Search Results (86)

The oil-bearing rose (Rosa damascena Mill.), traditionally cultivated in Bulgaria for centuries, and the rose oil produced from it are of major cultural and economic importance. Its distinctive fragrance and rich aromatic profile are highly valued worldwide. In this study, a set of 15 start codon-targeted (SCoT) molecular markers was used to evaluate the genetic diversity and relationships of 38 rose accessions. The analyzed materials included Bulgarian-bred R. damascena cultivars, a locally improved population (‘Population 5’), three oil-bearing species (Rosa alba L., Rosa gallica L., and Rosa centifolia L.), Romanian heritage roses, and an unidentified rose genotype from an old Bulgarian plantation (Rosa sp.). The SCoT primers yielded a cumulative count of 238 bands, with an average of 12.9 bands per primer. The range of diversity markers, such as PIC (0.20–0.78), number of different alleles (1.5–2.00), Shannon’s information index (0.24–0.69), and gene diversity (0.15–0.50), provided evidence of genetic differences among the examined accessions. Analysis of Molecular Variance (AMOVA) revealed higher genetic variation within groups (61%) than among the groups (39%). Multivariate analyses (UPGMA, PCoA, and STRUCTURE) resolved the accessions into major genetic clusters corresponding to their taxonomic identity or breeding history. The unidentified Rosa sp. formed a distinct genetic group, showing closer affinity to R. gallica. The locally improved R. damascena ‘Population 5’ exhibited higher genetic diversity than the Bulgarian cultivars. Overall, our results demonstrate the effectiveness of SCoT markers and the value of local and traditional rose germplasm as reservoirs of genetic diversity. The study provides a molecular framework to support breeding, conservation, and sustainable management of oil-bearing rose genetic resources. Full article

Sugar beet (Beta vulgaris L.) is an economically important crop that accounts for approximately 20% of global sugar production. The success of future breeding programs depends on the effective utilization of existing genetic resources. The aim of this study was to assess the genetic diversity and population structure of 192 sugar beet (Beta vulgaris L.) genotypes, including commercial cultivars and accessions obtained from the USDA gene bank, using SCoT and ISSR molecular markers, and to identify potential genetic resources for sugar beet breeding programs. In this study, a total of 192 sugar beet genotypes, including 187 accessions from the USDA (U.S. Department of Agriculture) gene bank and 5 commercial cultivars, were evaluated for genetic diversity using Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers. A total of 68 scorable bands were obtained from five SCoT and three ISSR primers, and all bands were found to be polymorphic (100% polymorphism). Parameters such as polymorphic information content (PIC), Nei’s genetic diversity, and Shannon’s index indicated a high level of variation within the gene pool, with SCoT markers being more informative than ISSR markers. Dendrogram analyses based on Nei’s genetic distance revealed that the populations were separated into two main groups, while the sub-clusterings contained broad genetic variation. STRUCTURE analysis identified four (K = 4) populations for the SCoT data and three (K = 3) populations for the ISSR data; the inclusion of a high number of individuals in the admixture population indicated extensive gene flow. Principal component analysis (PCA) revealed both homogeneous groups and differentiated genotypes contributing to within-population diversity. The results demonstrate that the combined use of SCoT and ISSR markers provides powerful and complementary tools for assessing genetic diversity in sugar beet. The findings provide a solid scientific basis for the development of new, high-yielding and high-quality sugar beet cultivars as well as for the conservation of existing genetic resources. Molecular data constitute an important reference for guiding sugar beet breeding programs and for the effective utilization of genetic resources. Full article

Rye (Secale cereale L.) is a small-grain cereal traditionally cultivated under low-input conditions, where locally adapted populations have contributed substantially to the maintenance of genetic diversity. Despite this importance, Greek rye germplasm has received limited attention at the molecular level. In the present study, 33 rye accessions, including gene bank landraces, locally cultivated populations and one commercial variety, were analyzed using inter-simple sequence repeat (ISSR), start codon-targeted (SCoT), and exon-based amplified polymorphism (EBAP) markers. All three marker systems generated high proportions of polymorphic loci and comparable estimates of expected heterozygosity, indicating considerable genetic variability within the studied material. Multivariate analyses revealed moderate population structuring and consistently identified a small number of genetically divergent accessions, most notably T-492, K-163, and K-166. No clear clustering according to geographical origin was detected, as in most cases of landraces or local populations. Taken together, the results provide a detailed molecular overview of Greek rye germplasm—which has never been performed before for Greek rye genetic material—and offer a useful basis for conservation priorities and future pre-breeding efforts. Full article

Lavender has been cultivated in Bulgaria for over a century. The high essential oil content and quality of Bulgarian lavender varieties have established the country as a leading global producer. Studies into the crop’s genetic diversity are essential for selecting varieties best suited to specific environmental conditions, maximizing resilience and yield. Therefore, identifying appropriate genetic markers to monitor lavender diversity is a key prerequisite for developing effective crop selection strategies, particularly in response to the challenges posed by global climate change. In this study, we evaluate the versatility of markers for assessing genetic diversity of lavender genotypes. A total of 96, 97 and 96 bands were recorded using the 13 Start Codon Targeted Polymorphism (SCoT), 13 Inter-Simple Sequence Repeat (ISSR) and 14 Cis-Element Aligned Polymorphism (CEAP) primers, respectively. All amplification programs used were successful in the studied genotypes. Additionally, four informative primers of each marker system were applied for assessment of the within-field genetic variability in two lavender plantations from Bulgaria. This is the first report on the combined use and comparison of CEAP, SCoT and ISSR primers in lavender genotypes in Bulgaria. Full article

Lavender (Lavandula angustifolia Mill.) is a traditional and economically important crop in Bulgaria. The cultivated areas are primarily planted with seven Bulgarian varieties: ‘Hemus’, ‘Druzhba’, ‘Sevtopolis’, ‘Yubileina’, ‘Raya’, ‘Hebar’, and ‘Karlovo’. Except for ‘Karlovo’, these cultivars are widely grown due to their proven agronomic performance and adaptability across different regions of the country. However, their genetic diversity and relationships have not been deeply examined. In this study, 13 Start Codon Targeted (SCoT) markers were used to assess the genetic diversity of those seven Bulgarian cultivars. This research provides the first report on the application of SCoT markers in lavender accessions. The results revealed considerable polymorphism, confirming the effectiveness of the SCoT marker system for L. angustifolia. The obtained data indicate moderate genetic diversity among the cultivars, supported by the effective number of alleles and polymorphic information content. Cluster analysis (UPGMA) and Principal Coordinates Analysis (PCoA) demonstrated clear genetic differentiation, grouping the cultivars according to their genetic proximity. These findings provide valuable baseline information for future selection, conservation, and genetic evaluation of Bulgarian lavender. Full article

The success of plant tissue cryopreservation strongly depends on maximizing explant survival during storage in liquid nitrogen and recovery, which requires species-specific protocol optimization and ongoing refinement. This study examined the effect of Plant Vitrification Solution 3 (PVS3) supplemented with nanoparticles (NPs) or melatonin (MEL) on the recovery of Lamprocapnos spectabilis (L.) Fukuhara explants after cryostorage. Treatments with ZnO + Ag NPs, as well as different MEL concentrations, were applied to evaluate their influence on explant survival, photosynthetic efficiency, and genetic stability. The highest recovery (40–44%) was obtained with PVS3 containing 50 mg L⁻¹ ZnO + 0.1% Ag NPs and PVS3 supplemented with 8 mg L⁻¹ MEL, which was 17.5–20% higher than in the control. These treatments, however, did not ensure the highest photosynthetic efficiency of recovered plants. PVS additives likely support recovery by slowing metabolism and reducing oxidative stress, with lower photosynthetic activity suggesting a lag phase in plastid regeneration. Using the Start Codon Targeted (SCoT) marker system, no significant genetic alterations were detected in recovered plants of any tested variant. These findings demonstrate the feasibility of optimizing cryopreservation protocols for L. spectabilis and encourage further research on combined NPs and MEL treatments or alternative nanocarriers. Full article

It is essential to introduce new cultivars to diversify the pomelo industry in China. This paper compared the agronomic and environmental performances of new Tabtim Siam (TS) and Xishi (XS) pomelos with the local cultivars (Red-fleshed Sweet (RS) and Shatian (ST)) in Dabu County. We have generally evaluated the phenological, physiological, fruit quality, stress resistance, and storage characteristics. Findings indicated that TS and XS grew up well, and the phenological stages were adjusted to the local conditions. They had a high pollen viability and equivalent photosynthetic capacity. XS and TS had the highest yield and good fruit quality in terms of higher edible rates, more juice rate, and balanced sugar–acid content. Both the introduced cultivars had greater cold resistance compared with the control with lower semi-lethal temperatures. Polyethylene film at low temperatures to preserve the quality of storage was effective. Compared with RS and ST, TS and XS had a higher price in the market economically. The use of molecular markers (SCoT and SRAP) was able to discriminate all cultivars, which proved genetic uniqueness. In summary, TS and XS have potential to be grown in the Meizhou area and provide high quality, good adaptability, and greater market potential. Full article

Introduction: Stevia rebaudiana Bertoni has recently gained significant attention due to the presence of intensely sweet yet low-calorie steviol glycosides (SGs) in its leaves, making it a promising natural sugar alternative with applications in the food, pharmaceutical, and cosmetics industries. The primary goal of this study was to determine whether generating somaclonal variation from plant material obtained by indirect regeneration results in further genetic changes identifiable using the SCoT marker (Start Codon Targeted). Methods: In the first stage, callus tissue was initiated from first-generation somaclones on MS medium supplemented with 4.0 mg/L 6-benzylaminopurine (BAP), 2.0 mg/L 1-naphthaleneacetic acid (NAA), and 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D). Their morphogenetic potential was analyzed on four media with different BAP and Kinetin concentrations. Donor plants, first and second generation somaclones, were also analyzed for genetic diversity using SCoT markers. Results: All first-generation somaclones demonstrated a very high callus initiation capacity, ranging from 95 to 100%. It was found that for most of the studied somaclones, the greatest number of shoots were developed by explants grown in a medium supplemented with 0.5 mg/L BAP and 0.25 mg/L Kin. The studied group of somaclones exhibits a high degree of polymorphism (55.2%). The analysis of genetic similarity of somaclones presented in the form of individual dendrograms indicates that in most cases, greater genetic diversity was revealed as a result of indirect regeneration in the first generation of somaclones compared to the second. Indirect organogenesis allows for the production of subsequent generations of genetically unstable somaclones, creating the potential for obtaining new phenotypic variants useful in plant breeding. Full article

The Chinese holly (Ilex chinensis Sims.), an evergreen tree species native to China, is distributed mainly in regions south of the Qinling Mountains and Huai River. This research aimed to characterize the molecular profiles and genetic relationships of 40 Chinese holly genotypes via inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphism markers. Genetic diversity analysis revealed that the ISSR markers detected 111 polymorphic bands from 13 primers, with a polymorphism rate of 88.10%. The analysis generated parameters such as the observed allele number (Na = 1.876), effective allele number (Ne = 1.461), Shannon’s information index (I = 0.271), and expected heterozygosity (H = 0.411). In comparison, the SCoT markers produced 65 polymorphic bands from the 6 primers, resulting in a 100% polymorphism rate, with Na = 2.000, Ne = 1.695, I = 0.393, and H = 0.575. Cluster analysis classified the 40 genotypes into two main clusters with genetic similarity coefficients of 0.69 (ISSR) and 0.55 (SCoT). The ISSR markers presented the greatest similarity between the ZSS and ZLS genotypes, whereas the ZZDH and ZWW genotypes presented lower similarity. Conversely, the SCoT markers identified ZZP and ZJDS as the most similar, with ZLJ and ZHX showing less similarity. These results provide a theoretical basis for hybrid breeding, germplasm innovation, and conservation strategies of Chinese holly in China. Full article

Background: Tissue culture might be a method supplementing traditional plant propagation in various fields, like agriculture, medicine, industry, and the active conservation of plant species. For the purpose of plant restoration, it is important that the obtained progenies are identical with the mother plants to ensure the true-to-typeness of the future population. Methods: In the present study, the stability of Aldrovanda vesiculosa regenerants obtained in vitro through phenotypic and genetic analysis was estimated. Clones of aldrovanda plants were cultivated in tissue culture in the 1/10 MS liquid medium under the same conditions for over a year, with five weeks of subculturing. Results: It was observed that two clones formed plants that displayed atypical growth structures, the shoots were shorter with many lateral shoots, and they had a lower fresh weight. They also formed fewer and smaller snap-traps, which, in the case of carnivorous plants, determines the capability of catching prey. The 35 in vitro regenerated plants and 5 specimens obtained from the natural habitat were subjected to genetic analyses with two molecular markers: start codon targeted (SCoT) polymorphism and sequence-related amplified polymorphism (SRAP). Despite the visible morphological variants, the genetic stability of all the regenerants with the individuals from natural stands was confirmed. All of them were monomorphic except three bands that were obtained for reference, where individuals were amplified with SCoT28 and me12-em13 SRAP primers. Conclusions: As shown in the presented research, it might be recommended to use different methods to evaluate the stability of in vitro cultivated plants. Full article

Ajuga bracteosa is a herb with high medicinal value and a low range of distribution. It is used in several herbal and traditional medicines, including diabetes. In the present study, we designed the methodology for the micropropagation of A. bracteosa from internodal segments. The highest shoot multiplication was achieved on Murashige and Skoog (MS) medium supplemented with 6-benzyl-amino-purine (BAP) (5.0 µM) + indole-3-acetic acid (IAA) (1.5 µM) + adenine sulphate (ADS) (15.0 µM), which produced the maximum number of 20.45 ± 0.12 shoots/explants with 6.43 ± 0.006 cm shoot length. Rooting in the microshoots was attained on half-strength MS medium containing indole-3-butyric acid (IBA) (1.5 µM), with the highest root number of 16.44 ± 0.015 roots/shoot, and root length of 2.25 ± 0.011 cm. To assess genetic fidelity, SCoT marker analysis was performed on nine randomly selected in vitro regenerated plantlets and the mother plant, all of which exhibited monomorphic banding patterns, confirming genetic stability. Scanning electron microscopy (SEM) reveals normal stomatal structure in the regenerated plants post-acclimatization, indicating successful physiological recovery. Furthermore, Gas Chromatography–Mass Spectrometry (GC-MS) analysis confirms the presence of major phytocompounds in both the in vitro regenerated plants and the mother plant, supporting the conservation of phytochemical integrity. Given the restricted distribution and overharvesting pressure on this species, the established protocol provides an efficient strategy for rapid, large-scale, and genetically stable propagation to support conservation and pharmaceutical utilization. Full article

Barnyard grass is the most problematic weed in paddy fields in Ningxia. Its substantial morphological variation complicates both identification and control, yet the genetic diversity of barnyard grass infesting paddy fields in Ningxia has not been thoroughly studied. In this research, we analyzed the genetic diversity of 46 barnyard grass populations from Ningxia’s paddy fields based on the assessment of morphological traits, DNA barcoding, and SCoT-targeted gene markers. Nine morphological traits were quantitatively analyzed, among which three phenological traits, i.e., leaf length, stem diameter, and plant height, exhibited notable variations. Correlational analysis revealed a positive relationship between morphological traits and multi-herbicide resistance profiles. To assess genetic diversity, four DNA barcodes (ITS, psbA, matK, and trnL-F) were used, among which ITS demonstrated the strongest potential in single-gene barcoding for barnyard grass species identification. Cluster analysis based on ITS barcode sequences was performed to group the populations into five main categories. Additionally, SCoT marker analysis using six primers was performed to classify the 46 barnyard grass samples into five groups. The results showed that the predominant barnyard grass species in Ningxia were E. colona, E. crus-galli var. Formosensis, E. crusgalli, E. oryzoides, and E. crusgalli var. Zelayensis, with E. colona being the most prevalent. The differences observed between the morphological and molecular marker-based classifications were method-dependent. However, both SCoT molecular marker technology and DNA barcoding contributed to identifying the genetic diversity of barnyard grass. Taken together, our study revealed significant morphological and genetic variations among barnyard grass populations, which correlated with herbicide sensitivity in Ningxia’s paddy fields, underscoring the necessity for an integrated weed management approach to combat this troublesome weed species. Full article

Background: Chrysanthemum is an economically important ornamental species whose genetic diversity assessment forms the foundation for effective breeding programs. Methods: Phenotypic characterization of 12 traits (7 quantitative and 5 qualitative traits) was conducted alongside SCoT marker analysis to assess genetic diversity and perform marker–trait association analysis in 65 chrysanthemum accessions. Results: Quantitative traits showed 14.81–26.43% variation (peduncle length most variable), while qualitative traits exhibited Shannon–Weiner indices of 0.23–2.28 (flower color most diverse). Phenotypic analyses consistently grouped accessions into two clusters. SCoT markers generated 160 bands (159 polymorphic; 6.957 bands/marker) with high PIC values (0.408–0.896). Molecular analyses also revealed two genetic groups, though with partial discordance to phenotypic clusters. Eight significant marker–trait associations were identified, linking SCoT28/3/30/31/35/20/14/36 to flowering duration, plant height, peduncle diameter, flower color, and pest resistance traits. Conclusions: The study revealed substantial diversity in local chrysanthemum germplasm, with SCoT markers effectively capturing genetic variation. While phenotypic and molecular groupings showed partial mismatch, identified marker–trait associations (e.g., SCoT28 linked to flowering duration) provide practical tools for marker-assisted breeding. Full article

In nature, orchid seed germination is extremely low, making in vitro asymbiotic seed germination essential for the propagation and conservation of endangered Vanda coerulea. This study optimized a micropropagation protocol and evaluated the genetic homogeneity of regenerated orchids. The synergistic effect of kinetin (KN) with auxins in the Mitra (M) medium best supported protocorm formation and seedling development. The highest shoot multiplication (5.62 ± 0.09) was achieved with 1.2 mg L⁻¹ KN and 0.6 mg L⁻¹ IBA (indole-3-butyric acid) in the medium. Enhanced leaf production (4.81 ± 0.37) was observed when 3.2 mg L⁻¹ KN was combined with 1.8 mg L⁻¹ IAA (indole-3-acetic acid), while root development was superior when 3.2 mg L⁻¹ KN together with 2.4 mg L⁻¹ IAA was incorporated in the medium. Anatomical sections confirmed well-developed leaf and root structures. Genetic fidelity assessment using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), inter-primer binding site (iPBS), and start codon targeted (SCoT) markers revealed 97.17% monomorphism (240/247 bands) and low Nei’s genetic distances (0.000–0.039), indicating high similarity among the regenerants. Dendrogram clustering was supported by a high cophenetic correlation coefficient (CCC = 0.806) and strong resolution in Principal Coordinate Analysis (PCoA) (44.03% and 67.36% variation on the first two axes). The Mantel test revealed a significant correlation between both ISSR and SCoT markers with the pooled marker data. Flow cytometry confirmed the genome stability among the in vitro-propagated orchids, with consistently low CV (FL2-A) values (4.37–4.94%). This study demonstrated the establishment of a reliable in vitro protocol for rapidly propagating genetically identical V. coerulea via asymbiotic seed germination. Full article

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus species and 28 cultivars of European plum. Compared to SCoT-only analyses, the SCoT–FaSt combination produced fewer total bands but a higher percentage of polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, and Shannon’s index. SCoT–FaSt markers generated bands across a broader size range, which made gel patterns less dense, enabling the more accurate detection of differentially amplified fragments. Neighbor-joining and principal component analyses confirmed that SCoT–FaSt markers provided sufficient phylogenetic resolution at both interspecific and intraspecific levels. The sequencing of 32 SCoT–FaSt amplicons revealed FaSt elements in 26 fragments, with SCoT primers preferentially annealing to GC-rich exonic and intergenic regions. Seventeen protein-coding and one RNA-coding gene were partially identified, with FaSt elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of FaSt elements between the Cerasus and Prunus subgenera. In silico findings suggest that FaSt elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT–FaSt marker system is effective for evaluating Prunus genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon. Full article