Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data.

Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.

Essential Oil Composition of Five Thymus Species from Bulgaria.

In this study, the essential oil composition of five Thymus species, belonging to Sect. Hyphodromi (A. Kerner) Halácsy - Thymus atticus Celak., T. leucotrichus Halácsy, T. striatus Vahl, T. zygioides Griseb. and T. perinicus (Velen.) Jalas. was studied by GC/MS/FID. T. atticus, T. leucotrichus, and T. striatus were characterized by high amounts of sesquiterpenoids (57.7, 78.9 and 79.7 %, respectively) with ß-caryophyllene and caryophyllene oxide as the main constituents. Aromatic compounds (61.2 %) were the most abundant group in T. zygioides essential oil, with thymol (51.2 %) as the principal component. The essential oil from the endemic species T. perinicus contained almost equal amounts of monoterpenoids (37.8 %) and aromatic compounds (36.0 %) with borneol (17.9 %) and thymol (20.9 %) as the major components. The obtained results revealed the existence of new chemotypes of T. atticus (caryophyllene oxide/ß-caryophyllene), T. leucotrichus (ß-caryophyllene/elemol/germacrene D) and T. striatus (ß-caryophyllene/germacrene D/caryophyllene oxide). The essential oil content of endemic T. perinicus is reported for the first time. Principal component analysis (PCA) and cluster analysis (CA) were used to investigate the variations in the essential oils of different Thymus species from Sect. Hyphodromi (A. Kerner) Halácsy.

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.

DNA Barcoding Study of Representative Thymus Species in Bulgaria.

We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers-matK, rbcL, trnH-psbA and ITS-were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward-morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.

Metabolic Profiles, Genetic Diversity, and Genome Size of Bulgarian Population of Alkanna tinctoria.

Alkanna tinctoria (L.) Tausch Boraginaceae is a medicinal plant whose root is used for its antimicrobial and anti-inflammatory properties. A. tinctoria roots have been subject to numerous studies. However, the aerial parts have been explored less. The objective of the present study was to compare the chemical profile of aerial parts and roots as well as the total alkannin content in roots of 11 populations of the species from different floristic regions of Bulgaria. Methanolic extracts from 22 samples were analyzed by GC/MS. Phenolic, fatty, and organic acids, sterols, polyols, fatty alcohols, and sugars were identified. Ononitol (4-O-methyl-myo-inositol) was found as the main compound in the aerial parts. The total alkannin content in the roots was evaluated by the spectrophotometric method and compared with that of the commercial product. Populations with high alkannin content and rich in other bioactive compounds were identified. A relatively low genetic diversity in the studied populations was observed. The present study is the first comprehensive study on metabolite profiles and genetic diversity of the Bulgarian populations of A. tinctoria. The occurrence of ononitol in the aerial parts of the species is reported for the first time, as well as the phenolic acid profiles of the species in both aerial parts and roots. The results showed that aerial parts of the plant are also promising for use as a source of valuable biologically active substances.

On the Reproductive Potential in Primula veris L. (Primulaceae): Embryological Features, Pollen and Seed Viability, Genetic Diversity.

Primula veris (Primulaceae) is a valuable medicinal plant. The main characteristics for assessing the reproductive potential (embryological features; mode of reproduction; pollen and seed viability) and the genetic diversity of populations of the species from Bulgaria were studied. The anthers are tetrasporangiate. Their wall development follows the Dicotyledonous-type and consists of: epidermis, a fibrous endothecium, an ephemeral middle layer and a secretory (glandular) tapetum. After meiosis in pollen mother cells and simultaneous microsporogenesis tetrahedral tetrads are formed predominantly in the anthers. Many ovules (approximately 20) develop in the unilocular ovary and are anatropous, tenuinucellate and bitegmic. The embryo sac (ES) develops after Polygonum (monosporic)-type from the chalazal cell of linear megaspore tetrad in the ovule. After double fertilization, a Caryophyllad-type embryo and initially nuclear endosperm form. In the studied populations, high pollen viability of more than 95% was established. Extremely low viability (about 4%) of the seeds obtained from natural populations was established. The results reveal P. veris to be a predominantly amphimictic (sexually reproducing) species, although rare vegetative propagation is also observed. As a result of this study, essential data were obtained about the reproductive structures and processes and for assessing the reproductive potential of P. veris.

Influence of the Land Use Type on the Wild Plant Diversity.

Studies on the impact of agricultural practices on plant diversity provide important information for policy makers and the conservation of the environment. The aim of the present work was to evaluate wild plant diversity across the agroecosystems in two contrasting regions of Bulgaria; Pazardzhik-Plovdiv (representing agroecosystems in the lowlands) and Western Stara Planina (the Balkan Mountains, representing agroecosystems in the foothills of the mountains). This study conducted a two-year assessment of plant diversity in different types of agricultural and forest ecosystems, representing more than 30 land use types. Plant diversity, measured by species number, was affected by the land use type only in Pazardzhik-Plovdiv region. More pronounced was the effect of the groups of land use types on the diversity, measured by the mean species number per scoring plot. Climatic conditions, measured by 19 bioclimatic variables, were the most important factor affecting plant species diversity. Six bioclimatic variables had a significant effect on the plant diversity, and the effect was more pronounced when the analysis considered pooled data of the two regions. The highest plant diversity was found on grazing land with sparse tree cover, while the lowest one was in the land use types representing annual crops or fallow. The study also established a database on weed species, relevant to agriculture. A number of common weeds were found in the Pazardzhik-Plovdiv region, while the most frequent species in the Western Stara Planina region were indigenous ones. Overall, the natural flora of Western Stara Planina was more conserved; eleven orchid species with conservation significance were found in the pastures and meadows in that region. The present study is the first attempt in Bulgaria to characterize the plant diversity across diverse agroecosystems representing many different land use types and environmental conditions. The results can contribute to nature conservation, biodiversity, and the sustainable use of plant resources.

Genetic differentiation of the Western Capercaillie highlights the importance of South-eastern Europe for understanding the species phylogeography.

The Western Capercaillie (Tetrao urogallus L.) is a grouse species of open boreal or high altitude forests of Eurasia. It is endangered throughout most mountain range habitat areas in Europe. Two major genetically identifiable lineages of Western Capercaillie have been described to date: the southern lineage at the species' southernmost range of distribution in Europe, and the boreal lineage. We address the question of genetic differentiation of capercaillie populations from the Rhodope and Rila Mountains in Bulgaria, across the Dinaric Mountains to the Slovenian Alps. The two lineages' contact zone and resulting conservation strategies in this so-far understudied area of distribution have not been previously determined. The results of analysis of mitochondrial DNA control region sequences of 319 samples from the studied populations show that Alpine populations were composed exclusively of boreal lineage; Dinaric populations of both, but predominantly (96%) of boreal lineage; and Rhodope-Rila populations predominantly (>90%) of southern lineage individuals. The Bulgarian mountains were identified as the core area of the southern lineage, and the Dinaric Mountains as the western contact zone between both lineages in the Balkans. Bulgarian populations appeared genetically distinct from Alpine and Dinaric populations and exhibited characteristics of a long-term stationary population, suggesting that they should be considered as a glacial relict and probably a distinct subspecies. Although all of the studied populations suffered a decline in the past, the significantly lower level of genetic diversity when compared with the neighbouring Alpine and Bulgarian populations suggests that the isolated Dinaric capercaillie is particularly vulnerable to continuing population decline. The results are discussed in the context of conservation of the species in the Balkans, its principal threats and legal protection status. Potential conservation strategies should consider the existence of the two lineages and their vulnerable Dinaric contact zone and support the specificities of the populations.