Search Results (21)

Avocado (Persea americana Mill.) is cultivated in a wide range of environments, from tropical and semitropical to subtropical regions. Its fruit, of high nutritional value, is increasingly demanded worldwide. Spain is the main European producer, but avocado cultivation in certain areas, such as the Canary Islands, requires the genetic identification of West-Indian rootstocks because they often show tolerance to low-quality water and soil salinization. In the present study, eight novel Retrotransposon-Based Insertion Polymorphism assays, derived from previously characterized inter-Primer Binding Site markers, have been developed and evaluated by multiplex PCR across 58 P. americana cultivars. The results showed 100% specificity and sensitivity in detecting the West-Indian genomic component, both in pure and hybrid avocado cultivars. This cost-effective and fast molecular tool provides a valuable resource for characterization and selection programs of avocado cultivars genetically related to the West-Indian horticultural race. Full article

Analysis of the genetic diversity of natural populations of economically valuable plants is important for conservation and selection strategies. In this study, the genetic diversity of 11 natural populations of Hippophae rhamnoides L.—sea buckthorn from different regions of Kazakhstan—was studied using Inter-Primer Binding Site Polymorphism (iPBS) markers based on conserved sequences of tRNA primer-binding sites (PBSs) that initiate retrotransposon replication. Universal PBS primers yielded reproducible and informative amplicons, forming unique profiles for each sample. Analysis of molecular variance showed that 60% of the total genetic variation was due to intrapopulation differences and 40% was due to interpopulation differentiation. The highest genetic diversity was found in the Shetlasty and Tersayryk sea buckthorn populations, whereas the Karatal and Topkain populations were characterised by minimal values, although unique alleles were observed in the latter population, indicating possible adaptation to local environmental conditions or genetic isolation. Principal coordinate analysis, UPGMA clustering, and Bayesian structure analysis (K = 4) confirmed geographical structuring. This study provides insights into the genetic structure of sea buckthorn populations in Kazakhstan and demonstrates the effectiveness of iPBS markers for assessing intraspecific diversity. The obtained results provide a basis for the conversation of H. rhamnoides gene pool and underscore the need for both in situ conservation of genetically rich populations and ex situ protection of vulnerable groups. Full article

This study investigated interspecific and intraspecific polymorphism in Rheum (Polygonaceae) from Kazakhstan using the inter-primer binding site (iPBS) retrotransposon marker system. The results revealed considerable variation in the level and nature of genetic polymorphism both within and among Rheum species and ecopopulations across different regions of Kazakhstan. Rh. compactum and the ecopopulation Rh. tataricum from the Zhambyl Region (ZH) exhibited the lowest levels of polymorphism, supporting their designation as conservation priorities. Genetic differentiation analysis among species and ecopopulations identified clear distinctions, resulting in the formation of well-defined clusters with high bootstrap support. Minimal genetic distances were observed between the two ecopopulations of Rh. tataricum, along with a high degree of intraspecific genetic homogeneity in Rh. compactum and Rh. nanum. A distinct genetic divergence between Rh. compactum and the other taxa was detected, reinforcing its status as a separate species rather than a synonym of Rh. altaicum. The iPBS markers proved effective for investigating genetic variation in Rheum, offering valuable insights for future studies aimed at understanding the evolutionary history of the genus. 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

Drought stress significantly impacts global agricultural productivity, necessitating the identification of resilient genotypes and genetic markers to develop stress-tolerant crops. This study evaluates 48 watermelon (Citrullus lanatus L.) genotypes under controlled drought conditions to assess their morphological, physiological, and molecular responses. Key parameters such as root length, plant height, stem diameter, SPAD index (Soil and Plant Analysis Development index), and MDA levels (Malondialdehyde) were measured. Genotypes W20, W48, W13, and W60 exhibited superior drought tolerance, characterized by enhanced biomass retention, water-use efficiency, and photosynthetic capacity. Correlation analysis revealed significant relationships among traits, such as a strong positive correlation between plant height and stem diameter (r = 0.84) and a negative correlation between MDA and root length (r = −0.99), underscoring the physiological trade-offs under stress. Molecular analyses using inter-primer binding site (iPBS) markers showed a high polymorphism rate (93.2%) and identified 18 markers significantly associated with drought-related traits. Markers iPBS-2239 and iPBS-2400 emerged as highly informative, offering the potential for marker-assisted breeding. This integrative approach highlights the complex mechanisms underlying drought tolerance in watermelons and provides valuable genetic resources and candidate genotypes for developing drought-resilient cultivars. These findings contribute to advancing breeding strategies to address the challenges of climate change and water scarcity in agriculture. Full article

The analysis of genetic diversity in natural populations of valuable medicinal plant species experiencing overexploitation is a key aspect of their natural conservation strategy. Mobile genetic elements and other interspersed repeats, which are major components of eukaryotic genomes, serve as effective tools for studying plant biodiversity and variability. The genetic diversity of four valuable medicinal plant Rhodiola rosea L. populations was investigated using the inter-repeat amplified PCR method with inter-priming binding sites (iPBSs) for genome profiling. At the interpopulation level, unique amplicons characteristic of specific R. rosea populations were identified. Molecular variance analysis revealed that the biodiversity of R. rosea populations in the Kazakh Altai region is 56% attributed to interpopulation differences and 44% to intrapopulation differences. It was shown that populations located in favorable environmental conditions have greater genetic diversity compared to those in extreme habitats. This study identified a high degree of polymorphism among R. rosea populations using the inter-repeat amplified PCR method. The genetic diversity of the populations ranged from 0.105 to 0.156, with an average heterozygosity of 0.134. The findings provide new insights into the population structure of R. rosea in the Kazakh Altai, enabling the identification of different genotypes, which will significantly complement traditional methods for conserving this valuable medicinal plant. Full article

Both morphological and molecular markers have been extensively used to evaluate genetic diversity; however, molecular markers are considered more reliable and can lead to improved reproductive efficiency. This study utilized inter-primer binding site (iPBS) markers to examine the genetic diversity and population structure of thirty mulberry accessions from the districts of Sahiwal and Faisalabad, Pakistan. These mulberry accessions belonged to three species: Morus nigra (n = 13), Morus alba (n = 12), and Morus rubra (n = 5). The use of nine iPBS primers in this study provided a comprehensive understanding of genetic diversity among the selected mulberry accessions. Nine iPBS primers were used in the study and generated 431 bands with allelic frequencies ranging from 21 to 75 and band sizes from 200 to 1500 base pairs. The primer 2230 showed the highest polymorphic information content (PIC) value of 0.47 and the highest Shannon’s information index (I = 0.53). The Morus nigra accessions had the highest levels of expected heterozygosity (He = 0.30), unbiased expected heterozygosity (µHe = 0.33), and Shannon’s information index (I = 0.45). The molecular variance analysis (AMOVA) revealed a high degree of genetic variation, as estimated by the pairwise PhiPT value of 0.21, which was significant at the p < 0.001 *** level. The neighbor joining tree, principal coordinate analysis, and structure analysis grouped the 30 mulberry accessions into four main clusters. The distinct grouping of accessions SWLS14, SWLS6, FSDS30, and SWLS7 validated their notable genetic distinctiveness. Overall, these findings contribute valuable insights into the genetic landscape of mulberry accessions, which are essential for conservation and breeding strategies. Full article

Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation. Full article

The adaptive potential and biochemical properties of the Amaranthaceae species make them promising for introduction into agriculture and markets, particularly in arid conditions. Molecular genetic polymorphism analysis is the most powerful tool for studying plant resources; therefore, the current study aimed to investigate the polymorphisms of allelic variations in the ARF and SOD gene families, as well as the genetic diversity of six Amaranthaceae species, using retrotransposon-based fingerprinting with the multi-locus EPIC-PCR profiling approach. Additionally, the iPBS PCR amplification was employed for genome profiling, revealing variations in genetic diversity among the studied Amaranthaceae samples. The observed genetic diversity in Amaranthaceae species contributes to their enhanced tolerance to adverse environmental conditions. The knowledge about the genetic diversity of genes crucial in plant development and stress resistance can be useful for the genetic improvement of cultivated Amaranthaceae species. Full article

Numerous factors can impact the efficiency of callus formation and in vitro regeneration in wheat cultures through the introduction of exogenous polyamines (PAs). The present study aimed to investigate in vitro plant regeneration and DNA methylation patterns utilizing the inter-primer binding site (iPBS) retrotransposon and coupled restriction enzyme digestion–iPBS (CRED–iPBS) methods in wheat. This investigation involved the application of distinct types of PAs (Put: putrescine, Spd: spermidine, and Spm: spermine) at varying concentrations (0, 0.5, 1, and 1.5 mM). The subsequent outcomes were subjected to predictive modeling using diverse machine learning (ML) algorithms. Based on the specific polyamine type and concentration utilized, the results indicated that 1 mM Put and Spd were the most favorable PAs for supporting endosperm-associated mature embryos. Employing an epigenetic approach, Put at concentrations of 0.5 and 1.5 mM exhibited the highest levels of genomic template stability (GTS) (73.9%). Elevated Spd levels correlated with DNA hypermethylation while reduced Spm levels were linked to DNA hypomethylation. The in vitro and epigenetic characteristics were predicted using ML techniques such as the support vector machine (SVM), extreme gradient boosting (XGBoost), and random forest (RF) models. These models were employed to establish relationships between input variables (PAs, concentration, GTS rates, Msp I polymorphism, and Hpa II polymorphism) and output parameters (in vitro measurements). This comparative analysis aimed to evaluate the performance of the models and interpret the generated data. The outcomes demonstrated that the XGBoost method exhibited the highest performance scores for callus induction (CI%), regeneration efficiency (RE), and the number of plantlets (NP), with R² scores explaining 38.3%, 73.8%, and 85.3% of the variances, respectively. Additionally, the RF algorithm explained 41.5% of the total variance and showcased superior efficacy in terms of embryogenic callus induction (ECI%). Furthermore, the SVM model, which provided the most robust statistics for responding embryogenic calluses (RECs%), yielded an R² value of 84.1%, signifying its ability to account for a substantial portion of the total variance present in the data. In summary, this study exemplifies the application of diverse ML models to the cultivation of mature wheat embryos in the presence of various exogenous PAs and concentrations. Additionally, it explores the impact of polymorphic variations in the CRED–iPBS profile and DNA methylation on epigenetic changes, thereby contributing to a comprehensive understanding of these regulatory mechanisms. Full article

Phytohormones are chemical compounds found naturally in plants that have a significant effect on their growth and development. The increase in research on the occurrence of mammalian sex hormones (MSHs) in plants has prompted the need to investigate the functions performed by these hormones in plant biology. In the present study, we investigated the effects of MSHs on DNA damage and DNA methylation of wheat (Triticum aestivum L.) during the seedling growth stage, using the CRED-iPBS (coupled restriction enzyme digestion/inter primer binding site) assay and iPBS analysis to determine DNA methylation status. Exogenous treatment with four MSHs (17-β-estradiol, estrogen, progesterone, and testosterone) was carried out at four different concentrations (0, 0.05, 0.5, and 5 µM). The highest genomic template stability (GTS) value (80%) was observed for 5 µM 17-β-estradiol, 0.5 µM testosterone, and 0.05 µM estrogen, while the lowest value (70.7%) was observed for 5 µM progesterone and 0.5 µM estrogen. The results of the CRED-iPBS analysis conducted on MspI indicate that the 0.05 µM estrogen-treated group had the highest polymorphism value of 40%, while the 5 µM progesterone-treated group had the lowest value of 20%. For HpaII, treatment with 0.5 µM 17-β-estradiol had the highest polymorphism value of 33.3%, while the group treated with 0.05 µM 17-β-estradiol and 0.05 µM progesterone had the lowest value of 19.4%. In conclusion, MSH treatments altered the stability of the genomic template of wheat plants and affected the cytosine methylation status at the seedling growth stage. Upon comprehensive examination of the results, it was seen that the employed methodology successfully detected alterations in cytosine methylation of genomic DNA (gDNA), as well as changes in the pattern of genomic instability. Full article

The use of mutagens in plant breeding is used to create new germplasm, increase agricultural yield, quality, and resistance to diseases and pests. Mutagens are physical or chemical factors that can alter the DNA or RNA structure of an organism, causing mutations above the expected level. One of the most common and potent chemical mutagens is EMS (ethyl-methane sulfonate), which produces point mutations in plants, but to a lesser degree can also cause the loss or deletion of a chromosomal region. This study used inter-primer binding site (iPBS) and coupled restriction enzyme digestion inter-primer binding site (CRED-iPBS) technique analysis to determine the effect of EMS mutagens on methylation rates in wheat genotypes at seedling growth stage. Treatments with five different EMS concentrations (0%; control, 0.1%, 0.2%, 0.3%, and 0.4%) at four different times (0; control, 3, 6, and 9 h) were used. Inter-primer binding site (iPBS) markers were employed to assess genomic instability and cytosine methylation in treated wheat. In seeds treated with EMS at different concentrations and times, the disappearance of regular bands and the formation of new bands due to the effects of the EMS mutagen revealed that genetic diversity exists. The CRED-iPBS analysis revealed that the 3 h + 0.1% EMS treatment produced the highest MspI polymorphism value (19.60%), while the 9 h + 0.1% EMS treatment produced the lowest value (10.90%). The mutagenic effects of EMS treatments had considerable polymorphism on a variety of impacts on the cytosine methylation and genomic instability of wheat. According to the current research, EMS mutagenesis may be a practical method for accelerating breeding programs to produce enough genetic diversity in wheat populations. Mutation-assisted breeding and the subsequent selection of desirable mutants using genetic markers may also be carried out in wheat utilizing an integrated strategy. Full article

Wheat, which is scientifically known as Triticum aestivum L., is a very nutritious grain that serves as a key component of the human diet. The use of mutation breeding as a tool for crop improvement is a reasonably rapid procedure, and it generates a variety that may be used in selective breeding programs as well as functional gene investigations. The present experiment was used to evaluate the potential application of a conventional chemical mutagenesis technique via sodium azide (NaN₃) for the germination and seedling growth stage in wheat. Experiments with NaN₃ mutagenesis were conducted using four different treatment periods (0, 1, 2, and 3 h) and five different concentrations (0, 0.5, 1, 1.5, and 2 mM). The genomic instability and cytosine methylation of wheat using its seeds were investigated after they were treated. In order to evaluate the genomic instability and cytosine methylation in wheat that had been treated, interprimer binding site (iPBS) markers were used. The mutagenic effects of NaN₃ treatments had considerable polymorphism on a variety of impacts on the cytosine methylation and genomic instability of wheat plants. The results of the experiment showed considerable changes in the iPBS profiles produced by the administration of the same treatments at different dosages and at different times. Coupled restriction enzyme digestion interprimer binding site (CRED-iPBS) assays identified changes in gDNA cytosine methylation. The highest polymorphism value was obtained during 1 h + 2 mM NaN₃, while the lowest (20.7%) was obtained during 1 h + 1.5 mM NaN₃. Results showed that treatments with NaN₃ had an effect on the level of cytosine methylation and the stability of the genomic template in wheat plants in the germination stage. Additionally, an integrated method can be used to for mutation-assisted breeding using a molecular marker system in wheat followed by the selection of desired mutants. Full article

Representatives of the Crassulaceae family’s genus Rhodiola are succulents, making them distinctive in a changing environment. One of the most significant tools for analyzing plant resources, including numerous genetic processes in wild populations, is the analysis of molecular genetic polymorphism. This work aimed to look at the polymorphisms of allelic variations of the superoxide dismutase (SOD) and auxin response factor (ARF) gene families, as well as the genetic diversity of five Rhodiola species, using the retrotransposons-based fingerprinting approach. The multi-locus exon-primed intron-crossing (EPIC-PCR) profiling approach was used to examine allelic variations in the SOD and ARF gene families. We implemented the inter-primer binding site (iPBS) PCR amplification technique for genome profiling, which demonstrated a significant level of polymorphism in the Rhodiola samples studied. Natural populations of Rhodiola species have a great capacity for adaptation to unfavorable environmental influences. The genetic variety of wild populations of Rhodiola species leads to their improved tolerance of opposing environmental circumstances and species evolutionary divergence based on the diversity of reproductive systems. Full article

This study investigated the genetic diversity and population structure of 63 genotypes from Turkish bread wheat germplasm using iPBS-retrotransposons primers. The thirty-four iPBS primers produced a total of 1231 polymorphic bands, ranging from 8 (iPBS-2375) to 60 (iPBS-2381) alleles per marker, with an average number of 36.00 alleles. The polymorphism information content (PIC) per marker varied between 0.048 (iPBS 2087) and 0.303 (iPBS 2382), with an average of 0.175. The numbers of effective alleles (ne), genetic diversity of Nei (h), and Shannon’s information index (I) value were calculated as 1.157, 0.95, and 0.144, respectively. The greatest genetic distance (0.164) was between Eastern Anatolia Agricultural Research Institute genotypes and Çukurova Agricultural Research Institute genotypes. The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram placed the 63 wheat genotypes into three clusters. The percentage of genetic diversity explained by each of the three main coordinates of the basic coordinate analysis was determined to be 44.58, 12.08, and 3.44, respectively. AMOVA (Analysis of Molecular Variance) showed that the variation within populations was 99% and that between populations was 1%. The result of genetic structure analysis suggests that the greatest value of K was calculated as 3. The F-statistic (Fst) value was determined as 0.4005, 0.2374, and 0.3773 in the first to third subpopulations, respectively. Likewise, the expected heterozygosity values (He) were determined as 0.2203, 0.2599, and 0.2155 in the first, second, and third subpopulations, respectively. According to the information obtained in the study, the most genetically distant genotypes were the G1 (Aksel 2000) and G63 (Karasu 90) genotypes. This study provided a deep insight into genetic variations in Turkish bread wheat germplasm using the iPBS-retrotransposons marker system. Full article