in variable environments. Medicago truncatula was used as a model to study physical seed dormancy at the ecological and genetics level. The effect of alternating temperatures, as one of the causes releasing physical seed dormancy, was tested in 178 M. truncatula accessions over three years. Several coefficients of dormancy release were related to environmental variables. Dormancy varied greatly (4-100%) across accessions as well as year of experiment. We observed overall higher physical dormancy release under more alternating temperatures (35/15 °C) in comparison with less alternating ones (25/15 °C). Accessions from more arid climates released dormancy under higher experimental temperature alternations more than accessions originating from less arid environments. The plasticity of physical dormancy can probably distribute the germination through the year and act as a bet-hedging strategy in arid environments. On the other hand, a slight increase in physical dormancy was observed in accessions from environments with higher among-season temperature variation. Genome-wide association analysis identified 136 candidate genes related to secondary metabolite synthesis, hormone regulation, and modification of the cell wall. The activity of these genes might mediate seed coat permeability and, ultimately, imbibition and germination.

Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits.

BACKGROUND: Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. METHODS: Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). RESULTS: Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g-1) than those of non-dormant (mean 1.77 mg g-1) and responsive accessions (mean 1.87 mg g-1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.

Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross-pollination and strong effect of geographic but not environmental distance.

Knowledge of current genetic diversity and mating systems of crop wild relatives (CWR) in the Fertile Crescent is important in crop genetic improvement, because western agriculture began in the area after the cold-dry period known as Younger Dryas about 12,000 years ago and these species are also wild genepools of the world's most important food crops. Wild pea (Pisum sativum subsp. elatius) is an important source of genetic diversity for further pea crop improvement harbouring traits useful in climate change context. The genetic structure was assessed on 187 individuals of Pisum sativum subsp. elatius from fourteen populations collected in the northern part of the Fertile Crescent using 18,397 genome wide single nucleotide polymorphism DARTseq markers. AMOVA showed that 63% of the allelic variation was distributed between populations and 19% between individuals within populations. Four populations were found to contain admixed individuals. The observed heterozygosity ranged between 0.99 to 6.26% with estimated self-pollination rate between 47 to 90%. Genetic distances of wild pea populations were correlated with geographic but not environmental (climatic) distances and support a mixed mating system with predominant self-pollination. Niche modelling with future climatic projections showed a local decline in habitats suitable for wild pea, making a strong case for further collection and ex situ conservation.

Correction: Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross-pollination and strong effect of geographic but not environmental distance.

[This corrects the article DOI: 10.1371/journal.pone.0194056.].