Origin and genetic differentiation of pink-flowered Sorbus hybrids in the Western Carpathians.

Background and Aims: Diversity of the genus Sorbus has been affected by interspecific hybridizations. Pink-flowered hybrid species have been insufficiently studied so far. They comprise bigenomic hybrid species derived from crosses S. aria s.l. × S. chamaemespilus and trigenomic ones, where S. aucuparia was involved as well. The main objective of the present study was to reconstruct their hybrid origins as well as to assess genetic distinction among several morphologically recognized hybrid species. Methods: Samples from putative maternal species and eight pink-flowered and two white-flowered hybrid species were collected in the Western Carpathians and the Sudetes. In total, 370 specimens were analysed. Six chloroplast microsatellites were used to infer parentage, whereas nuclear amplified fragment length polymorphism (AFLP) markers were employed for the identification of clones and patterns of genetic variation. Ploidy levels were estimated by flow cytometry on a subset of 140 individuals. Key Results: Genetic data supported their hybrid origins proposed based on flower and leaf morphology, and chloroplast DNA (cpDNA) revealed recurrent origins ( S. caeruleomontana , S. haljamovae ), even from bidirectional hybridization events ( S. zuzanae ). All bigenomic and trigenomic hybrid species (except triploid S. zuzanae ) were found to be tetraploid. In addition to polyploidy, low genetic variation and the presence of clones within and among populations were observed, suggesting predominantly apomictic reproduction of the hybrid species. Most of the described hybrid species appeared also genetically distinct. Conclusions: The data suggest that multiple hybridization events in the Western Carpathian Sorbus have led to the formation of separate, partially reproductively isolated genetic lineages, which may or may not be discriminated morphologically. Even bidirectional hybridization can produce individuals classified to the same taxon based on phenotype. For some hybrid taxa, hybridization pathways were proposed based on their genetic proximity to parental species and differences in genome sizes.

Pollen viability and longevity in Juniperus taxa native to Slovakia.

Pollen viability, dispersion ability and longevity during deep-freezer storage were studied in three Juniperus taxa distributed in Slovakia. All these characteristics of pollen are closely related to the pollination and/or fertilization success of the junipers in nature. Pollen viability varied considerably between the three populations of J. communis and one population of each, J. sibirica and J. communis var. intermedia. Pollen germination rate ranged between 40.75% and 75.06%, and pollen tube length between 30.32 and 40.41 µm. A clear tendency indicates a higher germination rate of J. communis pollen from lower altitudes and reduced germination of J. sibirica and J. communis var. intermedia pollen from higher altitudes. The dispersion potential of the J. communis pollen during its shedding seems relatively low. In 2021, pollen cloud density was diluted at 68.1% at the 4 m distance from the test shrub, in 2022 of 52.1% at the 17 m distance from the pollen source. A deep-freezer storage of juniper pollen in a double-walled polyethylene bag with silica gel was not efficient enough, as indicated by the drop of pollen germination rate of 31.2% in J. communis and of 79.4% in J. sibirica during a 1-year storage period at - 81 °C.

Genomic variation of European beech reveals signals of local adaptation despite high levels of phenotypic plasticity.

Local adaptation is key for ecotypic differentiation and species evolution. Understanding underlying genomic patterns can allow the prediction of future maladaptation and ecosystem stability. Here, we report the whole-genome resequencing of 874 individuals from 100 range-wide populations of European beech (Fagus sylvatica L.), an important forest tree species in Europe. We show that genetic variation closely mirrors geography with a clear pattern of isolation-by-distance. Genome-wide analyses for genotype-environment associations (GEAs) identify relatively few potentially adaptive variants after correcting for an overwhelming signal of statistically significant but non-causal GEAs. We characterize the single high confidence genomic region and pinpoint a candidate gene possibly involved in winter temperature adaptation via modulation of spring phenology. Surprisingly, allelic variation at this locus does not result in any apparent fitness differences in a common garden. More generally, reciprocal transplant experiments across large climate distances suggest extensive phenotypic plasticity. Nevertheless, we find indications of polygenic adaptation which may be essential in natural ecosystems. This polygenic signal exhibits broad- and fine-scale variation across the landscape, highlighting the relevance of spatial resolution. In summary, our results emphasize the importance, but also exemplify the complexity, of employing natural genetic variation for forest conservation under climate change.

Long-term cryopreservation of Greek fir embryogenic cell lines: recovery, maturation and genetic fidelity.

In coniferous species, including Greek fir (Abies cephalonica Loud), the involvement of somatic embryo plants in breeding and reforestation programs is dependent on the success of long-term cryostorage of embryogenic cultures during clonal field testing. In the present study on Greek fir, we assayed the recovery, morphological characteristics and genetic fidelity of embryogenic cell lines 6 and 8 during proliferation and maturation after long-term cryostorage. Our results indicate successful recovery of both cell lines after 6 years in cryostorage. In the maturation phase, both cell lines were capable of producing somatic embryos although some differences were detected among experiments. However, these changes were more dependent on the differences in the components of the maturation media or in the experimental set-up than on the long-term cryostorage. During both proliferation and maturation phases, the morphological fidelity of the embryogenic cultures as well as of the somatic embryos were alike before and after cryopreservation. The genetic fidelity of the cryopreserved cell line 6 that was assayed by random amplified polymorphic DNA (i.e. RAPD) markers demonstrated some changes in the RAPD profiles. The results indicate possible genetic aberrations caused by long-term cryopreservation or somaclonal variation during the proliferation stage. However, in spite of these changes the embryogenic cultures did not lose their proliferation or maturation abilities.

Soil microbial characteristics at the monitoring plots on windthrow areas of the Tatra National Park (Slovakia): their assessment as environmental indicators.

This study focused on the responses of soil microorganisms to different management regimes on disturbed windthrow areas. Microbial parameters potentially serving as indicators of environmental changes within a long-term monitoring of forest development after large-scale disturbance events were assessed. Basal and substrate-induced respiration, N mineralisation, catalase activity, microbial biomass as well as functional diversity based on Biolog assay were determined in soil samples from three disturbed plots and an undisturbed reference plot in the Tatra National Park (Slovakia) since 2006. A relative congruence of inter-annual trends of microbial activity indicators at all plots results from a common response of microbiota to changes of climate at the landscape level after forest stands were destroyed. While catalase activity and functional diversity proved to be useful indicators of temporal trends, microbial biomass seems to reflect different management regimes at the disturbed plots.

Longevity and germination of Juniperus communis L. pollen after storage.

Pollen storage belongs among the most important activities associated with pollen handling. It overcomes the differences in pollen shedding and ovule receptivity during controlled pollination experiments. It is especially important for species like common juniper (Juniperus communis L.) with an extremely low quality of seeds due to pollination failure. Additionally, it is a substantial part of germplasm preservation programmes in pollen banks. In the present paper, the effect of short-term storage of pollen was studied using pollen samples from five shrubs in an in vitro germination test. Two temperature regimes were tested. The pollen viability of freshly collected pollen varied considerably between individual shrubs, exhibiting 67.3-88.6% germination rate and 248.0-367.3 µm of pollen tubes. Storage at + 4 °C for four months was accompanied by a profound decline in pollen viability. The germination percentage was reduced to 49.2-75.2% and the pollen tube length to 32.5-69.0%, depending on individual shrubs. The corresponding decline in pollen viability characteristics during storage at - 20 °C was only negligible in two of the tested shrubs. In the remaining three shrub samples, an increase in germination percentage was observed. Pollen tube growth responded more sensitively to freezing, but, on average, the decrease in length was lower than that at + 4 °C. The rate of reduction in pollen tube length varied between 11.5 and 45.4%. Cytological events accompanying in vitro germination of freezer-stored pollen exhibited some delay in releasing the exine from pollen grains during the early stages of germination as compared with freshly collected pollen. In conclusion, short-term storage of the common juniper pollen in a freezer is better for the preservation of its viability than storage at + 4 °C.

From allozymes to NGS: population genetics of forest trees in Slovakia in the past 40 years.

This review summarizes the development of population genetics and population genomics studies of forest trees in Slovakia during the past 40 years. Various protein and DNA markers have been applied during this period to address several topics in evolutionary genetics and biogeography of trees: allozymes, uniparentally inherited chloroplast and mitochondrial markers, simple sequence repeats and single nucleotide polymorphisms. The main object of studies of phylogeny and postglacial migration were Fagus sylvatica s.l. and eastern-Mediterranean firs (Abies Mill. section Abies), where the divergence of genetic lineages (species and subspecific taxa) in time, as well as colonization of the current ranges during the Holocene were reconstructed. The studies on intraspecific gene flow and homoploid hybridization focused on hybrid swarms Pinus sylvestris/P. mugo and firs. Unusual maternal inheritance of chloroplast DNA was revealed in P. mugo × P. sylvestris crosses. Contrasting geographical structures of hybrid zones were revealed in wind-dispersed vs. animal-dispersed trees. Within the studies of adaptation, signals of selection were identified both in field observations and common-garden experiments on Picea abies, F. sylvatica and A. alba. Perspectives of ongoing research employing next-generation sequencing were shortly outlined.

Photosynthetic performance of silver fir (Abies alba) of different origins under suboptimal growing conditions.

Understanding of the intraspecific variability in the physiological stress response of trees may enable to mitigate the impact of climate change on forest ecosystems in the future. We studied the photosynthetic performance of five silver fir (Abies alba Mill.) provenances originating from climatically distinct localities. The study was performed in the trial plot of the silver fir provenance experiment IUFRO 2005 on two dates: in the early summer and in the late summer. Heat waves and a decrease in water availability occurred between the two measurement dates, allowing us to study the response of the provenances to suboptimal growing conditions. The provenances were evaluated at the level of PSII photochemistry and CO2 assimilation by measuring photosynthesis-related pigment content, chlorophyll a fluorescence, and gas exchange parameters. Significant climatic clines were confirmed: the photosynthetic performance before and after the stress period increased with the increasing altitude and precipitation at the site of origin. In contrast, photosynthetic performance declined with the increasing temperature and Ellenberg's quotient of the origin site. We concluded that provenances originating from high altitudes, corresponding well with more humid and colder conditions in Central Europe, showed the greatest photosynthetic performance and were less responsive to moderate heat and drought. This documents inter-population variation in physiological traits, which needs to be considered in setting rules and recommendations for the transfer of forest reproductive materials.

A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae).

The eastern-Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern-Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the structure analysis and distance-based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi-trojani: both they represent evolutionary branches of Abies bornmuelleriana.

Do Cupins Have a Function Beyond Being Seed Storage Proteins?

Plants continue to flourish around the site of the Chernobyl Nuclear Power Plant disaster. The ability of plants to transcend the radio-contaminated environment was not anticipated and is not well understood. The aim of this study was to evaluate the proteome of flax (Linum usitatissimum L.) during seed filling by plants grown for a third generation near Chernobyl. For this purpose, seeds were harvested at 2, 4, and 6 weeks after flowering and at maturity, from plants grown in either non-radioactive or radio-contaminated experimental fields. Total proteins were extracted and the two-dimensional gel electrophoresis (2-DE) patterns analyzed. This approach established paired abundance profiles for 130 2-DE spots, e.g., profiles for the same spot across seed filling in non-radioactive and radio-contaminated experimental fields. Based on Analysis of Variance (ANOVA) followed by sequential Bonferroni correction, eight of the paired abundance profiles were discordant. Results from tandem mass spectrometry show that four 2-DE spots are discordant because they contain fragments of the cupin superfamily-proteins. Most of the fragments were derived from the N-terminal half of native cupins. Revisiting previously published data, it was found that cupin-fragments were also involved with discordance in paired abundance profiles of second generation flax seeds. Based on these observations we present an updated working model for the growth and reproductive success of flax in a radio-contaminated Chernobyl environment. This model suggests that the increased abundance of cupin fragments or isoforms and monomers contributes to the successful growth and reproduction of flax in a radio-contaminated environment.

Genetic effects of air pollution on forest tree species of the Carpathian Mountains.

The effects of air pollution on the genetic structure of Norway spruce, European silver fir and European beech were studied at four polluted sites in Slovakia, Romania and Czech Republic. In order to reduce potential effects of site heterogeneity on the health condition, pair-wise sampling of pollution-tolerant and sensitive trees was applied. Genotypes of sampled trees were determined at 21 isozyme gene loci of spruce, 18 loci of fir and 15 loci of beech. In comparison with Norway spruce, fewer genetic differences were revealed in beech and almost no differentiation between pollution-tolerant and sensitive trees was observed in fir. In adult stands of Norway spruce, sensitive trees exhibited higher genetic multiplicity and diversity. The decline of pollution-sensitive trees may result thus in a gradual genetic depletion of pollution-exposed populations of Norway spruce through the loss of less frequent alleles with potential adaptive significance to altered stressing regimes in the future. Comparison of the subsets of sensitive and tolerant Norway spruce individuals as determined by presence or absence of discolorations ("spruce yellowing") revealed different heterozygosity at 3 out of 11 polymorphic loci.

Changes in ATP, glucose-6-phosphate and NAD(P)H cellular levels during the proliferation and maturation phases of Abies alba Mill. embryogenic cultures.

The aim of the present study was to evaluate the adenosine triphospate (ATP), glucose-6-phosphate (glu-6P) and reduced form of nicotinamide adenine dinucleotide phosphate (NAD(P)H) cellular levels during the proliferation and maturation phases of Abies alba Mill. somatic embryos. For a better understanding of the dynamics of these parameters during the proliferation cycle, four embryonic cell lines were tested. During the maturation period, three independent experiments were conducted, focused on the effects of PEG-4000 (5 or 10% (w/v)) and abscisic acid (16, 32 or 64 µM) applied together (Experiments A and B) or with addition of gibberellic acid (Experiment C) on the dynamics of bio-energetic molecules and on the mean number of cotyledonary somatic embryos. Our results demonstrated that the cellular levels of bio-energetic molecules strongly depended on the composition of maturation media. Generally, the higher the number of cotyledonary embryos produced, the higher the level of ATP observed after a 2-week maturation period. The cellular level of ATP, glu-6P and NAD(P)H increased, particularly after the transition from the proliferation to the maturation phase when the differentiation and growth of somatic embryos occurred.

Genotypic variability and phenotypic plasticity of cavitation resistance in Fagus sylvatica L. across Europe.

Xylem cavitation resistance is a key physiological trait correlated with species tolerance to extreme drought stresses. Little is known about the genetic variability and phenotypic plasticity of this trait in natural tree populations. Here we measured the cavitation resistance of 17 Fagus sylvatica populations representative of the full range of the species in Europe. The trees were grown in three field trials under contrasting climatic conditions. Our findings suggest that the genotypic variability of cavitation resistance is high between genotypes of a given population. By contrast, no significant differences were found for this trait across populations, the mean population cavitation resistance being remarkably constant in each trial. We found a significant site effect and a significant site × population interaction, suggesting that cavitation resistance has a high phenotypic plasticity and that this plasticity is under genetic control. The implications of our findings for beech forest management in a context of climate change are discussed.

A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences.

Here, palaeobotanical and genetic data for common beech (Fagus sylvatica) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread. Four large datasets are presented, including over 400 fossil-pollen sites, 80 plant-macrofossil sites, and 450 and 600 modern beech populations for chloroplast and nuclear markers, respectively. The largely complementary palaeobotanical and genetic data indicate that: (i) beech survived the last glacial period in multiple refuge areas; (ii) the central European refugia were separated from the Mediterranean refugia; (iii) the Mediterranean refuges did not contribute to the colonization of central and northern Europe; (iv) some populations expanded considerably during the postglacial period, while others experienced only a limited expansion; (v) the mountain chains were not geographical barriers for beech but rather facilitated its diffusion; and (vi) the modern genetic diversity was shaped over multiple glacial-interglacial cycles. This scenario differs from many recent treatments of tree phylogeography in Europe that largely focus on the last ice age and the postglacial period to interpret genetic structure and argue that the southern peninsulas (Iberian, Italian and Balkan) were the main source areas for trees in central and northern Europe.