Digital descriptors sharpen classical descriptors, for improving genebank accession management: A case study on Arachis spp. and Phaseolus spp

High-throughput phenotyping brings new opportunities for detailed genebank accessions characterization based on image-processing techniques and data analysis using machine learning algorithms. Our work proposes to improve the characterization processes of bean and peanut accessions in the CIAT genebank through the identification of phenomic descriptors comparable to classical descriptors including methodology integration into the genebank workflow. To cope with these goals morphometrics and colorimetry traits of 14 bean and 16 forage peanut accessions were determined and compared to the classical International Board for Plant Genetic Resources (IBPGR) descriptors. Descriptors discriminating most accessions were identified using a random forest algorithm. The most-valuable classification descriptors for peanuts were 100-seed weight and days to flowering, and for beans, days to flowering and primary seed color. The combination of phenomic and classical descriptors increased the accuracy of the classification of Phaseolus and Arachis accessions. Functional diversity indices are recommended to genebank curators to evaluate phenotypic variability to identify accessions with unique traits or identify accessions that represent the greatest phenotypic variation of the species (functional agrobiodiversity collections). The artificial intelligence algorithms are capable of characterizing accessions which reduces costs generated by additional phenotyping. Even though deep analysis of data requires new skills, associating genetic, morphological and ecogeographic diversity is giving us an opportunity to establish unique functional agrobiodiversity collections with new potential traits.

Viability and dormancy of the Clematis vitalba aerial seed bank

Old man's beard (Clematis vitalba L.) is a liana species that has become invasive in many areas of its introduced range. Seeds are produced in abundance and are both physiologically and morphologically dormant upon maturity. To understand the importance of seeds to its invasiveness, changes in viability and dormancy of the aerial seed bank were tracked throughout the after-ripening period and during storage. Seeds collected every second month for 2 years were subjected to germination tests. Other seeds stored in outdoor ambient conditions or in a dry, chilled state were dissected before, during, and after imbibition, as well as during incubation, to measure embryo size. Less than 72% of seeds on the mother plant were viable. Viable seeds remained completely morpho-physiologically dormant throughout autumn, even when treated with nitrate. Physiological dormancy declined in response to seasonal changes, yet morphological dormancy did not change until seeds had been exposed to appropriate germination conditions for several days. Fully dormant autumn seeds decayed at higher rates during incubation than partially or fully after-ripened seeds, which were also more germinable and less dormant. Furthermore, seeds incubated in complete darkness were more likely to decay or remain dormant than those exposed to light. This study demonstrates that fewer than three-quarters of seeds produced are viable and further decay occurs after dispersal, yet total fertility is still very high, with enormous propagule pressure from seeds alone. Viable seeds are protected with two forms of dormancy; morphological dormancy requires additional germination cues in order to break after seasonal changes break physiological dormancy.

Responses of soil seed bank and its above-ground vegetation to various reclamation patterns

Coastal land reclamation has become a primary strategy for alleviating conflicts between human development and land resource utilization. However, anthropogenic activities associated with land reclamation inevitably result in significant changes to coastal wetland ecosystems. Previous studies have mainly focused on the ecological consequences of land reclamation on above-ground vegetation, while overlooking the distinctions between different reclamation patterns and the critical role of soil seed bank in maintaining ecosystem stability. In this study, the responses of soil seed bank and vegetation to various reclamation patterns, as well as the factors influencing changes in seed bank characteristics, were analyzed in a natural coastal wetland (NCW), a reclaimed wetland with sea embankments constructed on native wetland (SEW), and another reclaimed wetland formed through land reclamation from the sea (LRW). These findings suggest that seed banks and their vegetation adopt different adaptation strategies under various reclamation patterns. In the NCW, the proportion of non-halophytes (1.39%), diversity, and density of the seed bank were at their lowest levels, whereas the species compositions derived from the seed bank and vegetation were very similar (similarity coefficient = 0.67). Conversely, the seed bank in the SEW demonstrated the highest species diversity, which differed significantly from the species composition of its above-ground vegetation (similarity coefficient = 0.21). However, the highest proportion of non-halophytes (36.60%), vegetation diversity, and seed bank density occurred in LRW. Furthermore, differences in seed bank characteristics under different reclamation patterns may be related to changes in soil salinity and plant reproductive strategies after reclamation. Adjusting reclamation patterns and restoring soil properties could potentially optimize the types of local plant species and their distribution in reclaimed areas.

Exploring the effect of region on diversity and composition of weed seedbanks in herbicide-resistant crop systems in the United States

BACKGROUND

Soil seedbanks have been recognized as one of the crucial components of agricultural ecosystems. However, studies on the shift in structure and biodiversity of soil seedbanks in herbicide-resistant crop systems are limited, and a functional trait perspective of the soil seedbank is often overlooked.

RESULTS

A 6 years experiment was conducted to investigate the roles of region, crop system, and weed management strategy on species richness, functional trait diversity, and composition of the weed seedbank. Species richness was different across the interaction of region and crop system, while functional trait diversity only showed difference across regions. Species and functional trait compositions were affected by the interaction of region and crop system. Specifically, the compositional difference among crop systems was mainly determined by the significant heterogeneity of group dispersion.

CONCLUSION

Growers and practitioners should consider weed functional traits in developing lasting agricultural management strategies. Long-term weed research should draw attention to the impact of transgenic crop systems and specific management tactics on weed dispersal, functional composition, and resistance evolution of weed species in such agroecosystems. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Investigating seed bank potential of crustose coralline algae using DNA metabarcoding

To examine the potential for the autogenic ecosystem engineers, crustose coralline algae (CCA), to serve as seed banks or refugia for life stages of other species, it is critical to develop sampling protocols that reflect the diversity of life present. In this pilot study on two shallow water species of CCA collected from Raoul Island (Kermadec Islands; Rangitāhua) New Zealand, we investigated two preservation methods (ethanol vs. silica gel), sampled inner and outer regions of the crusts, and used DNA metabarcoding and seven genes/gene regions (16S rRNA, 18S rRNA, 23S rRNA, cox1, rbcL, and tufA genes and the ITS rRNA region) to develop a protocol for taxa identification. The results revealed immense diversity, with typically more taxa identified within the inner layers than the outer layers. As highlighted in other metabarcoding studies and in earlier work on rhodoliths (nodose coralline algae), reference databases are incomplete, and to some extent, the use of multiple markers mitigates this issue. Specifically, the 23S rRNA and rbcL genes are currently more suitable for identifying algae, while the cox1 gene fares better at capturing the diversity present inclusive of algae. Further investigation of these autogenic ecosystem engineers that likely act as marine seed banks is needed.

[Effects of coal mine waste dump on soil seed bank and vegetation distribution pattern]

Long-term occupation of coal gangue dumping sites (CGDS) may destroy ecological environment of nearby area. However, how the CGDS affects the distribution pattern of soil seed banks and vegetation in the nearby area is not clear. In this study, we investigated soil seed bank and vegetation at different distances from the second CGDS of Yangchangwan in Ningdong mining area, Lingwu, Ningxia. The results showed that soil seed bank was mainly distributed in 0-10 cm layer and decreased with increasing soil depth. Species richness of soil seed bank and vegetation first increased and then tended to be stable with increasing distance to the CGDS. The influence range of CGDS on soil seed banks was 300-500 m and was 100-300 m on aboveground vegetation. The CGDS did not affect the vertical distribution pattern of soil seed bank, but significantly affected the horizontal distribution pattern of soil seed banks and aboveground vegetation. The key area of vegetation restoration around the CGDS was between 100 m and 300 m.

Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

The coastal wetland is easily invaded by alien species due to locating in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to the community restoration and species diversity protection. To reveal the long-term Spartina alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariqueter, ruderal and unvegetated site) and soil depths (0-5 and 5-10 cm) in the coastal salt marsh wetland, Chongming island, eastern China. The results showed that the soil seed bank richness and species density under different vegetation types were higher than the aboveground vegetation, and those of 0-5 cm seed banks were higher than 5-10 cm, except for the unvegetated site. The species richness and S. alterniflora seed proportion in the seed banks under S. alterniflora communities (S.AS) were lower and larger respectively than those of other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0-5 and 5-10 cm depths were interpreted 3.03% and 2.25% by the aboveground communities, while 4.92% and 5.55% were interpreted by the soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks richness at the 0-5 cm depth and 5-10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks species density at the 0-5 cm depth and 5-10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0-5 cm seed banks richness and species density, while its height and biomass only affected the 5-10 cm seed banks species density. The 0-10 cm soil depth microbial biomass indirectly affected the 0-5 cm seed banks richness and species density, while affected the 5-10 cm seed banks richness. Soil physical and chemical properties only indirectly affected the 0-5 cm seed banks species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China, and guidance for the protection and restoration of the native plant communities.

A source of hidden diversity: soil seed bank and aboveground populations of a common herb contain similar levels of genetic variation

In many landscapes, successful re-establisment of plant populations depends on the presence of diaspores, either near or directly beneath sites to be restored. The soil seed bank is, therefore, an important part of ecosystem resilience and a vital pillar for regeneration of genetic diversity in many plant populations. However, regeneration from the soil seed bank and the siubsequent restoration can only be considered successful when genetic diversity of restored populations is not eroded nor genetic differentiation inflated. We compared genetic variation within and among soil seed bank and aboveground populations of Origanum vulgare, to test whether genetically variable populations can be restored from the soil seed bank. We explored levels of genetic diversity within aboveground populations and the corresponding soil seed banks. Furthermore, we assessed the extent to which the soil seed bank differs genetically from the aboveground population. Levels of genetic diversity were to generally similar in aboveground populations and the corresponding soil seed banks. Only levels of inbreeding were slightly higher in the lower layer of the soil seed bank compared to the aboveground populations, probably because of selection processes acting against homozygotes accumulating in the seed bank. Furthermore, significant genetic differentiation between the aboveground population and the corresponding seed banks was completely absent. Across all sites, genetic differentiation between the soil seed bank was similar to that between aboveground populations, probably due to the absence of severe climate conditions, strong bottlenecks or disturbance events. Our conclusions support the possibility of successful re-establishment of healthy, genetically variable plant populations after aboveground destruction or following soil re-allocation from persistent seed banks.

Spatial variation of soil seed banks along a gradient of anthropogenic disturbances in tropical forests on coral islands

Poor regeneration of natural vegetation is a major factor contributing to the degradation of tropical coral islands. Soil seed banks (SSB) are important for maintaining the resilience of plant communities. However, the community characteristics and spatial distribution of SSBs and the controlling factors along human disturbance on coral islands are unclear. To fill this gap, we measured the community structure and spatial distributions of forest SSBs on three coral islands in the South China Sea, with varying degrees of human disturbance. The results showed that strong human disturbance increased the diversity, richness, and density of SSBs, as well as increased the richness of invasive species. With increased human disturbance, the heterogeneity pattern of SSBs spatial distribution changed from difference between forest east and west to forest center and edge. The similarity between the SSBs and above-ground vegetation also increased, and the distribution of invasive species extended from the edge to the central area of the forests, demonstrating that human disturbance limited the outward dispersal of seeds of resident species but increased the inward dispersal of seeds of invasive species. Interaction between soil properties, plant characteristics, and human disturbance explained 23-45% of the spatial variation of forest SSBs on the coral islands. However, human disturbance reduced the correlations of plant communities and spatial distribution of SSBs with soil factors (i.e., available phosphorus and total nitrogen) and increased the correlations of the community characteristics of SSB with landscape heterogeneity index, road distance, and shrub and litter cover. Resident seed dispersal on tropical coral islands might be enhanced by reducing building height, constructing buildings in down-wind locations, and preserving corridors that support animal movement among forest fragments.

Weak seed banks influence the signature and detectability of selective sweeps

Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait implies it is ignored when developing tools to detect selective sweeps. But, as dormancy lengthens the ancestral recombination graph (ARG), increasing times to fixation, it can change the genomic signatures of selection. To detect genes under positive selection in seed banking species it is important to (1) determine whether the efficacy of selection is affected, and (2) predict the patterns of nucleotide diversity at and around positively selected alleles. We present the first tree sequence-based simulation program integrating a weak seed bank to examine the dynamics and genomic footprints of beneficial alleles in a finite population. We find that seed banking does not affect the probability of fixation and confirm expectations of increased times to fixation. We also confirm earlier findings that, for strong selection, the times to fixation are not scaled by the inbreeding effective population size in the presence of seed banks, but are shorter than would be expected. As seed banking increases the effective recombination rate, footprints of sweeps appear narrower around the selected sites and due to the scaling of the ARG are detectable for longer periods of time. The developed simulation tool can be used to predict the footprints of selection and draw statistical inference of past evolutionary events in plants, invertebrates, or fungi with seed banks.

Quantifying shrub encroachment through soil seed bank analysis in the Ethiopian highlands

This study aimed to understand the impact of shrub encroachment on native species in the Guassa Community Conservation Area in Ethiopia. We assessed the soil seed bank composition and density across different elevations and aspects, and management systems within the area. The vegetation was stratified and eight blocks were selected across a range of elevation (<3350 m and >3350 m) and aspect (northeast, northwest, southeast, southwest). Within each block we established twenty 5m x 5m plots for a total of 160. We then collected soil samples from five subplots (1 m x 1 m) at three depths (0-3 cm, 3-6 cm and 6-9 cm) for a total of 480 samples, which were established in pots in greenhouse. We calculated species abundance by totaling the number of seedlings that emerged from each sample. To determine the variability in the abundance of Festuca macrophylla and Helichrysum splendidum in the soil seed bank along altitudinal gradient, we used two-way ANOVA using SAS statistical software version 9.0.1. Shannon diversity index was used to determine species diversity in the soil seedbank. After counting all the seeds, we identified 74 plant species represented in the soil seedbank which belong to 55 genera and 23 families. Eleven species are endemic to Ethiopia. At the lower elevation range, the effects of aspect (P <0.0088) and soil depth (P <0.005) are not significant to determine the abundance of seeds of H. splendidum and F. macrophylla. But when the factors are segregated, both aspect and soil depth play a significant role (p<0.0001) regarding the abundance of the seeds of the competing species at lower elevation. At higher elevation, only the effect of soil depth is significant (P<0.0001) for determining the abundance of H. splendidum. Soil depth and aspect have no significant effects on soil seed bank abundance at this elevation.

Can the soil seed bank of Rumex obtusifolius in productive grasslands be explained by management and soil properties?

Rumex obtusifolius is a problematic weed in temperate grasslands worldwide as it decreases yield and nutritional value of forage. Because the species can recruit from the seed bank, we determined the effect of management and soil properties on the soil seed bank of R. obtusifolius in intensively managed, permanent grasslands in Switzerland (CH), Slovenia (SI), and United Kingdom (UK). Following a paired case-control design, soil cores were taken from the topsoil of grassland with a high density of R. obtusifolius plants (cases) and from nearby parcels with very low R. obtusifolius density (controls). Data on grassland management, soil nutrients, pH, soil texture, and density of R. obtusifolius plants were also collected. Seeds in the soil were germinated under optimal conditions in a glasshouse. The number of germinated seeds of R. obtusifolius in case parcels was 866 ±152 m-2 (CH, mean ±SE), 628 ±183 m-2 (SI), and 752 ±183 m-2 (UK), with no significant difference among countries. Densities in individual case parcels ranged from 0 up to approximately 3000 seeds m-2 (each country). Control parcels had significantly fewer seeds, with a mean of 51 ±18, 75 ±52, and 98 ±52 seeds m-2 in CH, SI, and UK, respectively, and a range between 0 and up to 1000 seeds m-2. Across countries, variables explaining variation in the soil seed bank of R. obtusifolius in case parcels were soil pH (negative relation), silt content (negative), land-use intensity (negative), and aboveground R. obtusifolius plant density (positive). Because a large soil seed bank can sustain grassland infestation with R. obtusifolius, management strategies to control the species should target the reduction in the density of mature plants, prevention of the species' seed production and dispersal, as well as the regulation of the soil pH to a range optimal for forage production.

Responses of soil seed banks to drought on a global scale

The global increase in drought frequency and intensity in large areas has potentially important effects on soil seed banks (SSBs). However, a systematic evaluation of the impact of drought on SSBs at a global scale has not yet been well understood. We evaluated the effects of drought on SSBs and identified the association key drivers in the current meta-analysis. The overall effects of drought on soil seed density and richness were weak negative and positive, respectively. Drought significantly increased soil seed density by 11.94 % in forest ecosystem, whereas soil seed richness were significantly increased in vascular plants (7.39 %). Linear mixed-effect results showed that soil seed density and richness significantly reduced as increasing drought intensity. In addition, geography (altitude) has significance in controlling the lnRR of soil seed density by altering climate (mean annual precipitation, drought) and soil properties (pH, soil organic carbon, and clay content) in the structural equation model, whereas soil seed richness was controlled by geography (altitude, and latitude) via climate (mean annual precipitation). In summary, the results suggested the size of SSBs response to drought and its relationship with drought intensity in terrestrial ecosystems, it may shed light on ecosystem restoration, succession, and management using SSBs when estimating the future drought.

Light controls alpine meadow community assembly during succession by affecting species recruitment from the seed bank

Some research indicates that soil seed banks can promote species coexistence through storage effects. However, the seed bank mechanism that maintains plant assembly and its role in degraded grassland restoration are still not clear. We collected seed bank samples from early, mid and late secondary successional stages of an abandoned subalpine meadow on the Tibetan Plateau, and samples from each stage were exposed to full (i.e., natural), mid, and low light treatments in the field to represent light availability at the bottom/understory (soil surface) of a plant community in the early, mid and late stages of succession, respectively. Species richness, seed density, species composition, and community weighted mean values (CWMs) of seed mass of the species whose seeds germinated in soil samples were evaluated. In response to the light treatments, species richness increased significantly with increased light only for the late successional stage, seed density increased significantly with increased light only in the early and mid successional stages, and seed mass decreased significantly with increased light only in the mid and late successional stages. Species composition differed significantly among the light treatments only in the late successional stage. For the successional series, species richness and seed mass of the species that germinated increased significantly with succession only under mid and full light treatments. Seed density decreased significantly with succession in each light treatment. Species composition differed significantly between the early- and late stage and between the mid and late stage in each light treatment. Both the abiotic (light) and biotic (seed mass) factors influence seed bank recruitment to the plant community. Regeneration of small-seeded species in the seed bank was inhibited under low light in the late successional stage. The balance of stochastic and deterministic processes along a successional gradient was determined by regeneration from the seed bank depending on light intensity change. Differences in seed response to light intensity change largely determined plant community assembly. Our findings should help in the development of effective conservation and restoration strategies.

Extinct in the wild: The precarious state of Earth's most threatened group of species

Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species-already compromised by their small number of founders-are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.

Negative impacts of human disturbances on the seed bank of subalpine forests are offset by climatic factors

Precipitation and temperature in the subalpine region have increased dramatically in recent decades due to global warming, and human disturbances have continued to impact the vegetation in the region. Seed bank plays an important role in population recovery, but there are few studies on the synergistic effects of human disturbances and climate change on seed bank. We analyzed the synergistic effects of human disturbances and climate change on seed bank samples from 20 sites in the subalpine coniferous forest region using grazing and logging as the disturbance intensity gradient and precipitation and temperature as climate variables. The species diversity of aboveground vegetation all changed significantly (p < 0.05) with precipitation, temperature and disturbance level, while the seed bank richness and density did not. Furthermore, the species composition of the seed bank varied significantly less than that of the aboveground vegetation at different levels of disturbance (p < 0.001). Thus, seed bank showed a strong buffering capacity against the risk of local extinction caused by environmental changes that shift the species composition and diversity of aboveground vegetation. In addition, soil and litter are important influences controlling seed bank density in subalpine forests, and the results of structural equation modelling suggest that both disturbance and climate change can indirectly regulate the seed bank by changing the physicochemical properties of soil and litter. We conclude that increases in precipitation and temperature driven by climate change can buffer the negative effects of disturbances on the seed bank.

[Morphology of Caragana korshinskii seeds across different stand ages in sandy-hilly region of northwest Shanxi Province, China]

We investigated the morphological characteristics of C. korshinskii seeds with three different sizes under plantations with different stand ages (6, 12, 18, 40 and 50 years old) in the typical sandy-hilly region of northwest Shanxi Province, to explore the restoration potential of artificial vegetation from the perspective of reproduction strategies. The results showed that seed production of C. korshinskii plantation increased with stand age, reaching the maximum (584 grain·plant^-1) in 50-year-old stand. Seed length, seed width, and seed shape index decreased with stand age, reaching the minimum (5.09 mm, 2.76 mm and 0.05) in 50-year-old stand. Seed germination percentage showed an upward-downward-upward fluctuating trend, reaching the maximum (97.2%) at 12-year-old stand. Seed production was significantly negatively correlated with seed weight. Seed germination percentage was closely related to seed weight. Seeds with low weight had a low germination percentage and were easier to form a persistent seed bank. In addition, seed production was significantly positively correlated with the height of mother plant, aboveground biomass and belowground biomass, while the shape index of C. korshinskii seeds was significantly negatively correlated with number of new branches. It indicated that with the increases of stand age, the reproduction strategy of C. korshinskii changed from the K strategy with larger seeds in the early stage (6-12 year-old) to the r strategy of small seeds in the later stage (18-50 year-old). Specifically, C. korshinskii kept both the high number and high persistence of seeds by producing a larger number of small and round seeds.

nov., a fungal species associated with seeds of pioneer trees in the soil seed bank of a lowland forest in Panama

As currently circumscribed, Acrogenospora (Acrogenosporaceae, Minutisphaerales, Dothideomycetes) is a genus of saprobic hyphomycetes with distinctive conidia. Although considered common and cosmopolitan, the genus is poorly represented by sequence data, and no neotropical representatives are present in public sequence databases. Consequently, Acrogenospora has been largely invisible to ecological studies that rely on sequence-based identification. As part of an effort to identify fungi collected during ecological studies, we identified strains of Acrogenospora isolated in culture from seeds in the soil seed bank of a lowland tropical forest in Panama. Here we describe Acrogenospora terricola sp. nov. based on morphological and phylogenetic analyses. We confirm that the genus has a pantropical distribution. The observation of Acrogenospora infecting seeds in a terrestrial environment contrasts with previously described species in the genus, most of which occur on decaying wood in freshwater environments. This work highlights the often hidden taxonomic value of collections derived from ecological studies of fungal communities and the ways in which rich sequence databases can shed light on the identity, distributions and diversity of cryptic microfungi.

[Diversity of soil seed banks under different vegetation types in the southeastern margin of the Tengger Desert, China]

To explore the dynamics and distribution of soil seed banks under different vegetation types in desert, and reveal the community succession tendency and diversity characteristics of different vegetative types, we took Populus euphratica community, Caragana intermedia community, Leymus secalinus community and Agriophyllum squarrosum community as the research objects in the southeastern margin of the Tengger Desert. Samples of 0-2 cm, 2-5 cm, 5-10 cm, and 10-20 cm soil layers were collected. We examined the characteristics of soil seed banks and their relationships with vegetation. The results showed that there were 13 plant species in the soil seed banks of the four vegetation types, belonging to 3 families and 12 genera, with the annual and biennial herbs dominated and much Chenopodiaceae species. The soil seed bank density was generally low, with an order of C. intermedia community > L. secalinus community > P. euphratica community > A. squarrosum community. The seed bank density and species richness decreased with increasing soil depth. Based on the Shannon index, Simpson index, Pielou index and Patrick richness analysis, the order of species diversity in soil seed banks was P. euphratica community > L. secalinus community > C. intermedia community > A. squarrosum community. The similarity coefficient between soil seed bank and vegetation was the highest in C. intermedia community, followed by P. euphratica community, and the lowest in P. euphratica community and L. secalinus community. On the whole, the arbor forest P. euphratica community was the most stable one, while the sandy land A. squarrosum community was the most vulnerable.

[Changes of persistent soil seed bank along a precipitation gradient in forest-steppe ecotone]

This study aimed to examine the responses of persistent soil seed bank to future precipitation reduction of global climate change in the forest-steppe ecotone of Hulunbuir. Samples of soil seed bank were collected from 0-10 cm soil layer along a precipitation gradient. We examined the density, species composition, diversity of seed bank and their relationship with vegetation. Structural equation model was used to explore the direct impact of annual precipitation on soil seed bank and the indirect impact through vegetation, soil nitrogen, soil phosphorus, and soil pH. The results showed that seed bank density and species richness were negatively correlated with annual precipitation. The species diversity of soil seed banks in grasslands was higher than that in forests. The similarity between soil seed bank and vegetation was generally low. The results of structural equation model showed that the effects of annual precipitation on seed bank density and species richness were negative, with the standard path coefficients of -0.051 and -0.122, respectively. The direct effect of annual precipitation on seed bank density and species richness were positive. Precipitation had indirect and positive effect on seed bank density and species richness through soil nitrogen, a significantly indirect negative effect on seed bank species richness through soil pH and soil available phosphorus, and a significantly indirect negative effect on seed bank density through soil pH. The reduction of precipitation under furture climate change might alter the hedging strategies of plants. The persistent soil seed bank in the forest-steppeecotone had a potential buffering effect against future precipitation reduction.

Changes in the composition of the soil seed bank of grassland after giant ragweed (Ambrosia trifida L.) invasion

Giant ragweed (Ambrosia trifida L.), an invasive weed, has an expanding distribution area and has recently started to spread in grasslands. This unusual event threatens grasslands worldwide. In this study, we aimed to evaluate the changes in the grassland soil seed banks caused by the giant ragweed invasion in Yili Valley, Xinjiang, China. Using the space-for-time substitution approach, we compared and quantified the soil seed bank communities in a grassland over eight years following giant ragweed invasion and after its removal. The results showed that the duration of invasion determined whether giant ragweed might pose a significant threat to the native seed bank community. Four years after the invasion, the in-site seed bank density of native community significantly decreased (30.44%), while the relative coverage of giant ragweed aboveground reached 83.75%. Furthermore, the species richness in the seed bank decreased significantly (12.36%), while the relative coverage of giant ragweed reached 100% six years after the invasion. Eight years after the invasion, the seed bank density and species richness of the native community decreased by 83.28% and 39.33%, respectively, whereby the seed banks tended to be homogeneous. After the removal of giant ragweed, the potential for regeneration was limited by the residual seed bank densities of the native community. Although the native seed bank density had increased significantly after three years of restoration, new growth was dominated by weedy species, rather than by the distinctive components of the grassland habitat. Our study clarifies the process by which giant ragweed causes damage to grasslands and serves as a reference for grassland restoration and management efforts.

Soil seedbank: Importance for revegetation in the water level fluctuation zone of the reservoir area

Vegetation succession in the water level fluctuation zone (WLFZ) is driven by periodical water fluctuations, the mechanisms of response and synergistic evolution between aboveground vegetation (AGV) and soil seed bank (SSB) in the WLFZ remain unclear. To illustrate the response between AGV and SSB and the importance of SSB for revegetation in the WLFZ, the Three Gorges Reservoir (TGR) was taken as the target in the current study, and five sampling sites that lie in the center of reservoir and major tributaries of the TGR were selected. Plant community survey along the three water level gradients (i.e., 165-170 m, 170-175 m and 175-180 m) was conducted. Simultaneously, SSB samples on the topsoil (0-5 cm) were collected for germination experiments. A total of forty-nine species were observed from the SSB, belonging to 24 families and 47 genera, of which Asteraceae (8 species) and Poaceae (6 species) dominated. The number of total germinated seedlings species from soil samples from the sampling sites differed, i.e., was lower in Fengjie and Wushan compared to Yunyang, Gaoyang and Fengdu. The seed density in 165-170 m was significantly lower than that of 170-175 m and 175-180 m (p < 0.05). The Sørensen similarity coefficients between AGV and SSB tended to decrease with the increase of water level gradient, ranging from 0.04 to 0.42. SSB species composition was significantly associated with total carbon and total nitrogen contents of the soil (both p < 0.05). The SSB density was significantly negatively correlated with concentration of soil total nitrogen (p < 0.05), the species richness of SSB was significantly negatively correlated with soil pH value (p < 0.05). Hence, the relationship between the SSB and the soil habitat might be an important factor driving the construction of vegetation in the WLFZ. The correlation between dynamic of SSB and TGR hydrological regimes should be considered for revegetation in the WLFZ.

Direct and indirect effects of soil salinization on soil seed banks in salinizing wetlands in the Songnen Plain, China

Soil salinization has become a widespread threat to the structure and ecological functioning of inland wetlands globally. Soil seed banks can be important for plant regeneration in salinizing wetlands. To explore the effects of soil salinization on soil seed banks and their potential role in revegetation, we studied the structure and composition of plant communities and soil seed banks along a soil salinization gradient, and analyzed the responses of Carex-dominated and Phragmites-dominated communities to saline-alkaline stress in the Songnen Plain, China. We found that the dominant species of aboveground vegetation were different along the soil salinization gradient. Carex spp. dominated in the non-salinized and mild salinity wetlands, and Phragmites australis dominated in wetlands with moderate and high levels of salinity. The species richness of aboveground vegetation, and the density and richness of soil seed banks were higher in wetlands with lower salinity. The structural equation model indicated that the difference in soil salinization was directly associated with the aboveground species richness, and density and richness of the soil seed banks, while it was indirectly associated with the density and richness of the soil seed banks by directly affecting the composition and the species richness of the aboveground vegetation. Soil seed banks in Phragmites communities were more tolerant of saline-alkaline stress than Carex communities. This study indicates that soil salinization affects the size and composition of soil seed banks and limits their role in plant regeneration in wetlands of the Songnen Plain. In addition to hydrological regulation, the reduction of soil salinity is necessary to protect and restore biodiversity in salinizing wetlands.

Restoration of aquatic macrophytes with the seed bank is difficult in lakes with reservoir-like water-level fluctuations: A case study of Chaohu Lake in China

Aquatic vegetation in lakes along the middle and lower reaches of the Yangtze River has been seriously degraded by human disturbances such as river-lake disconnection and water eutrophication. Chaohu Lake is a typical lake with reservoir-like water-level fluctuations (WLFs). Since a sluice was built in 1962, the coverage of aquatic vegetation in Chaohu Lake has been very low (0.77%). In this study, field investigations of the aquatic vegetation and seed bank of Chaohu Lake were conducted, and aboveground vegetation diversity was found to be low. Forty-eight species were recorded, of which submerged, floating-leaved, and emergent macrophytes were 1, 5, and 10, respectively. Currently, artificially planted Phragmites australis and Salix communities have become the main community types. A total of 18 aquatic macrophytes were identified in the seed bank, of which the number of submerged, floating-leaved, and emergent macrophytes and hygrophytes were 2, 2, 3, and 11, respectively; the seed density was 2.05, 2.05, 16.93, and 9.30 ind./m², respectively. The seed density of aquatic macrophytes was much lower in Chaohu Lake than in the lakes with quasi-natural WLFs, and the seeds were mainly distributed in the estuary area. Only two emergent macrophyte species (Typha) germinated in the open water area. Spearman correlation analysis showed that the distance to bank was the main environmental factor that affected aquatic macrophyte diversity and seed density in the seed bank. It is not feasible to promote the natural reconstruction and restoration of aquatic macrophytes in Chaohu Lake by decreasing the water level or increasing water transparency, but the area near the estuary can be identified as a priority restoration area (PRA) for aquatic macrophytes. Artificial transformation of the micro-topography can be used to guide some hydrochorous seeds in the tributaries to the PRA and restore aquatic vegetation in the local area.

Seed size-seed number trade-offs: influence of seed size on the density of fire-stimulated persistent soil seed banks

PREMISE

Does the seed size-seed number allocation trade-off model apply to long-term persistent soil seed banks? This trade-off between seed size versus number of seeds produced is usually applied at a single population on an annual basis. Our question is how this model might apply to close relatives that produce dormant seed forming long-term persistent soil seed banks. These two criteria allow a focus on divergent evolution of conspecifics and permits us to isolate seed size in the spectrum of life history traits that may be influencing seed traits, and on how seed size influences accumulation and persistence in the soil.

METHODS

In California, Arctostaphylos species only produce physiologically dormant seed that are fire-stimulated and that vary in seed size permitting seed size-seed bank density relationship as a test of the seed size-seed number allocation model. Soil seed banks of 10 species of Arctostaphylos were sampled with fruit volumes ranging from 21-1063 mm³ . Seed bank density was determined by hand extraction from soil samples.

RESULTS

We found that seed bank densities were significantly negatively related to fruit or seed size.

CONCLUSIONS

Rather than an issue of allocational trade-off between size and number, we interpret these results as reflecting seed predation and postfire seedling establishment. Seed bank densities, even after decades, generally were less than one or two-year's seed production, suggesting intense seed predation. Burial by scatter-hoarding rodents provided sufficient seeds deep enough for survival of fire. Variation on seed size suggests seedling establishment constraints, but it needs further research.

The role of maternal age, growth, and environment in shaping offspring performance in an aerial conifer seed bank

PREMISE

Maternal effects have been demonstrated to affect offspring performance in many organisms, and in plants, seeds are important mediators of these effects. Some woody plant species maintain long-lasting canopy seed banks as an adaptation to wildfires. Importantly, these seeds stored in serotinous cones are produced by the mother plant under varying ontogenetic and physiological conditions.

METHODS

We sampled the canopy seed bank of a highly serotinous population of Pinus pinaster to test whether maternal age and growth and the environmental conditions during each crop year affected seed mass and ultimately germination and early survival. After determining retrospectively the year of each seed cohort, we followed germination and early survival in a semi-natural common garden.

RESULTS

Seed mass was related to maternal age and growth at the time of seed production; i.e., slow-growing, older mothers had smaller seeds, and fast-growing, young mothers had larger seeds, which could be interpreted either as a proxy of senescence or as a maternal strategy. Seed mass had a positive effect on germination success, but aside from differences in seed mass, maternal age had a negative effect and diameter had a positive effect on germination timing and subsequent survival.

CONCLUSIONS

The results highlight the importance of maternal conditions combined with seed mass in shaping seedling establishment. Our findings open new insights in the offspring performance deriving from long-term canopy seed banks, which may have high relevance for plant adaptation.

Edge effects on the realised soil seed bank along microclimatic gradients in temperate European forests

Despite the crucial role of the seed bank in forest conservation and dynamics, the effects of forest edge microclimate and climate warming on germination responses from the forest seed bank are still almost unknown. Here, we investigated edge effects on the realised seed bank and seedling community in two types of European temperate deciduous forest, one in the Oceanic and one in the Mediterranean climatic region. Responses in terms of seedling density, diversity, species composition and functional type of the seed bank at the forest edge and interior were examined along latitudinal, elevational and stand structural gradients by means of soil translocation experiments. Moreover, we translocated soil samples from high to low elevation forests in the two regions, thus performing a warming simulation. Density, species diversity and mortality of the seedlings varied with region and elevation. Seedling density also differed between forest edge and interior position, while seedling cover mainly depended on forest structure. Both the edge and interior forest seed bank contained a high proportion of generalist species. In Belgium, a more homogeneous seed bank was found at the forest edge and interior, while in Italy compositional and ecological differences were larger: at the forest edge, more light and less moisture demanding seedling communities developed, with a higher proportion of generalists compared to the interior. In both regions, the upland-to-lowland translocation experiment revealed effects of warming on forest seed banks with thermophilization of the realised communities. Moreover, edge conditions shifted the seedling composition towards more light-demanding communities. The establishment of more light and warm-adapted species from the seed bank could in the long term alter the aboveground vegetation composition, with communities becoming progressively richer in light-demanding generalists and poorer in forest specialists.

The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems

Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.

LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.

Integration of the metabolome and transcriptome reveals the mechanism of resistance to low nitrogen supply in wild bermudagrass (Cynodon dactylon (L.) Pers.) roots

BACKGROUND

Nitrogen (N) is an essential macronutrient that significantly affects turf quality. Commercial cultivars of bermudagrass (Cynodon dactylon (L.) Pers.) require large amounts of nitrogenous fertilizer. Wild bermudagrass germplasm from natural habitats with poor nutrition and diverse N distributions is an important source for low-N-tolerant cultivated bermudagrass breeding. However, the mechanisms underlying the differences in N utilization among wild germplasm resources of bermudagrass are not clear.

RESULTS

To clarify the low N tolerance mechanism in wild bermudagrass germplasm, the growth, physiology, metabolome and transcriptome of two wild accessions, C291 (low-N-tolerant) and C716 (low-N-sensitive), were investigated. The results showed that root growth was less inhibited in low-N-tolerant C291 than in low-N-sensitive C716 under low N conditions; the root dry weight, soluble protein content and free amino acid content of C291 did not differ from those of the control, while those of C716 were significantly decreased. Down-regulation of N acquisition, primary N assimilation and amino acid biosynthesis was less pronounced in C291 than in C716 under low N conditions; glycolysis and the tricarboxylic acid (TCA) cycle pathway were also down-regulated, accompanied by a decrease in the biosynthesis of amino acids; strikingly, processes such as translation, biosynthesis of the structural constituent of ribosome, and the expression of individual aminoacyl-tRNA synthetase genes, most of genes associated with ribosomes related to protein synthesis were all up-regulated in C291, but down-regulated in C716.

CONCLUSIONS

Overall, low-N-tolerant wild bermudagrass tolerated low N nutrition by reducing N primary assimilation and amino acid biosynthesis, while promoting the root protein synthesis process and thereby maintaining root N status and normal growth.

Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement

Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.

Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers

Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

BACKGROUND

Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population.

RESULTS

Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch.

CONCLUSIONS

We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.

Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge

Cassava (Manihot esculenta Crantz.) has been a vital staple and food security crop in Tanzania for several centuries, and it is likely that its resilience will play a key role in mitigating livelihood insecurities arising from climate change. The sector is dominated by smallholder farmers growing traditional landrace varieties. A recent surge in virus diseases and awareness in the commercial potential of cassava has prompted a drive to disseminate improved varieties in the country. These factors however also threaten the existence of landraces and associated farmer knowledge. It is important that the landraces are conserved and utilized as the adaptive gene complexes they harbor can drive breeding for improved varieties that meet agro-ecological adaptation as well as farmer and consumer needs, thereby improving adoption rates. Here we report on cassava germplasm collection missions and documentation of farmer knowledge in seven zones of Tanzania. A total of 277 unique landraces are identified through high-density genotyping. The large number of landraces is attributable to a mixed clonal/sexual reproductive system in which the soil seed bank and incorporation of seedlings plays an important role. A striking divergence in genetic relationships between the coastal regions and western regions is evident and explained by (i) independent introductions of cassava into the country, (ii) adaptation to prevailing agro-ecological conditions and (iii) farmer selections according to the intended use or market demands. The main uses of cassava with different product profiles are evident, including fresh consumption, flour production, dual purpose incorporating both these uses and longer-term food security. Each of these products have different trait requirements. Individual landraces were not widely distributed across the country with limited farmer-to-farmer diffusion with implications for seed systems.

Persistent soil seed banks promote naturalisation and invasiveness in flowering plants

With globalisation facilitating the movement of plants and seeds beyond the native range, preventing potentially harmful introductions requires knowledge of what drives the successful establishment and spread of alien plants. Here, we examined global-scale relationships between naturalisation success (incidence and extent) and invasiveness, soil seed bank properties (type and densities) and key species traits (seed mass, seed dormancy and life form) for 2350 species of angiosperms. Naturalisation and invasiveness were strongly associated with the ability to form persistent (vs. transient) seed banks but relatively weakly with seed bank densities and other traits. Our findings suggest that seed bank persistence is a trait that better captures the ability to become naturalised and invasive compared to seed traits more widely available in trait databases. Knowledge of seed persistence can contribute to our ability to predict global naturalisation and invasiveness and to identify potentially invasive flowering plants before they are introduced.

A branching process model for dormancy and seed banks in randomly fluctuating environments

The goal of this article is to contribute towards the conceptual and quantitative understanding of the evolutionary benefits for (microbial) populations to maintain a seed bank consisting of dormant individuals when facing fluctuating environmental conditions. To this end, we discuss a class of '2-type' branching processes describing populations of individuals that may switch between 'active' and 'dormant' states in a random environment oscillating between a 'healthy' and a 'harsh' state. We incorporate different switching strategies and suggest a method of 'fair comparison' to incorporate potentially varying reproductive costs. We then use this concept to compare the fitness of the different strategies in terms of maximal Lyapunov exponents. This gives rise to a 'fitness map' depicting the environmental regimes where certain switching strategies are uniquely supercritical.

Multiple DNA marker-assisted diversity analysis of Indian mango (Mangifera indica L.) populations

Arbitrary (65 RAPD, 25 ISSR, 23 DAMD), gene-targeted (22 SCoT, 33 CBDP) and co-dominant sequence specific (40 SSR) markers were used individually, or in combinations, to examine the genetic variability within and among 70 selected Indian mango genotypes based on geographic origin (East India, West India, North India, South India) and fruit status (Selection, Hybrid, Landrace). The highest genetic variability was demonstrated by the East Indian populations, followed by those from South India, West India, and North India, when measured in terms of Na, Ne, H, I, PB%, Ht and Hs. Interestingly, the local genotypes of Odisha, which forms a part of East Indian populations, showed the highest diversity compared to hybrid or selection groups, suggesting that the indigenous genotypes hold a greater potential for exploiting the unique and favourable alleles. The maximum genetic variability was detected in geographical/fruit status populations with SSRs (Na-1.76/1.88, Ne-1.48/1.51, H-0.28/0.30, I-0.41/0.45, PB%-76.1/86.9, Ht-0.31/0.32 and Hs-0.28/0.30), followed by CBDPs and SCoTs, reflecting their preeminence for examining the level of genetic polymorphism and diversity. Outcome of AMOVA based analyses as well as low-to-moderate coefficient of genetic differentiation (Gst) and high gene flow (Nm) indicated a greater amount of intra-population genetic variation compared to heterogeneity at inter-population level. Information generated through this investigation could facilitate conservation and further exploitation of mango germplasm including genetic improvement through breeding.

Seed longevity of maize conserved under germplasm bank conditions for up to 60 years

BACKGROUND AND AIMS

The long-term conservation of seeds of plant genetic resources is of key importance for food security and preservation of agrobiodiversity. Nevertheless, there is scarce information available about seed longevity of many crops under germplasm bank conditions.

METHODS

Through germination experiments as well as the analysis of historical monitoring data, we studied the decline in viability manifested by 1000 maize (Zea mays subsp. mays) seed accessions conserved for an average of 48 years at the CIMMYT germplasm bank, the largest maize seedbank in the world, under two cold storage conditions: an active (-3 °C; intended for seed distribution) and a base conservation chamber (-15 °C; for long-term conservation).

KEY RESULTS

Seed lots stored in the active chamber had a significantly lower and more variable seed germination, averaging 81.4 %, as compared with the seed lots conserved in the base chamber, averaging 92.1 %. The average seed viability detected in this study was higher in comparison with that found in other seed longevity studies on maize conserved under similar conditions. A significant difference was detected in seed germination and longevity estimates (e.g. p85 and p50) among accessions. Correlating seed longevity with seed traits and passport data, grain type showed the strongest correlation, with flint varieties being longer lived than floury and dent types.

CONCLUSIONS

The more rapid loss of seed viability detected in the active chamber suggests that the seed conservation approach, based on the storage of the same seed accessions in two chambers with different temperatures, might be counterproductive for overall long-term conservation and that base conditions should be applied in both. The significant differences detected in seed longevity among accessions underscores that different viability monitoring and regeneration intervals should be applied to groups of accessions showing different longevity profiles.

Separation of timescales for the seed bank diffusion and its jump-diffusion limit

We investigate scaling limits of the seed bank model when migration (to and from the seed bank) is 'slow' compared to reproduction. This is motivated by models for bacterial dormancy, where periods of dormancy can be orders of magnitude larger than reproductive times. Speeding up time, we encounter a separation of timescales phenomenon which leads to mathematically interesting observations, in particular providing a prototypical example where the scaling limit of a continuous diffusion will be a jump diffusion. For this situation, standard convergence results typically fail. While such a situation could in principle be attacked by the sophisticated analytical scheme of Kurtz (J Funct Anal 12:55-67, 1973), this will require significant technical efforts. Instead, in our situation, we are able to identify and explicitly characterise a well-defined limit via duality in a surprisingly non-technical way. Indeed, we show that moment duality is in a suitable sense stable under passage to the limit and allows a direct and intuitive identification of the limiting semi-group while at the same time providing a probabilistic interpretation of the model. We also obtain a general convergence strategy for continuous-time Markov chains in a separation of timescales regime, which is of independent interest.

Distinctive seed dispersal and seed bank patterns of invasive African grasses favour their invasion in a neotropical savanna

High propagule availability compared to native species is often critical to invasion success, but it is unclear if this has contributed to invasions by African grasses in Neotropical savannas. We compared patterns of occurrence in the vegetation, seed rain and seed bank among African and native grasses in Cerrado sites in southeastern Brazil. In grasslands and savannas, we obtained the abundance of grasses in the vegetation, in the seed rain (monthly for one year) and in the seed bank (rainy and dry season), and assessed seed limitation and relationships among compartments. Invasive grasses showed low abundance in all compartments and high seed limitation in grasslands, where the seed bank and seed rain were dominated by small-seeded native grasses, but were at least as abundant as the natives in the seed bank and seed rain in savannas, mostly due to high abundance of Melinis minutiflora at these compartments. Native grasses dispersal occurred in the rainy season, whereas invasive grass dispersal occurred from mid rainy to mid dry season (Urochloa decumbens) and in the dry season (M. minutiflora). Melinis minutiflora showed a more persistent seed bank than U. decumbens and natives in savannas. Abundance of invasive and most of the native grasses in the vegetation was positively related to their abundance in the seed rain. Differences in seed production, the timing of seed dispersal and seed bank persistence compared to native grasses seem to favour invasive African grasses in the Cerrado, but this role may differ between grasslands and savannas.

Native Riparian Plant Species Dominate the Soil Seedbank of In-channel Geomorphic Features of a Regulated River

Flow regulation impacts on riparian vegetation composition, often increasing the prevalence of exotic and terrestrial plant species. Environmental flows may benefit native riparian vegetation via the promotion of plant recruitment from riparian soil seedbanks, but this is dependent on an intact native seedbank. Thus, we assessed the composition of the soil seedbank of different riverine geomorphic features to determine its potential response to environmental flows. Soil seedbank samples were taken from channel bars, benches and floodplains at six sites along the Campaspe River, Australia, a heavily regulated river that receives environmental flows. These geomorphic features represent a gradient in elevation and thus flooding frequency from frequently flooded (bars) to infrequently flooded (floodplain). Seedbank samples were 'grown out' in a glasshouse, and seedlings identified and classified according to taxa, flood tolerance and origin (native or exotic). We identified 6515 seedlings across all geomorphic features and sites, with monocots most abundant. Soil seedbank composition varied between geomorphic features. Overall, seedling abundances were greater for in-channel features (bars and benches) than floodplains, but taxa richness did not vary likewise. Soil seedbanks of in-channel features were dominated by flood tolerant and native taxa, while flood intolerant and exotic taxa were generally associated with floodplains. The dominance of native flood tolerant taxa in the soil seedbanks of in-channel geomorphic features suggest these seedbanks can play an important role in the resilience of native riparian plant communities. Moreover, environmental flows are likely to play a positive role in maintaining native riparian plant communities given such conditions.

Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential

Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.

Germination potential of baldcypress (Taxodium distichum) swamp soil seed bank along geographical gradients

Changing environments of temperature, precipitation and moisture availability can affect vegetation in ecosystems, by affecting regeneration from the seed bank. Our objective was to explore the responses of soil seed bank germination to climate-related environments along geographic gradients. We collected seed banks in baldcypress (Taxodium distichum) swamps along the Mississippi River and the Gulf of Mexico Coast in the United States, which have distinct temperature and/or precipitation gradients, and germinated them in a greenhouse. The frequency, richness and seed density of species germinated from the seed bank were compared between various geographic locations, experimental water regimes (saturated, flooded) and wetland types (tidal, non-tidal and inland swamps). We also analyzed the relationship of seed density to the environment by using a Non-metric Multi-dimensional Scaling (NMDS) model. Sixty-one species germinated from the seed bank, differing in pattern by geographic location, experimental water regime and wetland type. The foundation species (i.e., T. distichum and Cephalanthus occidentalis) germinated with a niche affinity for the northern part of the latitudinal gradient (Tennessee and Illinois) and these species may shift northward with climate change. Some species had higher seed density in the locations that were subject to more persistent drought conditions (e.g., Texas) including Cyperus rotundus and Gratiola virginiana, indicating that these species may be better adapted to sites with high temperature and low precipitation. In contrast, certain species including Saururus cernuus and Ludwigia palustris were present throughout the range of these gradients, and so may be more resilient to any future climate shifts. We found that the regeneration potential of baldcypress swamps might be altered by changes in local and climate environment because of nuances of responses of seed banks to climates along latitudinal and longitudinal gradients. Our study can help predict vegetation regeneration potential to climate change environments depending on the ability of these species to disperse and maintain seed banks.

Natural regeneration triggers compositional and functional shifts in soil seed banks

Secondary forests emerging during traditional shifting cultivation practices are increasingly recognized for their fulfillment of ecosystem services and mitigation potential of climate change and biodiversity losses. The soil seed bank as a recruit reservoir is a limiting factor for natural forest regeneration of such secondary forests and is decisive for the formation and restitution of the post-disturbance community. The aim of this study was to compare the composition of the soil seed bank along a natural regeneration chronosequence from the Caxiuanã National Forest, eastern Amazon, including old-growth reference sites. We sampled standing vegetation, soil properties and soil seed banks and compared the density and species richness of different life forms among different regeneration stages. Using nonmetric, multiple scaling, we compared the composition of the soil seed bank among different regeneration stages and with standing vegetation composition. Furthermore, we outlined the influence of stand age, vegetation structure and soil properties on the density, richness and functional characterization of the soil seed bank using mixed effect models. The soil seed bank was dominated by herb seeds in all regeneration stages, and the density and richness of tree seeds increased with regeneration time and recovery of vegetation structure. Seed bank composition changed gradually with regeneration advance and differed from standing vegetation, containing a high amount of allochthonous seeds, especially in older stands. This observation highlights the importance of dispersal and habitat connectivity for the natural regeneration of these secondary forests. Shifts in soil seed bank composition towards slow-growing, animal-dispersed, non-pioneer species with larger, recalcitrant seeds in older regeneration stands indicate changes in vegetation composition along succession. Thus, our data indicate the importance of connectivity for forest regeneration and long fallow periods (> 40 years) to increase the performance of ecosystem services, resilience and stability of secondary forests arising during shifting cultivation practices.

Comparative whole-genome and proteomics analyses of the next seed bank and the original master seed bank of MucoRice-CTB 51A line, a rice-based oral cholera vaccine

BACKGROUND

We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker-free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB.

RESULTS

We re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy.

CONCLUSIONS

All analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

The presence of invasive grasses affects the soil seed bank composition and dynamics of both invaded and non-invaded areas of open savannas

One of the major threats to tropical savannas globally is the invasion by alien grasses. In systems frequently disturbed, individuals can be recruited from the seed bank, and areas under natural regeneration can be more easily invaded when exotic newcomers are in the system, including the presence of invasive propagules in the soil seed bank. This study analyzed the dynamics of the soil seed bank in invaded and non-invaded areas of open savannas elucidating the potential of grass regeneration from the seed bank. Soil samples were collected in areas with different invasive grasses: Urochloa brizantha (Hochst. ex A. Rich.) R.D.Webster - synonym Brachiaria brizantha (Hochst. ex A. Rich.) Stapf, Melinis minutiflora Beauv. and areas with native vegetation. Soil seed bank was assessed using two techniques: seed counting and seedling emergence. Dominant species in each area influenced the seed bank composition, showing the highest densities from April to September. In invaded areas, the seed bank was composed mainly of invasive grasses that contributed to 98% (670 ± 382 seeds.m^-2) of total seeds. In non-invaded areas, the soil seed bank presented the highest density (65%, 135 ± 38 seeds.m^-2) of native species. However, the presence of invasive grasses was significant, with 35% of the total seeds belonging to U. brizantha. Although non-invaded areas have a higher potential for regeneration by native grasses, the presence of invasive grasses in the seed bank is an indication that the invasive species is already in the system and changes in the aboveground cover could accelerate the invasion process. Early management efforts towards establishing and/or established invasive species before seed dispersal could help reduce the soil seed bank load and should be carried out to control and avoid the establishment of African grasses, since they can dominate the seed bank in non-invaded areas if they are present in neighboring areas, affecting the dynamics of plant communities.

The barley pan-genome reveals the hidden legacy of mutation breeding

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

Evaluation of coatings for application in raffia big bags in conditioned storage of soybean cultivars in seed processing units

Different regions have different environmental conditions, which may be unfavorable for the preservation of the quality of stored soybean seeds over time. Thus, it is necessary to adopt specific technologies to control the storage environment conditions. Big raffia bags are widely used for the storage of soybean seeds, however these consist of a porous, permeable material that allows the exchange of gases between the packaging and the storage environment. In an effort to find a solution to this problem, in this study we evaluated low cost big bag coating alternatives, in order to minimize the effects of temperature and intergranular humidity on stored seeds. Thus, the aim of this work was to evaluate the quality of soybean cultivars subjected to different temperature and storage duration conditions and stored in raffia bags with or without internal coating. We used a completely randomized, three-factor (10 × 6 × 5) experimental design. We assessed 10 soybean cultivars, six storage environments, and five evaluation periods. Our results showed that seeds of the M-SOY 8866, M7110 IPRO, CD 2737 RR, and BMX DESAFIO 8473 RSF soybean cultivars preserved their physiological quality better in different storage environments. The storage duration had a cumulative effect on the negative factors that favor the deterioration of the quality of the stored seeds. The storage temperature was the main factor that affected the physiological quality of the stored seeds. The use of coated packaging was beneficial in preserving the physiological quality of stored soybean seeds; however, its effect was greater at ambient temperature than in a cold environment. The best storage environment for the preservation of the quality of the seeds was characterized by 10°C temperature conditions and the use of coated packaging, while the worst storage environment was characterized by ambient temperature conditions without the use of coated packaging. Thus, it was concluded that the use of coatings in raffia big bags can be an alternative for maintaining the quality of seeds of different soybean cultivars during storage in seed processing units.

Safeguarding a global seed heritage from Syria to Svalbard

Crop diversity underpins food security and adaptation to climate change. Concerted conservation efforts are needed to maintain and make this diversity available to plant scientists, breeders and farmers. Here we present the story of the rescue and reconstitution of the unique seed collection held in the international genebank of International Center for Agricultural Research in the Dry Areas (ICARDA) in Syria. Being among the first depositors to the Svalbard Global Seed Vault, ICARDA managed to safety duplicate more than 80% of its collection before the last staff had to leave the genebank in 2014 because of the war. Based on the safety duplicates, ICARDA since 2015 have rebuilt their collections and resumed distribution of seeds to users internationally from their new premises in Morocco and Lebanon. We describe the multifaceted and layered structure of the global system for the conservation and use of crop diversity that enabled this successful outcome. Genebanks do not work alone but in an increasingly strengthened and experienced multilateral system of governance, science, financial support and collaboration. This system underpins efforts to build sustainable and socially equitable agri-food systems.

Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.