Phylogeny, Seed Trait, and Ecological Correlates of Seed Germination at the Community Level in a Degraded Sandy Grassland

Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines

KEY MESSAGE

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

Germination Characteristics Is More Associated With Phylogeny-Related Traits of Species in a Salinized Grassland of Northeastern China

Knowing the determinants of seed germination helps us understand plant adaptive strategies to the environment and predict population and community regeneration under climate change. However, multiple factors, including plant and seed traits that influence germination and their relative importance, have received little attention. Here, seed germination experiments were conducted on newly collected seeds for 89 herbaceous species from salinized Songnen grassland. We tested the effects of multiple phylogeny-related plant traits and seed morphological and physiological traits on germination percentage and initial germination time and their relative contribution to shaping germination variation. We found that biennials had higher germination percentages and rates than annuals and perennials. Species with brown seeds had higher germination percentages than those with yellow and black seeds. Eudicots germinated faster than monocots, and seeds with morphophysiological dormancy required more time to initiate germination than those with other kinds of dormancy. Phylogeny-related factors explained more of the variation in germination than seed traits. Seed mass and volume of the large-seeded, but not small-seeded group species were positively correlated with germination percentage. Our findings provide important information for understanding germination variation across species and local adaptation for species in the salinized Songnen grassland.

Seed Dormancy and Soil Seed Bank of the Two Alpine Primula Species in the Hengduan Mountains of Southwest China

The timing of germination has long been recognized as a key seedling survival strategy for plants in highly variable alpine environments. Seed dormancy and germination mechanisms are important factors that determining the timing of germination. To gain an understanding of how these mechanisms help to synchronize the germination event to the beginning of the growing season in two of the most popular Primula species (P. secundiflora and P. sikkimensis) in the Hengduan Mountains, Southwest China, we explored their seed dormancy and germination characteristics in the laboratory and their soil seed bank type in the field. Germination was first tested using fresh seeds at two alternating temperatures (15/5 and 25/15°C) and five constant temperatures (5, 10, 15, 20, and 25°C) in light and dark, and again after dry after-ripening at room temperature for 6 months. Germination tests were also conducted at a range of temperatures (5-30, 25/15, and 15/5°C) in light and dark for seeds dry cold stored at 4°C for 4 years, after which they were incubated under the above-mentioned incubation conditions after different periods (4 and 8 weeks) of cold stratification. Base temperatures (T _b) and thermal times for 50% germination (θ ₅₀) were calculated. Seeds were buried at the collection site to test persistence in the soil for 5 years. Dry storage improved germination significantly, as compared with fresh seeds, suggesting after-ripening released physiological dormancy (PD); however, it was not sufficient to break dormancy. Cold stratification released PD completely after dry storage, increasing final germination, and widening the temperature range from medium to both high and low; moreover, the T _b and θ ₅₀ for germination decreased. Fresh seeds had a light requirement for germination, facilitating formation of a persistent soil seed bank. Although the requirement reduced during treatments for dormancy release or at lower alternating temperatures (15/5°C), a high proportion of viable seeds did not germinate even after 5 years of burial, showing that the seeds of these two species could cycle back to dormancy if the conditions were unfavorable during spring. In this study, fresh seeds of the two Primula species exhibited type 3 non-deep physiological dormancy and required light for germination. After dormancy release, they had a low thermal requirement for germination control, as well as rapid seed germination in spring and at/near the soil surface from the soil seed bank. Such dormancy and germination mechanisms reflect a germination strategy of these two Primula species, adapted to the same alpine environments.

Disentangling the influence of ecological and historical factors on seed germination and seedling types in a Neotropical dry forest

In tropical dry forests, although seed germination and seedling establishment are in general limited by the seasonal availability of water, high interspecific variability, nonetheless, exists in terms of seedling traits and germination dynamics. Differences among species in seed germination and seedling traits may be related to other plant life-history traits, such that assessing these relationships may increase our understanding of factors influencing plant establishment, which would affect the regeneration pathways of tropical dry forest communities. In this study, taking into consideration the effect species’ phylogeny, we evaluated the relationships of seed germination metrics (percentage, lag time, and rate of germination) and seedling types (i.e. cotyledons functional morphology), with plant life-history traits (growth form, seed mass, dispersal syndrome and dispersal phenology) for 110 species in a Neotropical dry forest in Mexico. A total of 92% of the species studied disperse their seeds during the dry season, mainly at the beginning of this season (66%), a strategy mostly associated with autochorous herbs. Seed germination was more frequent in species that dispersed seeds at the end of the dry season. Germination percentage was not related to any of the traits studied. However, germination lag time and rate were negatively related to seed mass, a trait that in turn depended on growth form and dispersal syndrome. The dominant seedling type in the community was phanerocotylar epigeal with foliaceous cotyledons (56%), which was mostly associated with small seed mass and herbaceous growth form. Our results provide evidence that several plant life-history traits explain an important part of the variation in seed germination and seedling characteristics observed among species. Therefore, these plant life-history traits may be useful for grouping species in terms of their establishment strategies and roles on the regeneration of tropical dry communities.

Temperature and storage time strongly affect the germination success of perennial Euphorbia species in Mediterranean regions

This study aims to explore the effect of environmental factors (temperature, light, storage time) on germination response and dormancy patterns in eight Mediterranean native wildplants, belonging to the Euphorbia L. genus. In detail, we considered E. amygdaloides subsp. arbuscula, E. bivonae subsp. bivonae, E. ceratocarpa, E. characias, E. dendroides, E. melapetala, E. myrsinites, and E. rigida. We collected seeds from natural plant populations and performed germination assays in climatic chambers at seven constant temperatures (from 5 to 35°C, with 5°C increments), and four fluctuating temperature regimes (8/15, 8/20, 8/25, and 8/30°C, with a 12/12 hr thermoperiod). Germination assays were set up both in dark (D) and in light/dark conditions (L/D, 12/12 hr photoperiod), after short and long seed storage (SS around 30 days and LS around 150 days). For all these species, except E. amygdaloides subsp. arbuscula, results show that the final germinated proportions were improved by a long storage period (>150 days), which supports the existence of nondeep physiological dormancy. Optimal temperature levels ranged from 14.3 to 21.3°C and base temperatures ranged from 5.6 to 12.1°C, while ceiling temperatures from 25.6 to 34.7°C. For none of these species, germinations were favored by an alternating daily temperature regime, while in several instances, germinations were quicker and more complete in darkness, than in an alternating light/dark regime. In some instances, extreme temperature levels (5 and 30°C) induced dormancy and germinations did not resume when seeds were exposed at optimal temperature levels. Results are discussed in terms of the dynamics of emergences and how this might be affected by climate changes.

Cracking the case: Seed traits and phylogeny predict time to germination in prairie restoration species

Traits are important for understanding how plant communities assemble and function, providing a common currency for studying ecological processes across species, locations, and habitat types. However, the majority of studies relating species traits to community assembly rely upon vegetative traits of mature plants. Seed traits, which are understudied relative to whole-plant traits, are key to understanding assembly of plant communities. This is particularly true for restored communities, which are typically started de novo from seed, making seed germination a critical first step in community assembly and an early filter for plant establishment. We experimentally tested the effects of seed traits (mass, shape, and embryo to seed size ratio) and phylogeny on germination response in 32 species commonly used in prairie grassland restoration in the Midwestern USA, analyzing data using time-to-event (survival) analysis. As germination is also influenced by seed dormancy, and dormancy break treatments are commonly employed in restoration, we also tested the effects of two pretreatments (cold stratification and gibberellic acid application) on time to germination. Seed traits, phylogeny, and seed pretreatments all affected time to germination. Of all traits tested, variables related to seed shape (height and shape variance) best predicted germination response, with high-variance (i.e., pointier and narrower) seeds germinating faster. Phylogenetic position (the location of species on the phylogenetic tree relative to other tested species) was also an important predictor of germination response, that is, closely related species showed similar patterns in time to germination. This was true despite the fact that all measured seed traits showed phylogenetic signal, therefore phylogeny provided residual information that was not already captured by measured seed traits. Seed traits, phylogenetic position, and germination pretreatments were important predictors of germination response for a suite of species commonly used in grassland restoration. Shape traits were especially important, while mass, often the only seed trait used in studies of community assembly, was not a strong predictor of germination timing. These findings illustrate the ecological importance of seed traits that are rarely incorporated into functional studies of plant communities. This information can also be used to advance restoration practice by guiding restoration planning and seed mix design.

Phylogeny and source climate impact seed dormancy and germination of restoration-relevant forb species

For many species and seed sources used in restoration activities, specific seed germination requirements are often unknown. Because seed dormancy and germination traits can be constrained by phylogenetic history, related species are often assumed to have similar traits. However, significant variation in these traits is also present within species as a result of adaptation to local climatic conditions. A growing number of studies have attempted to disentangle how phylogeny and climate influence seed dormancy and germination traits, but they have focused primarily on species-level effects, ignoring potential population-level variation. We examined the relationships between phylogeny, climate, and seed dormancy and germination traits for 24 populations of eight native, restoration-relevant forb species found in a wide range of climatic conditions in the Southwest United States. The seeds were exposed to eight temperature and stratification length regimes designed to mimic regional climatic conditions. Phylogenetic relatedness, overall climatic conditions, and temperature conditions at the site were all significantly correlated with final germination response, with significant among-population variation in germination response across incubation treatments for seven of our eight study species. Notably, germination during stratification was significantly predicted by precipitation seasonality and differed significantly among populations for seven species. While previous studies have not examined germination during stratification as a potential trait influencing overall germination response, our results suggest that this trait should be included in germination studies as well as seed sourcing decisions. Results of this study deepen our understanding of the relationships between source climate, species identity, and germination, leading to improved seed sourcing decisions for restorations.

Functional trade-offs and the phylogenetic dispersion of seed traits in a biodiversity hotspot of the Mountains of Southwest China

The diversity of traits associated with plant regeneration is often shaped by functional trade-offs where plants typically do not excel at every function because resources allocated to one function cannot be allocated to another. By analyzing correlations among seed traits, empirical studies have shown that there is a trade-off between seedling development and the occupation of new habitats, although only a small range of taxa have been tested; whether such trade-off exists in a biodiverse and complex landscape remains unclear. Here, we amassed seed trait data of 1,119 species from a biodiversity hotspot of the Mountains of Southwest China and analyzed the relationship between seed mass and the number of seeds and between seed mass and time to germination. Our results showed that seed mass was negatively correlated with seed number but positively correlated with time to germination. The same trend was found regardless of variation in life-form and phylogenetic conservatism. Furthermore, the relation between seed mass and other seed traits was randomly dispersed across the phylogeny at both the order and family levels. Collectively, results suggest that there is a functional trade-off between seedling development and new habitat occupation for seed plants in this region. Larger seeds tend to produce fewer seedlings but with greater fitness compared to those produced by smaller seeds, whereas smaller seeds tend to have a larger number of seeds that germinate faster compared to large-seeded species. Apart from genetic constraints, species that produce large seeds will succeed in sites where resource availability is low, whereas species with high colonization ability (those that produce a high number of seeds per fruit) will succeed in new niches. This study provides a mechanistic explanation for the relatively high levels of plant diversity currently found in a heterogeneous region of the Mountains of Southwest China.

A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale

Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome-environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.