Search Results (154)

Seed transfer guidelines are used in ecological restoration to reduce the maladaptation risk from non-local genotypes. Researchers often examine second-generation populations under uniform conditions to isolate adaptation from environmental responses. However, in outcrossing species, interpreting these traits may be challenging if uncontrolled gene flow and recombination among provenances influence offspring phenotypes. We compared seed germination and seedling traits of the wind-pollinated grass Festuca vaginata, a dominant species of open sand grasslands in Hungary, across seed transfer zones (STZs) and localities. We used a two-generation common garden experiment with uncontrolled gene flow. Our results reveal that under common garden cultivation, the transgenerational stability of population differentiation is traitspecific. While locality effects on germination disappeared in the second generation, phenotypic variation in biomass and leaf length persisted, suggesting that shared environments homogenize germination faster than vegetative traits. As wind-pollinated species often exhibit weak regional genetic structuring, STZs may not capture the primary axis of phenotypic variation in specific traits. While not invalidating the use of STZs, our findings suggest that seed sourcing strategies should, if feasible, consider locality-level variation when using wind-pollinated grasses for species reintroduction. Full article

The development of effective conservation and management strategies for wild Ribes populations requires a comprehensive understanding of genetic diversity and population structure of these taxa, but only a few genetic studies exist, and these have focused on cultivated material in the genus. We evaluated the use of MobiSeq as a reduced representation sequencing approach to detect genetic variation in three Ribes species, and we used the data to characterize the genetic diversity and population structure in the Netherlands and the relationships between the wild Ribes populations, the ex situ genebank collection, and cultivars. MobiSeq with a single primer designed for repetitive elements that occur in the three species produced 17,000–31,000 SNPs per species after filtering against markers with minor allele frequency (MAF) < 0.01 and markers deviating from Hardy-Weinberg equilibrium (HWE). The SNPs were called against consensus sequences, producing separate sets of markers for each of the species. All three species had moderate genetic diversity (H_S = 0.141–0.239) and relatively low differentiation (F_ST = 0.049–0.083) with no evidence of inbreeding, consistent with their predominantly outcrossing life-history traits. This suggests that Dutch wild populations have largely retained their genetic diversity despite the current habitat fragmentation. Several putatively wild individuals showed evidence of cultivated ancestry, possibly indicating historical introgression or naturalized escapes from cultivation, particularly in R. rubrum and R. uva-crispa. Low differentiation between in situ and ex situ material (F_ST = 0.004–0.026) suggests that the genebank collections already capture most of the genetic diversity present in wild populations. Full article

N. cadamba is a fast-growing and economically important tree species with significant industrial and medicinal values. Its spherical capitulum comprises hundreds of sessile florets densely aggregated on a receptacle. How this unique floral structure shapes the mating system of this species remains unknown, as this structure enhances the probabilities of both selfing and outcrossing. Here we clarify this question by investigating a natural population. We randomly sampled 11 half-sib families and 6 progenies per half-sib family and assayed samples with whole-genome resequencing. Population genomic analysis indicated that about 93.09% of 4,876,674 high-quality SNPs were under Hardy–Weinberg equilibrium, with a mean inbreeding coefficient of 0.0614 in the sample. Genome-wide nucleotide diversity (π) was 0.0024 on average. The linkage disequilibria ($r$²) decayed by half at approximately 2.31 kb between sites across genomes. Principal component analysis showed clear family structure among all samples. Analysis with independent SNPs and MLTR (Program for estimating multilocus outcrossing rate) showed that the multilocus outcrossing rate (t_m) and single-locus outcrossing rate (t_s) were 1.028 ± 0.048 and 1.015 ± 0.060, respectively, with an estimated difference between t_m and t_s of 0.013 ± 0.022. Analysis with BORICE (Bayesian outcrossing rate and inbreeding coefficient estimation) showed an outcrossing rate (t) of 0.948 ± 0.029 and an inbreeding coefficient (F) of 0.012 ± 0.010. Collectively, these results imply that N. cadamba could be essentially outcrossing, without selfing and biparental inbreeding. The potentially outcrossing system of N. cadamba implies differences from its close relative N. macrophylla (a mixed-mating system) in population structure, genome evolution, and natural geographical distribution. This finding also provided a useful reference for breeding and genetic improvement of this “miracle tree”. Full article

Oenothera biennis L. is an economically important oil and ornamental crop. However, the regulatory mechanisms underlying its flower bud differentiation remain poorly understood. To elucidate the interactions between the environmental cues and molecular networks governing this process, this study investigated natural populations from the Lesser Khingan Mountains. The results demonstrate that exposure to 0–10 °C for at least 15 d and long-day (LD) conditions correlated strongly with floral induction. Notably, 200 mg·L⁻¹ of exogenous GA₃ effectively substituted for vernalization, significantly promoting bolting and advancing flower development. Expression profiling revealed an antagonistic expression pattern between floral activators such as ObFT and ObAP2 and repressors such as ObFLC. Both vernalization and GA₃ upregulated floral activators while suppressing the repressors, and these processes were coincident with the transition to flowering. Flower bud differentiation goes through six continuous stages, spanning from inflorescence primordia to gynoecium primordia formation. Hybrid fruit setting, the pollen–ovule ratio (98) and the outcrossing index (OCI = 3) confirmed that O. biennisis is a facultative selfer, with reproduction predominantly relying on self-pollination. This study provides a systematic characterization of the integrated regulatory network coordinating vernalization, photoperiod, and gibberellin in Oenothera flowering, proposing a framework for the putative FT-FLC antagonism. These findings establish a molecular foundation for the precision management of flowering time and informed breeding strategies. Full article

Fruit production in many crops depends on pollen transfer by animals, and many self-sterile crops rely on long-distance pollen transfer by animals between different genotypes, i.e., between different cultivars. Foragers such as honeybees may need to visit and carry the pollen of more than one cultivar to be effective pollinators, but we currently have little understanding of how many foragers are carrying more than one cultivar of pollen. We determined the number of cultivars carried by honeybees returning to their hive with pollen at two locations in an orchard of a predominantly self-sterile tree crop, macadamia. The locations were either (i) close to only one macadamia cultivar or (ii) between two macadamia cultivars. We sampled honeybees early in the flowering period, when the floral resource availability was lower, and at peak flowering when the resource availability was higher. We identified the cultivars carried by individual honeybees using a SABER-MassARRAY method that distinguishes cultivar-specific SNPs in pollen DNA. We found that most honeybees carried pollen from only one identified macadamia cultivar, regardless of the hive location and time within the flowering period. Only 15% of the honeybees were carrying pollen from more than one identified macadamia cultivar. This suggests that most honeybee foraging visits to flowers in the orchard were unlikely to have resulted in cross-pollination. Pollenizer trees could be interplanted among the main cultivars in macadamia orchards to increase the number of honeybees carrying cross-pollen and increase their pollination efficiency. Full article

Self-incompatibility (SI) is an important plant mechanism that prevents inbreeding depression by recognizing and rejecting self-pollen, thereby promoting outcrossing. However, SI can also act as a barrier in breeding programs, presenting significant challenges to breeders. Passion fruit (Passiflora edulis), a tropical fruit species of substantial economic importance, also serves as a valuable system for investigating SI mechanisms within the Passifloraceae. Nevertheless, the molecular basis of SI in passion fruit has not yet been elucidated. In this study, we investigated the SI system in yellow passion fruit (P. edulis f. flavicarpa) and employed transcriptomic analysis to examine the time-course transcriptional responses following different pollination treatments. Transcriptomic analysis revealed distinct gene expression dynamics under different pollination treatments: self-pollinated samples exhibited stronger and earlier transcriptional changes, whereas the number of differentially expressed genes (DEGs) in cross-pollinated samples was relatively lower. Numerous pathways previously associated with sporophytic self-incompatibility (SSI) were enriched in the stigma samples after self-pollination. Reactive oxygen species (ROS) are crucial signaling molecules involved in pollen germination and pollen tube growth during SI responses. Our results showed that ROS-related pathways were enriched in stigma tissues after self-pollination. In addition, oxidative stress-related responses were detected in the style shortly after self-pollination, suggesting that plastid-associated or general oxidative stress processes may also be involved, although the precise source of ROS requires further validation. FERONIA, ROP9, and ARC1 are key genes related to the SI system in Brassica. In the passion fruit SI response, the expression levels of these genes increased in the style, indicating a spatial expression pattern different from that reported in classical Brassicaceae SSI systems. Together with cytological observations showing that self-pollen rejection occurs at the stigma surface, our results suggest that yellow passion fruit may employ an SSI-like regulatory framework while exhibiting a lineage-specific spatial deployment of SI-related regulators. Overall, this study provides new transcriptomic insights into the SI mechanism of yellow passion fruit, establishes a molecular framework for understanding SI in P. edulis f. flavicarpa, and offers novel insights into the diversity of plant SI systems. Full article

The steno-endemic Verbascum rupicola faces a precarious future due to its extreme habitat specialization on tectonically active hydrothermal quartz veins. This study presents a long-term assessment based on periodic population censuses spanning 18 years (2007, 2016, and 2025) to assess the demographic and spatial trends of its global population in the Tahtalı Dam basin, Türkiye. Field surveys, GIS-based habitat mapping, and controlled pollination experiments were integrated with seed germination kinetics and ex situ cultivation trials. Results reveal a precipitous 69.12% global population decline, primarily driven by a 33.41% habitat loss from agricultural expansion in 2011 and the total extirpation of three sub-populations by a major wildfire in 2017. Furthermore, a “reproductive squeeze” was identified, where climate-induced reductions in flower production (18.87%) are compounded by intensifying floral predation by Pieris rapae. Reproductive analysis revealed random monomorphic enantiostyly—reported for the first time in the genus—which functions as a flexible mating system prioritizing outcrossing while providing reproductive assurance. Despite high intrinsic seed viability (69.12%), ex situ cultivation largely failed (3.5% survival; 1 out of 28 transplanted individuals), underscoring the species’ obligate chasmophytic nature. Consequently, V. rupicola meets the criteria for Critically Endangered (CR) status, necessitating urgent “micro-reserve” protection of its remaining habitat and in situ restoration efforts. Full article

DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research. Full article

Tilia cordata Mill. is a long-lived, ecologically important broadleaved tree species that maintains high genetic diversity despite habitat fragmentation and historical range shifts. In this study, we assessed genetic diversity, clonal structure, and population differentiation in six genetic conservation units (GCUs) in Lithuania using nuclear microsatellite markers. A total of 1109 individuals were successfully genotyped, revealing 979 unique multi-locus genotypes, with 17% of individuals assigned to clonal lineages. Clonal groups were generally small and spatially restricted, indicating localized vegetative regeneration. Genetic diversity was high across all populations, with similar levels of observed and expected heterozygosity, consistent with predominantly outcrossing reproduction. Juvenile cohorts exhibited slightly higher allelic richness and latent genetic potential compared to mature trees, suggesting effective regeneration and maintenance of genetic variation. Genetic differentiation among populations was low but significant (F_ST = 0.013; G″_ST = 0.051), with evidence of clustering corresponding to provenance regions. High gene flow (Nm ≈ 10) likely contributes to weak population structure, although regional differentiation persists. The results demonstrate that Lithuanian T. cordata populations retain a robust genetic framework, combining high within-population diversity with moderate structuring. These findings highlight the importance of conserving multiple GCUs and implementing genetic monitoring to ensure long-term population viability under changing environmental conditions. Full article

The endemic Minuartia nifensis, the only known gynodioecious species of its genus, offers a suitable model for understanding the relationships between floral characteristics, pollination, and mating systems in species with narrow distributions and single populations. We analyzed population structure, floral morphology, pollen viability, stigma receptivity, mating system components, and pollinator assemblages using field observations, morphometric measurements, controlled pollination experiments (autogamy, allogamy, apomixis and open pollination), and standardized pollinator surveys. The population exhibited an approximately balanced hermaphrodite–female ratio (0.97:1) and clear sexual dimorphism, with hermaphrodite flowers significantly larger than female flowers. Despite this dimorphism, pollinator visitation was similar between morphs, with 52.54% of visits to hermaphrodite flowers and 47.46% to female flowers. A total of 1734 visits by seven visitor species were recorded, of which approximately 95% of potentially effective pollen transfer was attributable to three bee taxa. Pollen viability, stigma receptivity, and visitation frequency peaked between 12:00 and 14:00, accounting for 58% of total insect visits. Controlled pollination experiments showed highest reproductive success under cross-pollination and limited success under self-pollination, indicating a mixed but predominantly outcrossing mating system. Together, these results suggest that gynodioecy in M. nifensis may be supported by floral differentiation, temporal reproductive traits, and pollinator-mediated pollen transfer. Full article

Flag leaf angle (FLA) in rice (Oryza sativa L.) is one of the important traits affecting F₁ seed production by mechanization. Here, we report the map-based cloning and functional characterization of the FLA1 (FLAG-LEAF-ANGLE 1) gene, which resides at a major-effect quantitative trait locus (QTL). Through cell morphological observations and exogenous hormone treatment assays, we demonstrate that gibberellin (GA) modulates rice FLA by altering both the number of cell layers and cell length. Combining genetic and molecular biological analyses with genetic complementation and gene overexpression assays, we elucidated and validated the biological function of FLA1. In addition, we found that FLA1 is constitutively expressed and encodes a protein localized to both the cell membrane and nucleus. Via RT-qPCR assays, we further demonstrated that the FLA1^fla-R allele from the rice accession fla-R enhances GA biosynthesis by upregulating the expression of CLA1 and GA20ox2. Furthermore, yeast two-hybrid assays revealed that auxin-repressed protein 1 (ARP1) interacts with FLA1, suggesting a potential role of this interaction in the modulation of rice FLA. Collectively, our results demonstrate that optimizing rice FLA via molecular manipulation of FLA1 can resolve the problem of flag leaf shearing during F₁ hybrid rice seed production without compromising F₁ hybrid seed yield, thereby facilitating mechanized F₁ hybrid rice seed production. Full article

The MATα_HMGbox and HMG-box_ROX1-like domains of the MAT1-1-1 and MAT1-2-1 proteins, respectively, play essential roles in DNA binding and the subsequent regulation of gene transcription, controlling Ophiocordyceps sinensis sexual reproduction. Alternative splicing, differential occurrence and transcription of the MAT1-1-1 and MAT1-2-1 genes have been demonstrated in Hirsutella sinensis (GC-biased Genotype #1 of the 17 O. sinensis genotypes), suggesting self-sterility under heterothallic or hybrid outcrossing. In this study, the MATα_HMGbox domains of MAT1-1-1 proteins in wild-type Cordyceps sinensis isolates were shown to cluster into 5 clades in the Bayesian clustering tree and belong to diverse stereostructure morphs under 19 AlphaFold codes. The HMG-box_ROX1-like domains of MAT1-2-1 proteins, on the other hand, were shown to cluster into 2 branched Bayesian clades and belong to stereostructure morphs under 25 AlphaFold codes. Correlation analysis revealed that 1–3 amino acid substitutions in the DNA-binding domains of the mating proteins resulted in altered hydrophobicity and secondary and tertiary structures of the DNA-binding domains of the proteins, especially altered stereostructures of the hydrophobic cores formed by 3 critical α- helices within the functional domains of the proteins. Fungal origin analysis revealed possible heterospecific fungal sources of mating proteins with stereostructure variations in wild-type C. sinensis isolates, suggesting that alterations in DNA binding function and the subsequent regulation of mating-related gene transcription are involved in ensuring the accuracy and genetic diversity of heterothallic and hybrid reproduction of O. sinensis during the lifecycle of the C. sinensis insect–fungal complex. Full article

Plantations of the valuable Chinese timber species, Chamaecyparis hodginsii, established by planting, primarily rely on seed orchards for propagation. Therefore, effective management of the genetic composition of these orchards is essential to ensure a sustainable supply of high-quality seeds. However, the mating system and pollen dispersal mechanisms in its high-generation seed orchards remain unclear, limiting precise genetic management. To address this, we analyzed 30 parental clones and 75 of their open-pollinated progeny from a second-generation seed orchard using 15 polymorphic EST-SSR markers. Compared to reported natural populations of C. hodginsii, both parental and progeny populations maintained high genetic diversity (mean uHe = 0.438 and 0.449, respectively), with a significant excess of heterozygotes (mean Fis = −0.084 and −0.066, respectively). Population genetic structure analysis indicated weak genetic differentiation among the parental genetic groups (mean Fst = 0.012), which was further reduced in the progeny population (mean Fst = 0.003) due to open pollination, reflecting a trend toward genetic homogenization. The mating system was characterized exclusively by outcrossing (tm = 1.000). However, paternity analysis revealed highly skewed paternal contributions, a low effective number of pollen donors (Nep = 8.13), and contributions of S5, S11, and S17 as dominant pollen parents, with 17.33% external pollen flow. These findings elucidate the mechanisms underlying sustained genetic diversity despite unequal paternal contributions and provide a theoretical basis for optimizing parental configuration and pollen management. Full article

Loeselia mexicana (Polemoniaceae) is a Mexican shrub with significant medicinal value since pre-Hispanic times. Despite its ethnobotanical importance and apparent role in supporting pollinator communities, detailed information about its reproductive biology remains limited, hindering conservation efforts for this increasingly harvested species. We investigated the reproductive ecology of L. mexicana across two flowering seasons (2023–2024 and 2024–2025) in central Mexico through an integrated approach examining flowering phenology, floral morphology, sexual maturation sequence, nectar characteristics, floral visitors, and breeding system experiments. Flowering occurs from September to March, peaking in October. Flowers exhibit protandry, with anther dehiscence on days 1–2 and stigma receptivity from day 2 onward (flower lifespan: 2.85 ± 0.11 days). Maximum nectar production (1.46 ± 0.05 µL per flower; 193.13 ± 8.8 mg/mL) coincided with peak visitor activity. Despite possessing classic ornithophilous traits, we recorded 21 floral visitor species (5 hummingbirds, 3 hymenopterans, 13 butterflies) with similar visitation patterns, challenging previous assumptions about pollination specialization. Controlled pollination experiments confirmed self-incompatibility, with cross-pollination producing significantly more seeds than autonomous selfing. Our findings reveal that L. mexicana maintains a generalized pollination system, while protandry and self-incompatibility enforce outcrossing, providing critical baseline information for conservation strategies. Full article

Sonneratia ovata is an important tree species for ornamental, economic, ecological, and medicinal value and is identified as an endangered species. There are very few studies on the reproductive traits, genetic diversity, and population structure of S. ovata. Therefore, it is urgent to accurately understand its genetic background and reproductive status in order to better conserve and manage S. ovata. S. ovata has a mixed mating system, is partially self-compatible and needs pollinators, according to the outcrossing index, pollen–ovule ratio, pollination treatment results and outcrossing rate. Natural populations maintained high outcrossing coupled with inbreeding and low genetic diversity (H_e = 0.215), and the population DC was regarded as the center of genetic diversity. The Mantel test showed that there existed a positive correlation between geographic and genetic distance among populations, which was in line with the IBD model. Molecular variance was largely confined to within-population differences (75.4%), while inter-population differences accounted for 24.6%. Structure and PCoA analysis supported the UPGMA cluster. This study is the first to investigate reproductive traits, genetic diversity, and population structure through SSR. The results provide a scientific basis for cross breeding, conservation, and management of this species. In future, it is necessary to increase relevant research (human, environment, habitat factors, etc.) to better protect and utilize this species. Full article