Divergent selection and genetic structure of Sideritis scardica populations from southern Balkan Peninsula as revealed by AFLP fingerprinting

DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.

Sideritis scardica Extracts Demonstrate Neuroprotective Activity against Aβ25-35 Toxicity

Alzheimer's disease (AD) is the most prevalent neurodegenerative condition, primarily affecting seniors. Despite the significant time and money spent over the past few decades, no therapy has been developed yet. In recent years, the research has focused on ameliorating the cytotoxic amyloid beta (Aβ) peptide aggregates and the increased elevated oxidative stress, two interconnected main AD hallmarks. Medicinal plants constitute a large pool for identifying bioactive compounds or mixtures with a therapeutic effect. Sideritis scardica (SS) has been previously characterized as neuroprotective toward AD. We investigated this ability of SS by generating eight distinct solvent fractions, which were chemically characterized and assessed for their antioxidant and neuroprotective potential. The majority of the fractions were rich in phenolics and flavonoids, and all except one showed significant antioxidant activity. Additionally, four SS extracts partly rescued the viability in Aβ_25-35-treated SH-SY5Y human neuroblastoma cells, with the initial aqueous extract being the most potent and demonstrating similar activity in retinoic-acid-differentiated cells as well. These extracts were rich in neuroprotective substances, such as apigenin, myricetin-3-galactoside, and ellagic acid. Our findings indicate that specific SS mixtures can benefit the pharmaceutical industry to develop herbal drugs and functional food products that may alleviate AD.

Sideritis elica, a New Species of Lamiaceae from Bulgaria, Revealed by Morphology and Molecular Phylogeny

Sideritis elica, from the Rhodope Mountains, is described as a species new to science. Results of a detailed morphological analysis were combined with the data of molecular analyses using DNA barcoding as an efficient tool for the genetic, taxonomic identification of plants. The combination of morphological features distinguishes the new species well: Its first three uppermost leaf pairs are significantly shorter and wider, the branchiness of the stems is much more frequent, the whole plant is much more lanate, and it looks almost white, as opposed to the other closed species of section Empedoclia, which look grayish green. The molecular analysis, based on the rbcL and trnH-psbA regions, supports the morphological data about the divergence of Sideritis scardica and Sideritis elica. The studied populations of the two taxa were found to be genetically distant (up to 6.8% polymorphism for trnH-psbA) with distinct population-specific nucleotide patterns, while no polymorphism in the DNA barcodes was detected within the Sideritis elica population. The results confirm the existence of a new species called Sideritis elica, which occurs in the nature reserve Chervenata Stena, located in the northern part of the Central Rhodope Mountains. There were only 12 individuals found in the locality, which underlines the necessity of conservation measures.

Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm

Background

Morinda officinalis How (MO) is a perennial herb distributed in tropical and subtropical regions, which known as one of the “Four Southern Herbal Medicines”. The extent of genetic variability and the population structure of MO are presently little understood. Here, nine morphological traits, six chemical components and Single nucleotide polymorphism (SNP) markers were used in integrative research of MO germplasm variation among 88 individuals collected from ten populations across four geographical provinces of China.

Results

Both phenotype and chemical composition have significant genetic variation, and there is a certain correlation between them such as root diameter and the nystose content, as well as geographical distribution. The principal component analysis (PCA) showed the leaf length, leaf width, nystose, 1^F-furanosaccharide nystose, and the section color were the major contributors to diversity. The cluster analysis based on phenotypic and oligosaccharide data distinguished three significant groups, which was consistent with the result of a corresponding analysis with 228,615 SNP markers, and importantly, they all showed a significant correlation with geographical origin. However, there was little similarity between two cluster results. The Shannon’s information index (I) varied from 0.17 to 0.53 with a mean of 0.37, suggesting a high level of genetic diversity in MO populations, which mainly existed among individuals within populations, accounting for 99.66% of the total according to the analysis of molecular variance (AMOVA) results. Each population also maintains the connection because of certain gene communication, so that the genetic differentiation between populations was not very significant. The STRUCTURE software was used to analyse the population structure and the result showed that 88 accessions were clustered into three groups, and 67% of them were pure type, which was also confirmed through PCA.

Conclusions

The comprehensive study of phenotypic, chemical and molecular markers will provide valuable information for future breeding plans and understanding the phylogenetic relationship of MO population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08817-w.

Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient

Immortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of F_ST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.

Intense browsing by sika deer (Cervus nippon) drives the genetic differentiation of hairy nettle (Urtica thunbergiana) populations

Many studies have inferred the way in which natural selection, genetic drift and gene flow shape the population genetic structures, but very few have quantified the population differentiation under spatially and temporally varying levels of selection pressure, population fluctuation and gene flow. In Nara Park (6.6 km²), central Japan, where several hundred sika deer (Cervus nippon) have been protected for more than 1,200 years, heavily- or moderately-haired nettle (Urtica thunbergiana) populations have evolved probably in response to intense deer browsing. Here, we analysed the genetic structure of two Nara Park populations and five surrounding populations using amplified fragment length polymorphism markers. A total of 546 marker loci were genotyped from 210 individuals. A Bayesian method estimated 5.5% of these loci to be outliers, which are putatively under natural selection. Neighbour-joining, principal coordinates and Bayesian clustering analyses using all-loci, non-outlier loci and outlier loci datasets showed that the Nara Park populations formed a cluster distinct from the surroundings. These results indicate the genome-wide differentiation of the Nara Park populations from the surroundings. Moreover, these imply the following: (1) gene flow is limited between these populations and thus genetic drift is a major factor causing the differentiation; and (2) natural selection imposed by intense deer browsing has contributed to some extent to the differentiation. In conclusion, sika deer seems to have counteracted genetic drift to drive the genetic differentiation of hairy nettles in Nara Park. This study suggests that a single herbivore species could lead to genetic differentiation among plant populations.

Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot

Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with "resident" species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.

Genetic Diversity and Range Dynamics of Helleborus odorus subsp. cyclophyllus under Different Climate Change Scenarios

Research Highlights: The effects of climate change on habitat loss, range shift and/or genetic impoverishment of mid-elevation plants has received less attention compared to alpine species. Moreover, genetic diversity patterns of mountain forest herbaceous species have scarcely been explored in the Balkans. In this context, our study is the first that aims to examine Helleborus odorus subsp. cyclophyllus, a medicinal plant endemic to the southern part of the Balkan Peninsula. Background and Objectives: We compare its genetic diversity and structure along the continuous mountain range of western Greece with the topographically less structured mountains of eastern Greece, and predict its present and future habitat suitability, using several environmental variables. Materials and Methods: Inter Simple Sequence Repeat (ISSR) markers were used to genotype 80 individuals from 8 populations, covering almost the species’ entire distribution range in Greece. We investigated the factors shaping its genetic composition and driving its current and future distribution. Results: High gene diversity (0.2239–0.3319), moderate population differentiation (0.0317–0.3316) and increased gene flow (Nm = 1.3098) was detected. According to any GCM/RCP/climate database combination, Helleborus odorus subsp. cyclophyllus is projected to lose a significant portion of its current distribution by 2070 and follow a trend towards genetic homogenization. Conclusions: Populations exhibit in terms of genetic structure a west–east genetic split, which becomes more evident southwards. This is mainly due to geographic/topographic factors and their interplay with Quaternary climatic oscillations, and to environmental constraints, which may have a negative impact on the species’ future distribution and genetic composition. Pindos mountain range seems to buffer climate change effects and will probably continue to host several populations. On the other hand, peripheral populations have lower genetic diversity compared to central populations, but still hold significant evolutionary potential due to the private alleles they maintain.