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Fusarium oxysporum f. sp. pisi (Fop) is a highly destructive root rot pathogen for the pea (Pisum sativum L.) plant. In this study, the presence of F. oxysporum isolates was detected during the 2020–2021 growing season in plants showing symptoms of root rot in provinces of Turkey (Bursa, Afyonkarahisar, İzmir and Aydın) important for pea production. The pathogen was identified by its colony growth on various media, morphological characteristics and, molecular characterization based on DNA sequencing and SCoT markers. The pathogenicity of 183 isolates obtained from the roots of disease symptomatic plants was tested after artificial inoculation of pruned roots of seedlings by dipping in a conidia suspension of the isolates. Disease severity was scored and the length of brown lesions on the stem, extending from the base, was measured for each isolate. The isolates showed very large variation (0%-80%) for disease severity. A total of 50 isolates showing high stem-lesion lengths within different disease severity ranges were selected and evaluated for their effect on plant growth parameters such as plant height, number of seeds per pod and number of pods per plant. There were significant positive correlations between the reduction (%) in plant height and lesion length, and disease severity. These isolates can potentially cause yield losses in Turkey's pea cultivation based on the measured stem lesions which could be an indication of the pathogenicity of different Fop isolates. New information about pathogenic variability in Fop isolates from Turkey will be valuable for detecting races of this pathogen and resistance of pea genotypes. [ABSTRACT FROM AUTHOR]

High-altitude regions like the Himalaya, where various slopes are present on a very small spatial scale, are one of the best natural laboratories for investigating how genetic diversity and population structure are distributed across altitudinal gradients. In this study, we investigate the magnitude of genetic diversity and population structure of Rhododendron anthopogon D.Don along an altitudinal gradient in the Kashmir Himalaya. We used the start codon targeted (SCoT) marker to evaluate the genetic diversity and differentiation between different populations across five sites along an altitudinal gradient ranging from 3200 to 4000 m (amsl). Our results demonstrate that the magnitude of genetic diversity differs among the populations of R. anthopogon along the altitudinal gradient. We observed a decreasing trend in genetic diversity with increasing altitude from site-1 to site-3 (3200 to 3600 m), and an increasing trend from site-4 to site-5 (3601 to 4000 m). Furthermore, we also observed the highest genetic diversity at upper altitude (site-5) and the lowest at mid-altitude (site-3). Our results reveal a high genetic differentiation (Gst = 0.7349) and a low gene flow (Nm = 0.1804) among the populations. Analysis of molecular variance (AMOVA) reveals 71% variation among the populations and 29% variation within the populations. We also reveal positive associations between geographic and genetic distances, indicating isolation by distance effect across all altitudes. STRUCTURE and cluster analysis divided all the populations of R. anthopogon into five clusters according to their geographical location. Overall, the study adds to our understanding that altitude is the major driver of genetic variation and differentiation between populations of R. anthopogon which may help increase its range under ongoing projected climate change. Our study also reveals that populations at higher altitudes are not genetically isolated, suggesting that they might be an essential source for migration in the era of climate change. [ABSTRACT FROM AUTHOR]

Maize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Egyptian clover (Trifolium alexandrinum) has received limited attention regarding its genetic diversity, rendering it susceptible to climate change. To develop resilient Berseem cultivars, exploring its genetic resources is vital for enhancing the diversity within its germplasm, thereby optimizing breeding programs. The examination of 24 Berseem accessions. Using three different molecular marker types; Inter-Simple Sequence Repeat (ISSR) (10 primers), Start Codon Targeted polymorphism (SCoT) (22 primers), and Sequence-Related Amplified Polymorphism (SRAP) (17 primer combinations) revealed a high genetic variability. ISSR markers had the highest polymorphism rate (82.2%) compared to SCoT (69.6%) and SRAP (65.2%). Unweighted Pair Group Method with Arithmetic Mean clustering analysis divided the studied accessions into two major groups, supported by STRUCTURE analysis, which also split samples into two subpopulations (∆K = 2). Additionally, this classification was verified by both principal component analysis and a heat map. The study underscores the importance of Berseem's genetic diversity in crop development and breeding, with ISSR markers offering valuable insights due to their high polymorphism. Despite the diverse geographic origins of the accessions, the lack of geographic clustering implies significant genetic mixing, possibly because of high outcrossing facilitated by insect pollination or self-incompatibility. The combined use of multiple markers deepens our understanding of Berseem's genetics by providing more detailed and comprehensive coverage of the clover genome, allowing for increased resolution, validation of results, and a holistic perspective on the genomic landscape, furthermore, identifying and recommending specific Berseem accessions (NGB-43724, NGB-19680, Gemeiza1, and Giza6) as prospective candidates for future breeding programs in Egypt. [ABSTRACT FROM AUTHOR]

Sea buckthorn (Hippophae rhamnoides), a hardy deciduous shrub of the family Elaeagnaceae, is known for its economic and ecological importance due to its wide use in medicine, food, windbreaks, and sand fixation. In this study, the first genetic linkage map of H. rhamnoides was constructed based on an F1 population (H. rhamnoides subsp. mongolica 'wulangemu' × H. rhamnoides subsp. sinensis 'wucixiong') by using start codon targeted (SCoT), sequence-related amplified polymorphism (SRAP), and simple sequence repeat (SSR) markers. The linkage map contained 1143 markers with a total length of 1889.46 centimorgans (cM), including 12 linkage groups (LG) and covering 97.17% of the estimated genome, with an average marker density of 1.67 cM. According to the phenotypic variation analysis, 61 QTLs were identified. Among these QTLs, there were 18 QTLs for seedling height, 27 QTLs for ground diameter, two QTLs for primary branching angle, 11 QTLs for leaf width, and 3 QTLs for leaf shape index. The range of phenotypic variation explained by these QTLs was 10.7 ~ 21.9%. The QTLs identified by high-density linkage mapping reported in this study will be useful for the molecular breeding of sea buckthorn. [ABSTRACT FROM AUTHOR]

In light of the multitude of olive trees cultivated and the lack of the genetic diversity of available genotypes to select varieties and lines that are characterized by high diversity and better performance under the corresponding conditions, A comparison analysis of the genotyping and morphological characteristics of eight olive cultivars growing in Saudi Arabia's Al-Jouf region was conducted and analyzed. Morpho-anatomical and chemical characteristics along with both inter-simple-sequence repeats (ISSRs) and start-codon-targeted (SCoT) markers were used to evaluate the genetic diversity among eight olive varieties in Al-Jouf, Saudi Arabia. Analyses of 27 morphological, chemical, and anatomical characteristics concluded the existence of genetic differences among the studied varieties. Moreover, six ISSR and eight SCoT primer combinations produced a total of 48 loci, of which 18 (10 ISSR and 8 SCoT) were polymorphic. The average polymorphism information content (PIC values of 0.48 and 0.44, respectively) and marker index (MI of 0.79 and 0.48, respectively) detected for ISSR and SCoT markers revealed the prevalence of high genetic diversity among the studied olive varieties. Based on chemical and anatomical characteristics and the selected molecular markers, the eight olive cultivars were grouped into two distinct clusters. Clusters in the adjacent joint dendrogram produced using ISSR, SCoT and combined data were similar, and grouped all individuals into two groups. However, the dendrogram generated on the basis of SCoT separated individuals into subgroups containing at least two varieties. The findings showed that both methods were effective in assessing diversity, and that SCoT markers can be used as a reliable and informative method for assessing genetic diversity and relationships among olive varieties and can serve as a complementary tool to provide a more complete understanding of the genetic diversity available in Olea europaea populations in Saudi Arabia. [ABSTRACT FROM AUTHOR]

Corylus avellana L. stands as one of the world's most coveted nuts, thriving in the wild within the Fandoguloo forests of Iran's Ardabil province and showcasing remarkable diversity in this region. To assess the distribution of genetic diversity within and between populations, 78 genotypes from various regions of Iran, including Ardabil, Arasbaran, and Miyaneh, underwent analysis using Start Codon Targeted (SCoT) polymorphism. Additionally, the phytochemical characteristics of Corylus avellana L., such as ash, taxol, total phenol, palmitic acid, fiber, palmitoleic acid, carbohydrate, stearic acid, flavonoid, oleic acid, linoleic acid, fat, antioxidant compounds, and total phenol, were examined. The results revealed that 15 SCoT primers amplified 165 polymorphic polymerase chain reaction fragments, with the SC3 and SC21 primers exhibiting the highest and lowest polymorphic information content, respectively. The calculated marker index for the primers ranged from 2.6 to 6.1. The Ardabil population boasted the highest allele frequency, with a 100% polymorphism rate across all studied primers. The primers SC21, SC20, and SC5 showed the highest polymorphic rates among the populations with 14 fragments. The gene flow within populations was 0.4, whereas the gene flow between populations was 0.7, and the fixation index (Fst) was 0.4. This research underscores the effectiveness of the SCoT marker in gauging the genetic diversity of C. avellana, making it a promising foundation for future research on the population and evolutionary genetics of this economically significant species. [ABSTRACT FROM AUTHOR]

Petroselinum crispum (Mill.) Nym. ex A.W. Hill (Parsley) is a culinary and medicinal vegetable of the family Apiaceae, which has been used by humans since ancient time. A molecular genetic diversity study was conducted on 10 Iranian populations of P. crispum using start codon targeted (SCoT) molecular markers to investigate infraspecific genetic diversity and population structure. The nuclear genomes extraction were performed using the cetyltrimethylammonium bromide (CTAB) protocol, then amplified using 10 SCoT primers. We found a large amount of population genetic differentiation index (GST) and total genetic difference in the pooled populations (HT) among the examined populations, which were supported by HS, NM. Additionally, we detected a significant genetic diversity (PhiPT = 0.755, P = 0.001) among the populations and their individuals by the analysis of molecular variance (AMOVA) test, in which its great proportion was assigned to among populations. We detected the largest amounts of genetic polymorphism in populations 1 and 5, while a reverse condition was observed for population 7. We found four genotype groups among the populations that was similar with phytogeographic mapping. The level of genetic divergence between populations (PhiPT) of each genotype was relatively low. This species produce protandrous florets and cross-pollination plays a significant role in seed production. Therefore, the genetic structure of genotypes must be heterogeneous. In Iran, the genetic structure of all genotypes was nearly homogenous which resulted from a flat rate of gene flow, which agreed with our estimated amount of NM (0.13). We supposed a range of isolation mechanisms including, isolation by distance, isolation by environment, isolation by ecology, and isolation by resistance act as driving forces to create high genetic differentiation among the parsley populations. These genotypes can be used for future genetic and breeding research to develop new cultivars can survive under biotic and abiotic stresses and yield high biomass. [ABSTRACT FROM AUTHOR]

Concerns about food security worldwide have been raised due to the adverse impacts of climate change on agricultural productivity. Utilizing wild relatives of cultivated plants in breeding schemes is a potential solution to address the abovementioned challenges. Wild relatives refer to indigenous plant species that share genetic ancestry with recently cultivated plants. The capacity of plants to withstand abiotic stresses and enhance crop yield stability in cold and arid environments renders them a valuable prospective resource for breeding programs. Molecular markers are employed to assess the genetic variability of cultivated plants and their wild relatives under investigation. This study employed a set of five primers derived from ISSR (Inter Simple Sequence Repeats) and SCoT (Start Codon Targeted) to assess comparative research between cultivated species and their wild relatives from three families: Apiaceae (Apium gravolens L., A. leptophyllum (Pers.) F.Muell., Daucus carota L.& D. litoralis Sm.), Asteraceae (Lactuca sativa L. & L. serriola L.) and Brassicaceae (B. oleracea L., Brassica tourneforttii Gouan., Raphanus sativus L. & R. raphanistrum L.). The ISSR technique yields approximately 206 bands, whereas the SCoT primers generate approximately 207 bands. The ISSR primers yielded 169 polymorphic bands, exhibiting a polymorphism rate of 82.04%, whereas the SCoT primers produced 169 polymorphic bands with a polymorphism rate of 81.64%. The Brassicaceae has been found to exhibit the highest resolving power (RP) of 48.25, as determined by ISSR. The primary objective of DNA barcoding is to create a communal database of DNA sequences that can be utilized to identify organisms and clarify their taxonomic classification. The findings indicate that the internal transcribed spacer (ITS) regions exhibit high efficacy as a DNA barcoding tool. Overall, the results obtained from two molecular markers and DNA barcoding analyses suggest a significant degree of genetic diversity and relatedness among the cultivated taxa and their wild relatives examined in this study. [ABSTRACT FROM AUTHOR]

Parrotia persica (Hamamelidaceae) is a relict tree species restricted to the Hyrcanian district of Iran and Azerbaijan. Parrotia had a wide Eurasian distribution before the Pleistocene glaciations and the western Eurasian P. persica diverged from its East Asian sister species P. subaequalis during the Miocene. We investigated infraspecific genetic diversity and structure in 10 populations of P. persica using SCoT molecular markers. We determined a significant genetic diversity in the genomic DNA using AMOVA, which mainly to diversity among populations. Moreover, high levels of genetic differentiation (Gst), total genetic variation (Ht), and a low rate of gene flow were recorded between populations. In some populations, high levels of genetic polymorphism resulted from frequent mutations in their members. The Mantel test showed a significant correlation between genetic diversity and geographic distance. We found three genotype groups among the populations using STRUCTURE and clustering analyses. These genotypes did not conform to specific distribution patterns. Our results indicated that fragmented and small-sized populations, a flat rate of gene flow, a low rate of mutations, and the breeding system in Parrotia led to high levels of population differentiation along with a nearly uniform genetic structure in most populations. Three main diversity centers exist for Parrotia in Hyrcanian forests, which are of importance for conservation strategies. A comparison with previously published population genetic patterns in Hyrcanian relict tree species (Zelkova Spach and Pterocarya Nutt. ex Moq.) suggests that these have different genetic structures with higher rates of gene flow between populations. The detected genotypes can be used to generate new genotypes by cross pollination, and also they can cultivate as avenue trees and parks in urban areas around each genotype to conserve biodiversity in this species. [ABSTRACT FROM AUTHOR]

Background Bigfin squid is one of the economically important seafood resources in Vietnam's fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box--derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. Results Con Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. Conclusions For the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species. [ABSTRACT FROM AUTHOR]

Spinach seeds were irradiated with gamma-rays after that soaked in zinc oxide nanoparticles (ZnO–NPs) at 0.0, 50, 100 and 200 ppm for twenty-four hours at room temperature. Vegetative plant growth, photosynthetic pigments, and proline contents were investigated. Also, anatomical studies and the polymorphism by the SCoT technique were conducted. The present results revealed that the germination percentage was at the maximum values for the treatment of 100 ppm ZnO–NPs (92%), followed by 100 ppm ZnO–NPs + 60 Gy (90%). The application of ZnO–NPs resulted in an enhancement in the plant length. The maximum of chlorophylls and carotenoids content was recorded in the treatment, 100 ppm ZnO–NPs + 60 Gy. Meanwhile, the irradiation dose level (60 Gy) with all ZnO–NPs treatments increased proline content and reached its maximum increase to 1.069 mg/g FW for the treatment 60 Gy combined with 200 ppm ZnO–NPs. Also, the anatomical studies declared that there were variations between the treatments; un-irradiated and irradiated combined with ZnO–NPs plants which reveal that the leave epidermal tissue increased with 200 ppm ZnO–NPs in both the upper and lower epidermis. While irradiated plants with 60 Gy combined with 100 ppm ZnO–NPs gave more thickness of upper epidermis. As well as SCoT molecular marker technique effectively induced molecular alterations between the treatments. Where, SCoT primers targeted many new and missing amplicons that are expected to be associated with the lowly and highly expressed genes with 18.2 and 81.8%, respectively. Also, showed that the soaking in ZnO-NPs was helped for reducing molecular alteration rate, both spontaneous and induced by gamma irradiation. This nominates ZnO–NPs as potential nano-protective agents that can reduce irradiation-induced genetic damage. [ABSTRACT FROM AUTHOR]

An efficient shoot regeneration protocol has been developed for Thottea siliquosa (Lamk.) Ding Hou. via indirect shoot regeneration from root explants. Roots were collected from 45-day-old in vitro rooted shoots and cultured on Murashige and Skoog (MS) medium supplemented with various plant growth regulators for callus induction. Optimum callus induction (93%) was observed on 3.0 mg/l Kinetin (KN) and 1.0 mg/l 2, 4-Dichlorophenoxyacetic acid (2, 4- D). The highest shoot induction response from calli was obtained on 0.5 mg/l N6–Benzyladenine (BA) and 0.2 mg/l α-Naphthaleneacetic (NAA). Here, 100% of cultures responded with a mean number of 20.3 shoots per unit calli. The best rooting (90% induction with 20.8 roots per shoot) of shoots was obtained on half-strength MS medium supplemented with 1.0 mg/l Indole-3-butyric acid (IBA). The rooted shoots were acclimatized and transferred to the field with 92% success. The prolonged subculture of calli resulted in its decreased regeneration potential. The clonal fidelity of regenerated plants and mother plants analyzed by Start Codon Targeted (SCoT) primers revealed the genetic similarity between them. The field established in vitro propagated plants showed higher total polyphenol and flavonoid content and total antioxidant capacity than the field grown mother plant and root derived callus. The DPPH radicle scavenging activity showed higher antioxidant activity in field grown plants than the in vitro cultured plants. The in vitro regeneration protocol developed here will be utilized for the mass multiplication and genetic transformation of this medicinal plant. Key message: An efficient micropropagation protocol via root derived callus mediated shoot organogenesis was developed for Thottea siliquosa. The comparison of phytochemicals and antioxidant activity of callus, roots of in vitro and mother plants was studied. [ABSTRACT FROM AUTHOR]

Flemingia strobilifera is a rare phytochemically sound ethnomedicinal plant with a rich source of 2-Methoxy-4-vinyl phenol (2M4VP), a medicinally and industrially important compound. It has potential anti-cancerous and anti-inflammatory activities. The plant is a flavoring agent due to its rich aroma in alcoholic beverages, coffee, fragrances, smoke flavors, etc. All these plant properties grabbed the attention of mankind to capitalize on them. Unsustainable plant exploitation pushed it to the quagmire of becoming rare. We have successfully developed an efficient regeneration protocol using nodal stem segments to conserve medicinally important plant species. Murashige & Skoog (MS) medium fortified with BAP of 2.0 mg/l induced a maximum of 9.00 shoot buds from the nodal segments. BAP of 2.0 mg/l in combination with 0.5 mg/l of IBA was very effective in further increasing the shoots with a maximum of 14 shoots per explant and a shoot length of 6.26 cm. Optimum rooting of 81% was achieved on media containing 1.5 mg/l of IBA with a maximum of 17.78 roots per shoot. PCR amplification with SCoT primers reveals that all the regenerated plants are true to type with the mother plant and confirms the retention of genetic fidelity. Also, the GCMS evaluation of the 2M4VP levels confirmed the presence of chemical homogeneity between regenerated and elite mother plants. Key message: Flemingia strobilifera is an important medicinal plant with a rich source of 2-Methoxy-4-vinyl phenol (2M4VP). Efficient in vitro propagation was developed from nodal explants of F. strobilifera. The genetic homogeneity of in vitro propagated plants was confirmed using SCoT molecular markers. Biochemical fidelity in micropropagated plants carried out using GC–MS analysis. [ABSTRACT FROM AUTHOR]

Background: Basil (Ocimum sp.) exhibits significant morphological and genetic diversity. This variation provides an opportunity to identify novel traits that can be used in breeding programs to improve the productivity, quality, and disease resistance of basil plants. The integration of morphological and genetic data for basil varieties can improve our understanding of biodiversity, conservation, and breeding programs. Results: In 2019, we conducted a comprehensive investigation on 25 basil landraces collected from 12 Egyptian governorates to explore their morphological and genetic diversity. Morphological characterization revealed variability in plant vigor, flower color, cyme shape, and leaf shape, indicating distinct growth patterns and potential for specific applications. Productivity and biochemical evaluation demonstrated significant variation in yield and oil distillation, identifying top-performing landraces L5, L11, and L24 that can be used in breeding programs to optimize performance and reduce environmental impact. The genetic diversity of the landraces was investigated using 11 SCoT primers revealed high levels of genetic diversity among landraces, with a wide range of polymorphism variation. The phylogenetic analysis identified two distinct clades, providing valuable insights into genetic diversity and relationships between different landraces. An interesting observation was made in the study, whereby L6 and L13, collected from Fayoum and Port-Said, respectively, were found to be the closest landraces. Following closely were L7 and L14, which were also collected from the same governorates. These findings have significant implications for the conservation of these landraces, as they may have evolved from similar species. Conclusions: This study sheds light on the genetic diversity and relationships among 25 Egyptian basil landraces. Using SCoT markers, a high level of polymorphism was detected, indicating significant variation in the genetic makeup of the landraces. The study also revealed interesting observations regarding the relationships among the landraces, with some landraces appearing to have evolved from similar species. The phylogenetic analysis provided insights into the genetic relationships among the landraces, which can guide conservation efforts and breeding programs. Overall, this study provides valuable information for researchers, breeders, and farmers involved in the conservation, breeding, and utilization of basil genetic resources in Egypt. [ABSTRACT FROM AUTHOR]

Plumbago zeylanica L. is commonly known as chitrak, consumed since long time owing to its potent medicinal benefits. It is a major source of the yellow crystalline naphthoquinone called plumbagin, which is highly acclaimed for its anticancerous activities on different cancers i.e. prostrate, breast, ovarian, etc. The growing urges for this compound make this plant extremely demanding in the global market; hence, the plant is indiscriminately harvested from its very natural habitat. Therefore, in vitro biomass production of this plant can be a sustainable alternative for plumbagin production. In this present study, it has been found that, compared to other cytokinins, biomass production was enhanced by using aromatic cytokinin meta-topolin (mT). The highest shoot buds produced by mT (1 mg/l) was 13.60 ± 1.14 after 14 d of culture establishment. After 84 d in the same medium, 129.8 ± 2.71 shoots were produced, and the fresh weight of the total biomass was 19.72 ± 0.65 g. The highest number of roots was induced (37.80 ± 0.84) with 1.0 mg/l Indole-3-butyric acid (IBA). The well rooted plantlets were acclimatized in field condition with 87%survival. The regenerated plants' genetic fidelity was accessed through molecular markers i.e. Inter simple sequence repeat (ISSR), Start codon targeted (SCoT) and cytology studies. The monomorphic bands amplified by the primers across in vivo and in vitro plants confer the genetic homogeneity of the regenerants. The plumbagin content from different parts of the in vitro grown plants in vivo mother plant was quantified through High-Performance Liquid Chromatography (HPLC), and found that they do not differ significantly. Even all parts of the in vitro plants produce plumbagin, roots contain the maximum amount (14.67 ± 0.24 mg/g dry weight basis). [ABSTRACT FROM AUTHOR]

Grape (Vitis venifera L.), is one of the earliest domesticated fruit crops in Iran, cultivated across the different parts of the country. Due to its highly edible and economic importance, genetic diversity investigations are going on throughout the world for both wild and cultivated forms of grape plants. However, population genetic reports from Iran are very limited. The present study was performed on 123 plants of 25 table grape cultivars by using SCoT (start codon targeted markers). We obtained 48 SCoT bands in all the studied samples, with only one private band in two cultivars. A low to moderate genetic polymorphism was obtained in the studied populations, but these cultivars differed significantly in their genetic content as revealed by AMOVA. Clustering of the studied cultivars and their replications almost separated these cultivars into separate sub-clusters which indicates that SCoT markers are efficient in genetic fingerprinting of grape germplasm. Discriminating SCoT loci identified by discriminant analysis of principal components (DAPC) analysis, while genetic grouping of the studied cultivars by heat-map and linear discriminant analysis (LDA), placed the cultivars in four different groups. Some cases of homonymy were identified in the studied cultivars but need further approval by the other molecular markers. [ABSTRACT FROM AUTHOR]

Background: Herbal medicines have recently attracted increasing attention for use as food supplements with health benefits; however, species authentication can be difficult due to incomplete morphological characters. Here, a molecular tool was developed for the identification of species in the National List of Essential Medicinal Plants in Thailand. Methods: The identification process used DNA fingerprints including start codon targeted (SCoT) and inter simple sequence repeat (ISSR) polymorphisms, coupled with high resolution melting (HRM), to produce melting fingerprint (MF)-HRM. Results: Results indicated that MF-HRM, SCoT-HRM and ISSR-HRM could be used for DNA fingerprints as S34, S36, S9 and S8 of SCoT and UBC873, S25 and UBC841 of ISSR. The melting fingerprints obtained from S34 of SCoT exhibited the best primers for identification of herbal species with 87.5% accuracy and relatively high repeatability. The presence of intraspecific variation in a few species affected the shift of melting fingerprints within species. MF-HRM using S34 showed improved species prediction compared to DNA fingerprints. The concentration of DNA with 10 ng/µl was recommended to perform MF-HRM. MF-HRM enabled species authentication of herbal commercialized products at only 20% resulting from the low quality of DNA isolated, while admixture of multiple product species interfered with the MF process. Conclusion: Findings suggested that MF-HRM showed promise as a molecular tool for the authentication of species in commercial herbal products with high specificity, moderate repeatability and rapidity without prior sequence information. This information will greatly improve quality control and traceability during the manufacturing process. [ABSTRACT FROM AUTHOR]

The genus Calligonum L. Her (Polygonaceae) comprises 158 species with widespread distribution in regions such as India, China, North Africa, Pakistan, Afghanistan, Saudi Arabia, and South Europe. Calligonum L. is a prominent shrubby psammophyte found in deserts, known for its traditional medicinal uses. The aim of this study is to use Start Codon Target (SCoT) and Inter-Retrotransposon Amplified Polymorphism (IRAP) markers to evaluate the genetic diversity of Calligonum comosum and Calligonum tetrapterum in Saudi Arabia. In addition, it uses the raxmlHPC algorithm and DNA barcoding techniques (matK and rpoC1) to examine phylogenetic relationships. SCoT and IRAP markers revealed distinct genetic patterns, clustering Calligonum species based on their genetic similarities. DNA barcoding of matK and rpoC1 genes provided valuable insights into the evolutionary relationships within Calligonum species. Phylogenetic analyses highlighted well-supported structures with outgroup sequences showing early divergence. Conserved motifs analysis confirmed the presence of shared motifs in both isolated and identified genes, validating the potential use of isolated genes as biomarkers. This comprehensive genetic analysis enhances our understanding of Calligonum species’ genetic relationships, contributing valuable information for taxonomic classification and molecular marker validation. We are the first to add sequence of rpoC1 gene to Calligonum comosum and Calligonum tetrapterum in Gen-Bank. The identified conserved motifs and phylogenetic insights underscore the potential applications of Calligonum genes in various fields, including medicine and biodiversity conservation. [ABSTRACT FROM AUTHOR]

Salinity is the main impedance to world food security; it is considered one of the most serious environmental stresses that prohibit agricultural production in many countries. The development of salt-tolerant crop cultivars is indispensable. Eleven traits related to productivity and salinity tolerance were evaluated in the present study under different concentrations of salt stress. The data displayed that, Misr1, Misr2 and Shandaweel1 have maintained higher growth rates compared with the other cultivars under high salt concentrations. The results revealed a reduction in morphological and physiological parameters with the increase in saline conditions. Correlation coefficients among vegetative growth, physiological and biochemical traits show that the total number of leaves per plant was significantly positively correlated to all studied traits at (p < 0.05) except for both Na+ ppm and phenols content values which observed negative relationships. The genetic difference among the ten wheat cultivars used was resolved by simple sequence repeat (SSR), Sequence-related amplified polymorphism (SRAP), and Start codon targeted (SCoT) polymorphism. The results of the comparison between the different molecular markers showed that the most effective marker that showed the genetic diversity between wheat cultivars was the SSR with 63.8% polymorphism. Allelic frequency of the different SSR, SRAP and SCoT markers tested has differed among the ten wheat cultivars. These findings could be a good indicator of the salt tolerance mechanism present in the studied wheat cultivars. Therefore, these markers are of considerable value and can be utilized to screen large wheat populations for salt tolerance. [ABSTRACT FROM AUTHOR]

Lippia javanica is a multipurpose medicinal plant of the Verbenaceae family, which is commonly known for its volatile and essential oil compounds with numerous pharmaceutical applications. Due to medicinal importance, the plant was overexploited, which has been resulted in the rare availability of plant material. Through this study, an efficient and reproducible protocol was established for its in vitro micropropagation using nodal explants. Maximum number of shoots (7.11 ± 0.12) per nodal explant was induced on Murashige and Skoog (MS) medium augmented with 2.0 mg L−1 of 6-benzylaminopurine (BAP). When combination of phytohormones tested, highest number of multiple shoots (25.76 ± 0.37) was obtained on 2.0 mg L−1 of BAP and 0.5 mg L−1 of kinetin (Kn). Rooting of shoots with good response and maximum number of roots (21.19 ± 0.54) per explant was induced on half-strength MS medium with 1.0 mg L−1 of indole-3-butyric acid (IBA). Well rooted in vitro raised plantlets were hardened in paper cups possessing soilrite. The hardened plantlets were initially maintained in the pots for 3 weeks and finally acclimatized to soil conditions with an 80% of survival rate. The micro-morpho-anatomical characterization of in vitro and ex vitro hardened plantlets revealed detailed developmental information about structural features of leaf, stem, and the type and density of trichomes while adapting to natural conditions. Similarly, the genetic fidelity of micropropagated plantlets were screened by SCoT and ISSR molecular markers and the results confirmed the true to type nature of regenerated plantlets with the mother plant. Key message: Lippia javanica is a multipurpose medicinal plant with substantial industrial demand. An efficient in vitro micropropagation protocol was established from nodal explants of Lippia javanica. It is the first report on micro-morpho-anatomical studies and genetic fidelity analysis using molecular markers in Lippia javanica. [ABSTRACT FROM AUTHOR]

Accessions are a prospective source of genetic variability, as well as valuable genetic resources for crop improvement. Assessing the population structure and genetic diversity of Iraqi tomato accessions is therefore critical in breeding programs for the production of high-yielding cultivars, as well as widening the genetic base of tomato. Using fruit quality indices and molecular markers, a panel of 64 tomato accessions taken from six northern provinces of Iraq were analyzed for genetic diversity and population structure. In the analysis of variance, the fruit phenotypic data revealed a high level of significant variability (p ≤ 0.01) among tomato accessions. The most important characteristics for explaining fruit morphological variability, according to principal component analysis (PCA), were fruit weight, fruit size, fruit diameter, total soluble solids, and moisture content. Seven clades with different fruit characteristics were revealed in the cluster analysis. Genetic diversity and relationships among accessions were analyzed using thirteen inter simple sequence repeat (ISSR), twenty-six start codon-targeted (SCoT) polymorphisms, and fifteen conserved DNA-derived polymorphisms (CDDP). The ISSR, SCoT, and CDDP markers generated 121, 294, and 170 polymorphic bands, respectively, showing a high prevalence of polymorphism. The average polymorphism information content (PIC) values for ISSR, SCoT, and CDDP were 0.81, 0.84, and 0.84, respectively. The accessions were divided into two groups based on the cluster and STRUCTURE analysis results. The Mantel test revealed that three sets of markers had a positive and significant relationship. The increased genetic variation within the populations was found by the analysis of molecular variance (AMOVA), indicating considerable gene exchange between populations. To the best of our knowledge, this is the first extensive report on the use of gene-targeted molecular markers for genetic diversity analysis of tomato accessions in Iraq. Our findings demonstrated the utility of these markers for genetic diversity study in tomato accessions, as well as their potential for genome diversity and germplasm conservation. [ABSTRACT FROM AUTHOR]

Postphenomenology was envisaged to lay bare the black box of technology through a phenomenological approach. The vision, in this sense, was to identify how technology might mediate both the subjectivity of its immediate user and the world around her. In this paper I will argue that to cognize technology's effects fully, we need to enrich postphenomenology with further insights. In particular, SCOT and ANT may be integrated into postphenomenology. While the former can provide a historical narrative of how technology has evolved throughout time, the latter may embed technology within a network where the interplay of the technology, the first user, other individuals and the society, on the whole, can be depicted. After a preliminary theoretical discussion, I will go through some case studies to articulate how SCOT and ANT can make a contribution to a systematic investigation of technology. [ABSTRACT FROM AUTHOR]

Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development. [ABSTRACT FROM AUTHOR]

Background: Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. Methods and results: We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno–Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes. Conclusions: The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it. [ABSTRACT FROM AUTHOR]

Phytotherapeutic preparations from Uncaria guianensis (Aubl.) J.F. Gmel. (Rubiaceae) are marketed worldwide and are mainly used for their anti-inflammatory activity. The species has not yet been domesticated and is threatened by deforestation and overexploitation. It is, therefore, important to preserve and manage this genetic resource in germplasm banks, so that the extractive provision of plant material can be replaced by cultivated production. The aim of this study was to evaluate the genetic diversity among 20 genotypes maintained under in vitro conditions using 9 primers start codon targeted (SCoT) polymorphism, and to determine the concentrations of the pentacyclic oxindole alkaloids (POAs); mitraphylline and isomitraphylline in methanolic extracts by high-performance liquid chromatography (HPLC). Plantlets were cultivated on woody plant medium supplemented with 20 g.L−1 sucrose and 4.4 μM benzylaminopurine and incubated under a 16 h photoperiod for 45 days. SCoT analysis separated the genotypes into four divergent clusters and confirmed significant genetic diversity with up to 70% dissimilarity. Moreover, HPLC revealed considerable chemical variability and allowed the separation of the tested genotypes into high, medium and low producers of mitraphylline/isomitraphylline. Genotypes with the highest concentrations of POAs originated from the state of Acre and Amapá, while those with the lowest levels were from the state of Pará. The results demonstrate that the genetic diversity within the in vitro germplasm bank is sufficient to support breeding studies, selection of elite genotypes and the large-scale multiplication of plants that could serve as feedstock for the industrial-scale production of phytomedicines. [ABSTRACT FROM AUTHOR]

Coconut (Cocos nucifera L.) production sustains millions of smallholder farmers and their families around the globe, and also powers a thriving industry of climate-adaptive nutrition and biomaterials. Demand for high-quality planting materials has risen sharply in recent years, calling for greater understanding and potential utilization of the genetic diversity in coconut populations. Genetic diversity among several conserved coconut varieties in Vietnam was investigated to assess the suitability of 15 start codon targeted (SCoT) primers for future selective breeding programs. Amplification of 15 SCoT primers in 57 individuals from 19 coconut varieties revealed high intra-varietal diversity (Nei's genetic diversity index = 0.237, Shannon's Information index = 0.352), especially among the Vietnamese Dwarfs. Intriguingly, inter-varietal differentiation accounted for only 9.41% of total genetic variation. The designated SCoT primers were moderately informative. On average, each primer had 9.5 reproducible polymorphic bands per reaction. Polymorphism Information Content (PIC) per locus ranged between 0.217 and 0.390, with Resolving power (Rp) between 0.271 and 0.599. Principal Coordinate Analysis (PCoA) and Unweighted Pair Group Method with Arithmetic mean (UPGMA) analyses revealed distinct clusters for non-native Dwarf, native Dwarf, and Tall varieties. This paper represents the first-of-its-kind attempt to shed light on coconut genetic diversity in Vietnam using molecular markers. [ABSTRACT FROM AUTHOR]

Selection of elite accessions is important to get the maximum quantity of bioactive compounds in medicinal plants. In this study, thirteen accessions of Plumbago zeylanica L., a medicinal herb, was studied for phytochemical and genetic diversity analysis. Phytochemical analysis showed that accession number IC-524441 contains the highest amount of flavonoids, phenolic, tannin and plumbagin content, it also possesses maximum antioxidant activity. Genetic diversity analysis showed that 15 SCoT (Start codon targeted) and 20 CBDP (CAAT Box Derived Polymorphism) primers produced 86 and 110 amplicons in total and average were 5.73 and 5.5 amplicons/primer respectively. PIC values ranged from 0.12 to 0.37 and average is 0.25/primer in the case of SCoT marker whereas, in the case of CBDP marker it was 0.15 to 0.59 with average of 0.26/primer. Cluster analysis showed that SCoT marker provides three clusters where cluster 1 and cluster 2 have only 2 accessions while cluster 3 contains nine accessions. Similarly, CBDP marker provides three clusters where cluster 1 contains only 1 accession and cluster 2 and cluster 3 contains six accessions in each. Further AMOVA analysis of SCoT marker possesses maximum variation of 8% among agro-ecological regions whereas in case of CBDP marker its 5%. From the present investigation, it was found that IC-524441 is an elite accession and contains highest amount of bioactive compound. Our results also demonstrate that both SCoT and CBDP markers are informative and can be utilized for evaluation of genetic relationships among Plumbago zeylanica L. accessions. [ABSTRACT FROM AUTHOR]

Phytotherapeutic preparations from Uncaria guianensis (Aubl.) J.F. Gmel. (Rubiaceae) are marketed worldwide and are mainly used for their anti-inflammatory activity. The species has not yet been domesticated and is threatened by deforestation and overexploitation. It is, therefore, important to preserve and manage this genetic resource in germplasm banks, so that the extractive provision of plant material can be replaced by cultivated production. The aim of this study was to evaluate the genetic diversity among 20 genotypes maintained under in vitro conditions using 9 primers start codon targeted (SCoT) polymorphism, and to determine the concentrations of the pentacyclic oxindole alkaloids (POAs); mitraphylline and isomitraphylline in methanolic extracts by high-performance liquid chromatography (HPLC). Plantlets were cultivated on woody plant medium supplemented with 20 g.L−1 sucrose and 4.4 μM benzylaminopurine and incubated under a 16 h photoperiod for 45 days. SCoT analysis separated the genotypes into four divergent clusters and confirmed significant genetic diversity with up to 70% dissimilarity. Moreover, HPLC revealed considerable chemical variability and allowed the separation of the tested genotypes into high, medium and low producers of mitraphylline/isomitraphylline. Genotypes with the highest concentrations of POAs originated from the state of Acre and Amapá, while those with the lowest levels were from the state of Pará. The results demonstrate that the genetic diversity within the in vitro germplasm bank is sufficient to support breeding studies, selection of elite genotypes and the large-scale multiplication of plants that could serve as feedstock for the industrial-scale production of phytomedicines. [ABSTRACT FROM AUTHOR]

Background: Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. Results: Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. Conclusion: Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations. [ABSTRACT FROM AUTHOR]

An effective protocol for the plant regeneration via direct and indirect organogenesis has been developed from leaf explants of Asystasia gangetica (L.), cultured on Murashige and Skoog (MS) medium supplemented with various concentrations and combinations of auxin and cytokinins. Approximately 86% of explants produced direct shoots on MS medium containing 0.5 mg L−1 6-benzyladenine (BA) and 10 μg L−1 Triacontanol (TRIA) with a maximum of 4.82 ± 0.29 shoots per leaf segment. For production of callus-mediated plantlets (indirect), primarily callus was induced on MS medium containing 2 mg L−1 2,4-dichlorophenoxyacetic acid (2,4-D), which was then subcultured on medium with 0.1 mg L−1 naphthaleneacetic acid (NAA), 0.5 mg L−1 BA, and 1 to 8 mg L−1 2-isopentenyl adenine (2iP) in order to develop organogenic callus and subsequent shoot induction. A maximum of 6.84 ± 0.05 shoots per callus clump was obtained on MS media supplemented with 4 mg L−1 2iP, 0.5 mg L−1 BA, and 0.1 mg L−1 NAA. The shootlets produced roots when cultured on half-strength MS media supplemented with 2 mg L−1 indole-3-butyric acid (IBA). In vitro propagated plantlets were hardened on soil rite and acclimatized to field condition with 85% survivability. The chlorophyll content of acclimatized plants was comparable with that of the mother plant, while stomatal micromorphology of regenerated plants exhibited no abnormalities. The radical scavenging and antioxidant activity of methanolic extract of leaves were measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing ability of plasma (FRAP), and phosphomolybdenum test. In all experiments, regenerated plants exhibited enhanced antioxidant potential indicating micropropagated plants could be exploited for isolation of novel biomolecules. Further, the genetic homogeneity of acclimatized plants was confirmed by PCR-based start codon targeted (SCoT) markers and ycf1b DNA barcoding primers which exhibited monomorphic bands identical to the normal mother plant and no variations were observed. [ABSTRACT FROM AUTHOR]

We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon's information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species. [ABSTRACT FROM AUTHOR]

Date palm (Phoenix dactylifera) is an important crop plant both from nutritional and economic points of view. The assessment of genetic diversity and population differentiation of date palms are evaluative for its dynamic conservation and sustainable utilization of its genetic diversity. Estimates of genetic diversity based on molecular markers and fruit characteristics were performed in samples of 23 date palms growing in Ahvaz city (Khuzestan province of Iran). Clustering based on fruit morphological features separated the cultivars in different groups. These cultivars differed significantly in morphological features (P = 0.001). Start codon targeted (SCoT) polymorphism markers revealed a good level of genetic variability (10.17 to 45.76%) in these cultivars. Moreover, STRUCTURE analysis revealed the presence of within-population genetic variability. Analysis of molecular variance revealed a significant genetic difference among date palms, while it showed a higher degree of within-cultivar genetic variability compared with that of among-population diversity. Some degree of common shared alleles occurred between date palm cultivars. Gst versus Nm analysis showed that some of the SCoT markers have a high discrimination power and may have a potential local adaptive value. The Mantel test showed a significant association (r = 0.40, P = 0.001) between morphological and genetic distances. Therefore, both morphological and SCoT molecular data can be used in genetic screening of date palms in the available germplasm. [ABSTRACT FROM AUTHOR]

Fabaceae, the third-largest Angiosperm family, exhibits great morphological diversity with significantly high species diversification rate. Albizia, one of the largest genera of the legume family, possesses high ecological, economical and medicinal application prospects and displays a global distribution. The taxonomic classification among Albizia remains, however, unclear and has been subjected to changes. The resolution of phylogenetic relationships among members of genus Albizia is a priority. Nine Albizia species cultivated in Egypt; Albizia lebbeck, A. julibrissin, A. odoratissima, A. procera, A. anthelmintica, A. guachapele, A. myriophylla, A. richardiana and A. lucida were subjected to molecular classification via DNA fingerprinting techniques viz. Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted polymorphism (SCoT) using ten primers, five for each technique. The total number of bands produced by ISSR and SCoT primers was 28 and 40, respectively. The percentage of polymorphism varied from 64.28% in ISSR to 67.50% in SCoT analysis. Additionally, chemotaxonomic analysis was implemented based on UV spectroscopic profiling and total phenolic content coupled to unsupervised chemometric tools; Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Interspecific relationships were confirmed via molecular and phytochemical analyses between A. procera and A. guachapele; A. lebbeck and A. odoratissima; and A. julibrissin and A. lucida. The study reveals that chemotaxonomic data can reflect phylogenetic relationships among examined Albizia species and provides insights to the significance of utilizing the strengths of both molecular taxonomy and chemotaxonomy to resolve phylogenetic relationship among this genus which offers baseline for breeding programs. Future strategies to enrich taxonomic classification among Albizia includes extensive morphological characterization, DNA barcoding techniques and metabolomic profiling. [ABSTRACT FROM AUTHOR]

An efficient method of rapid micropropagation of Solanum khasianum Clarke was successfully established from the leaf, petiole, and nodal explants. The morphogenetic response of different concentrations of TDZ and BAP individually or in combination with auxins (IAA/IBA/2,4-D) was tested. Friable callus was obtained on different concentrations of BAP alone or in combination with IAA/IBA/2,4-D. Rapid multiple shoot induction was achieved from friable callus on MS medium supplemented with varying concentrations of TDZ and IBA. The leaf explants exhibited a high frequency of multiple shoots than petiole and nodal explants with an optimal percentage of response (92.73%), mean shoot number (53.5 ± 0.47), and shoot length (11.2 ± 0.53 cm) on MS medium augmented with TDZ (1.5 mg l−1) and IBA (1.5 mg l−1). Maximum rooting efficiency was achieved on MS medium with 1.5 mg l−1 IBA with 12.8 ± 0.36 mean number of roots. The in vitro rooted plants were acclimatized with a survival rate of 80%. The genetic fidelity of the regenerants assayed by the ISSR and the SCoT markers showed no genetic variation. The study examined the micropropagation responses of S. khasianum in the presence of various growth regulators and provided a simple and more suitable protocol adapted for the mass propagation of clones in this species. Key message: We have established a highly efficient micropropagation system for large scale production in Solanum khasianum. Evaluation of clonal fidelity by using ISSR and SCoT markers detected no somaclonal variations. The present study helps to the enhancement of potential alkaloids (solasodine) with the help of biotechnological tools. [ABSTRACT FROM AUTHOR]

Aenhenrya rotundifolia is a critically endangered terrestrial jewel orchid. It is monotypic and endemic to evergreen forests of southern western ghats of India. In the present study, identification of this plant species is validated with DNA barcoding using matK and rbcL chloroplast markers. Further, germ-free juvenile axillary bud explants were cultured on Mitra medium supplemented with different kinds of cytokinins like 6-benzyladenine, 6-furfurylaminopurine, N6-(Δ2-isopentyl) adenine, thidiazuron, zeatin and meta-topolin as well as auxins such as α-naphthaleneacetic acid, indole-3-acetic acid and indole-3-butyric acid at different concentrations and combinations for successful proliferation and establishment in vitro. After 12 weeks of culture, axillary bud explants produced an average of 30.12 ± 0.71 shoots per explant, 3.87 ± 0.06 cm shoot length, 1671 ± 2.82 mg fresh mass of proliferated shoots with a proliferation frequency of 100% on Mitra medium supplemented with 6.20 µM meta-topolin and 2.25 µM thidiazuron. No root formation was observed in in vitro proliferated microshoots. However, tiny hair like projections were observed in some elongated shoots on Mitra medium pertaining to 5.37 µM NAA. The tiny hair like structure bearing plantlets were hardened and acclimatized with 100% survival rate in the polytunnel chamber. After 8–10 months of establishment ex vitro, flowering was observed. Additionally, the genetic fidelity of in vitro derived plants was tested with ISSR and SCoT marker profiling. The test results revealed that the plants derived from the protocol has 99% genetic similarity to that of the donor mother plant. This study can be applied in forensic interventions of this species, describes the maintenance of germplasm in vitro and establishment of new viable population in its original habitats by restoring existing sites of this critically endangered jewel orchid. [ABSTRACT FROM AUTHOR]

Clerodendrum belonging to the family of Lamiaceae is used in indigenous systems of medicine to treat various life-threatening diseases. The genus has complex morphological variations which lead to limits in its precise taxonomic classifications. Genetic diversity study could enhance taxonomic authentication and evolutionary relationship among the species of Clerodendrum. In this study, nine species of Clerodendrum collected from different regions of North East India were screened using ISSR, RAPD, and SCoT molecular markers. The markers of ISSR, RAPD, and SCoT generated a total of 79, 126, and 145 amplicons with an average of 6.58, 7.86, and 8.53 amplicon per primer. The polymorphism information contents (PIC) for ISSR, RAPD, and SCoT ranged from 0.28 to 0.37, 0.39 to 0.69, and 0.30 to 0.62 with resolving power (Rp) varying from 5.26 to 11.11, 4.04 to 9.67, and 4.54 to 8.65, respectively. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based clustering methods grouped 94 genotypes into 6 clusters for ISSR and 3 clusters each for RAPD and SCoT markers. Similarly, population structure-based analysis divided 94 genotypes into 6 populations for ISSR and RAPD and 4 populations for SCoT markers. AMOVA analysis revealed that SCoT markers generated maximum genetic variations within and among genotypes, contrary to ISSR and RAPD markers. Results in this study, suggest that the competence of three markers was relatively the same in genotypes fingerprinting, but SCoT was more efficient in the detection of polymorphism for Clerodendrum species. Further, these results could be integrated in the exploration of diverse Clerodendrum species and germplasm utilization. [ABSTRACT FROM AUTHOR]

Eggplant is an important Solanaceous vegetable crop with distinct morphological forms, colours, and shape of the fruits. Limited genomic coverage of the crop is a major constraint to unfold the cause of morphological variations underlying the contrasting traits. Therefore, with the aim to initiate targeted breeding efforts and to render ready-to-use markers for application in mapping quantitative trait loci (QTLs)/genes and to facilitate MAS, arbitrary and microsatellite molecular markers were used to map an inter-specific mapping population of 114 F8-recombinant inbred lines (RILs) developed using two contrasting lines, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.). The arbitrary and microsatellite markers were screened for polymorphism with aim to cover the whole genome of eggplant. Of the total 1443 number of markers investigated, 6.07% RAPDs, 25% ISSR, 46.25% SCoT, and 22.46% SSRs revealed polymorphism between the parental lines, and were used for genotyping the RILs population. The results exhibit robust and sturdy nature of SCoT and microsatellite markers in unwrapping variations between both genotypes. Further, a high-density genetic linkage map was constructed with LOD threshold ≥ 4 clustered into 12 tentative linkage groups and spanning 1165 cM of the eggplant genome with an average marker density of 4.13 cM. The results shall further be used in mapping QTLs of agri-horticultural traits in eggplant. [ABSTRACT FROM AUTHOR]

Juglans regia L. is the most widely cultivated and economically important species of edible nuts. Iran is known as a center of origin of genetically rich walnut germplasm and expected to be found a large diversity within Iranian walnut populations. A detailed population genetic of local populations is useful for developing an optimal strategy for in situ conservation and can assist the breeders in crop improvement programmes. The main aim of the present study was genetic fingerprinting of 20 Persian walnut populations, including 3 wild and 17 cultivated populations by using SCoT markers. We also aimed to evaluate the discriminating power of SCoT markers in these populations. The correlation between genetic distance and geographical distance has also investigated. The results showed that SCoT marker has a good discrimination power and can differentiate the studied populations. This marker can be used to evaluate genetic diversity, identify genotypes and DNA finger printing of Persian walnut populations. The present study also revealed that there are at least two genetic groups in the studied Persian walnut populations and the geographical features of cultivated populations can be influenced grouping of them. The studied populations differed genetically and showed isolation by distance. [ABSTRACT FROM AUTHOR]

Camellia oleifera Abel. is a cultivable plant with important economic value. It is very helpful for the scientific utilization, cultivation and preservation of germplasm resources through evaluating the genetic diversity. In this study, we estimated the genetic distances of 135 accessions of C. oleifera using ISSR and SCoT markers, respectively. The genetic dissimilarity coefficients of ISSR markers ranged from 0.56 to 1.00. And the accessions were divided into five groups. While the genetic dissimilarity coefficients of SCoT markers ranged from 0.62 to 1.00, the accessions were divided into four groups. The results demonstrated that C. oleifera germplasms perform a little genetic variation. This is the first report to evaluate the genetic diversity of different C. oleifera germplasms using the ISSR and SCoT molecular markers, and the results provide the useful foundation for plant breeding of C. oleifera. [ABSTRACT FROM AUTHOR]

Phoenix dactylifera L. has about 400 date palm cultivars in Iran with very confined information on their genetic structure and content. Up to now, our date palm cultivation has been based on traditional approached and therefore we need to move towards modern approaches of molecular breeding and biotechnology. The present study was performed on 113 date palm trees of 13 known cultivars, cultivated in different regions of Iran. We used SCoT molecular marker for our genetic investigation with the following aims: 1—Investigate genetic diversity both among and with date palm cultivars, 2—Identify genetic groups within these 13 cultivars, and 3—produce data on the genetic structure of date palm cultivars. The results obtained revealed a high within-population genetic variability. The studied cultivars differed genetically as evidenced by analysis of molecular variance and Fst values obtained in STRUCTURE analysis. Gene flow and genetic admixture were observed among date palm cultivars. No association occurred between geographical distance and genetic distance of date palm populations studied. The results indicated the efficiency of SCoT markers in genetic diversity analysis and genetic fingerprinting of date palms. Similarly, data obtained may be used in future breeding and hybridization programs of Iranian date palms. [ABSTRACT FROM AUTHOR]

Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure. [ABSTRACT FROM AUTHOR]

In coffee, the micropropagation technique can be efficiently used in mass multiplication of superior F1 hybrids which is difficult using the conventional method. However, the in vitro regeneration protocol is genotype-specific. Therefore the development of an efficient regeneration protocol is critical to the success of large scale propagation of any coffee hybrids. In the present study, regeneration of two improved rust tolerant arabica hybrids S.4202 and S.4932 was achieved through somatic embryogenesis. The MS media supplemented with different concentrations of 2, 4-D, IAA and Kn were tested for callus induction using foliar explants. The optimum somatic embryogenesis in S.4202 and S.4932 was obtained when explants were incubated in callus induction media containing 0.4 to 0.6 mg/l 2, 4-D. The in vitro regenerated plants were planted in the field and were found to be phenotypically normal. The genetic fidelity of in vitro regenerated plants of both the genotypes along with their mother plant was tested using 20 SRAP and 12 SCoT markers. The average genetic similarity between the tissue culture-derived plants and mother plants of S.4202 was 0.977 using SRAP and 0.987 using SCoT markers. Similarly, the average genetic similarity between the mother plant and the in vitro derived plants of S.4932 was 0.966 and 0.993 using SRAP and SCoT markers respectively. The differential fragments amplified by SRAP primers in the regenerated plants were sequenced and in silico analysis of the fragments revealed the occurrence of somaclonal variation in the coding region with functional attribution to zinc finger protein. Key message: Plant regeneration through somatic embryogenesis was achieved in two improved cultivars of Coffea arabica. The genetic fidelity of in vitro regenerated plants was tested using both SRAP and SCoT molecular markers. The differential fragments amplified in in vitro regenerated plants using SRAP primers were sequenced and in silico analysis revealed the genomic alterations in the coding region. [ABSTRACT FROM AUTHOR]

Sunn pest is one of the most destructive insects in the western and central parts of Asia causing severe reductions of wheat yield and flour quality. Therefore, an effort was undertaken to find effective resistance by analyzing genetic variation among 25 wheat genotypes artificially infested in field-cages as well as using start codon targeted (SCoT) polymorphism and inter- retrotransposon amplified polymorphism (IRAP) markers. High variation was revealed amongst genotypes with Sunn pest resistance characteristics including Bayat, Bezostaya, Sayson, Line93, Line120, Rashagol, Golsepi and AarasGolsoor, which were classified as resistant to moderately resistant. SCoTs and IRAPs were determined as efficient markers for studying genetic diversity. The non-parametric Kruskal–Wallis test was conducted to evaluate the effect of specific SCoT and IRAP amplicons on Sunn pest resistance characteristics for wheat genotypes. The stepwise regression analysis exhibited seven informative SCoTs and IRAPs explaining the highest resistance characteristics variation ranging from 25.7–50.1 to 17.6–40.1, respectively. The relationship between resistance of genotypes and informative SCoT and IRAP amplicons was found based on canonical discriminant analysis showing the capacity of informative markers for functional marker selection method and screening the wheat germplasms for Sunn pest resistance characteristics. [ABSTRACT FROM AUTHOR]

Background: Bigfin squid is one of the economically important seafood resources in Vietnam's fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box-derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data., Results: Con Dao population possessed a higher diversity [expected heterozygosity (H e ) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (H e = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of H e = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (G ST ) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region., Conclusions: For the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species., (© 2023. The Author(s).)

Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies. [ABSTRACT FROM AUTHOR]

The knowledge about genetic diversity in the wild relatives of wheat provides useful information for breeding programs and gene pool management. In the present study, an assessment of agro-morphological diversity and molecular variability among 70 accessions of Triticum, belonging to T. boeoticum, T. urartu, T. durum and T. aestivum species, collected from different regions of Iran was made. According to phenotypic analysis, all traits except peduncle length, stem diameter and the number of seeds per spike indicated a high level of diversity among studied accessions. Also, principal component analysis identified six components that explained 87.53% of the total variation in agro-morphological traits. In molecular analysis, 15 start codon targeted (SCoT) polymorphism primers produced 166 bands, out of which, 162 (97.59%) were polymorphic. Analysis of molecular variance (AMOVA) indicated the 63% of the variation resided among populations. The maximum value of polymorphism information content (PIC), the observed (Na) and effective (Ne) number of alleles, Nie's gene diversity (He) and Shannon's information index (I) was detected for T. boeoticum than the other species. The SCoT-based tree revealed three different groups corresponding to the genomic constitution in Triticum germplasm, which was in part confirmed by STRUCTURE and principal coordinate (PCoA) analyses. Our results indicated a remarkable level of genetic diversity among studied Iranian Triticum species, especially T. boeoticum, which can be of interest for future breeding and other analyses associated with future studies of the wild relatives of wheat. More importantly, our results revealed that SCoT markers could be used to accurate evaluate genetic diversity and phylogenetic relationships among different Triticum species. [ABSTRACT FROM AUTHOR]

In order to provide information for further research and utilization of Erianthus arundinaceus (Retz.) Jesw., the phenotypic variation and genetic diversity in the collection of E. arundinaceus (Retz.) Jesw. germplasm in Guangxi, China were investigated. The coefficient of variation (CV) in four quantitative traits, plant height, stalk diameter, spikelet length and number of panicle nodes, of 50 E. arundinaceus (Retz.) Jesw. clones ranged from 12.71 to 16.14 %, stalk diameter had the highest coefficient of variation, followed by spikelet length, and number of panicle nodes showed the lowest. Fifteen start condon targeted polymorphism (SCoT) marker primers were used to assess the genetic diversity of the 50 collections of E. arundinaceus (Retz.) Jesw. germplasm. A total of 336 genotypes were investigated for SCoT polymorphism, which produced 284 amplicons with 83.97 % polymorphism, indicating that E. arundinaceus (Retz.) Jesw. germplasm had abundant diversity in Guangxi. The Jaccard's similarity coefficients among these accessions varied from 0.61 to 0.88 with an average of 0.71. The UPGMA clustering analysis showed the 50 E. arundinaceus (Retz.) Jesw. accessions could be divided into four major groups at the similarity coefficient level 0.73. The UPGMA dendrogram reflected the geographic distribution patterns of these accessions. [ABSTRACT FROM AUTHOR]

Genetic variation and relationships among 37 cultivars of Ziziphus mauritiana (Lamk.) native of India were analyzed using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. High level of polymorphism among SCoT (61.6%) and ISSR (61%) primers with higher PIC values ranging from 63.1 to 90.4% of SCoT and 47.3 to 88.8% of ISSR primers was recorded. SCoT and ISSR dendrograms revealed similarity coefficients ranging from 0.80 to 0.92 and 0.79 to 0.96, respectively, and clearly delineated all the cultivars of Z. mauritiana into well-supported distinct clusters. Greater Gst signifies higher amount of differentiation observed over multiple loci among seven Z. mauritiana populations. On the other hand, higher gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another. The genetic diversity of population 1 (Rajasthan) was the richest among all the seven populations. The largest genetic distance was measured between Maharashtra and West Bengal and the least between Rajasthan and Punjab cultivars. Most of the genetic diversity exists within population rather than among populations. Substantial variation in the ITS-1 region signifies its phylogenetic utility specifically in assessing genetic diversity in Z. mauritiana. The clustering patterns using three molecular marker systems vis-à-vis place of origin exhibited no consistency in grouping of Z. mauritiana cultivars as cultivars from the same place of origin were genetically cataloged into different SCoT, ISSR, and ITS phylogram clusters indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested. [ABSTRACT FROM AUTHOR]

Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement. [ABSTRACT FROM AUTHOR]