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Studies on genetic diversity could enhance taxonomic authentication and evolutionary relationship among the species of Ocimum. Therefore, diversity among 36 Ocimum accessions representing species from different regions of world were analyzed using Start Codon-Targeted Polymorphism (SCoT) and inter-simple sequences repeat (ISSR) marker. Marker systems used in this study was potentially targeted the different regions of the genome and included 18 SCoT and 15 ISSR primers, which showed successful amplification profile for Ocimum. Between these two, SCoT revealed the highest mean value of percentage of Polymorphism (84.6%), polymorphic information content (PIC, 0.65), and resolving power (Rp, 8.80), which were higher than ISSR. A total of 140 and 111 amplicons were obtained with SCoT and ISSR marker. The Mantel test indicted a significant correlation (r2 = 0.44) between ISSR and SCoT, which suggested a common genetical background among the accessions. The principal coordinate study showed the selection of different Ocimum genotypes by the cluster analysis. This study will help and support identification, genetic mapping, and molecular ecology to enhance the breeding program's efficiency for developing elite varieties to meet industrial demand globally. The present study is the first report of the genetic diversity, and relationship determination with SCoT-based molecular marker among Ocimum accessions.

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.

Astragalus L. is one of the largest angiosperm complex genera that belongs to the family Fabaceae, subfamily Papilionoideae or Faboideae under the subtribe Astragalinae of the tribe Galegeae. The current study includes the whole plant morphology, DNA barcode (ITS2), and molecular marker (SCoT). Ten taxa representing four species of Astragalus were collected from different localities in Egypt during the period from February 2018 to May 2019. Morphologically, identification and classification of collected Astragalus plants occurred by utilizing the light microscope, regarding the taxonomic revisions of the reference collected Astragalus specimens in other Egyptian Herbaria. For molecular validation, ten SCoT primers were used in this study, producing a unique banding pattern to differentiate between ten samples of Astragalus taxa which generated 212 DNA fragments with an average of 12.2 bands per 10 Astragalus samples, with 8 to 37 fragments per primer. The 212 fragments amplified were distributed as 2 monomorphic bands, 27 polymorphic without unique bands, 183 unique bands (210 Polymorphic with unique bands), and ITS2 gene sequence was showed as the optimal barcode for identifying Astragalus L. using BLAST searched on NCBI database, and afterward, analyzing the chromatogram for ITS region, 10 samples have been identified as two samples representing A. hauarensis, four samples representing A. sieberi, three samples representing A. spinosus and one sample representing A. vogelii. Based on the ITS barcode, A. hauarensis RMG1, A. hauarensis RMG2, A. sieberi RMG1, A. sieberi RMG2, A. sieberi RMG3, A. sieberi RMG4, A. spinosus RMG1, A. spinosus RMG2, A. spinosus RMG3, A. vogelii RMG were deposited into GenBank with accession # MT367587.1, MT367591.1, MT367593.1, MT367585.1, MT367586.1, MT367588.1, MT160347.1, MT367590.1, MT367589.1, MT367592.1, respectively. These results indicated the efficiency of SCoT markers and ITS2 region in identifying and determining genetic relationships between Astragalus species.

Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21%) were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC) was 0.358, the Shannon diversity index (H) was 0.534, the marker index (MI) was 4.040, the resolving power (RP) was 6.108, and the genotype index (GI) was 0.782. Genetic similarity coefficients (GS) between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA) based on GS largely confirmed the results of principal coordinate analysis (PCoA). PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel’s test (r = 0.2268, p = 0.9999). In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA) and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species.

In vitro propagation of Nyactanthes arbor-tristis L. was achieved by culturing N-phenyl-N'-benzothiazol-6-yl-urea (PBU)-pretreated nodal expiants in Murashige and Skoog (MS) medium without any phytohormones. Pretreatment of nodal expiants in liquid MS medium with 100 µM N-phenyl-N'-benzothiazol-6-yl-urea for 4 d showed the highest shoot proliferation by producing maximum number of shoots (17.40 ± 1.02) per expiant, with average shoot length of 5.96 ± 0.08 cm at the end of 8 wk. Effective rooting was accomplished by preincubating the cut-end of shoots with half-strength MS medium containing 6 indole-3-butyric acid for 1 wk, followed by implantation into half-strength MS medium; an average of 6.20 ± 0.049 roots per shoot were produced. Seventy-eight percent of the plantlets regenerated in vitro were successfully acclimatized and transferred to soil. These plantlets appeared to be morphologically similar to the donor plants. The genetic fidelity of these in vitroregenerated plantlets was confirmed by start codon targeted polymorphism (SCoT) marker analysis, followed by comparative evaluations of the bioactive metabolites (ursolic acid, rengyolone, arbortristoside-A, and nyctanthoside), antioxidant-rich phytochemicals, and radical scavenging activities. This optimized in vitro propagation protocol should be an aid for the conservation of N arbor-tristis germplasm, as well as cater to the needs of herbal industries for the production of therapeutic molecules.

The genetic relationships among 90 mating-type isolates of Sporisorium scitamineum collected from mainland China were evaluated based on the start codon-targeted (SCoT) marker technique. Fourteen selected SCoT primers amplified 135 DNA fragments, of which 98 (72.6 %) were polymorphic. The polymorphic information content values ranged from 0.649 to 0.910 with an average of 0.820, indicating that a high degree of genetic diversity exists among these Chinese S. scitamineum isolates. Cluster groups identified using the unweighted pair-group method with arithmetic mean (UPGMA) and principal component analysis (PCA) were similar and divided the 90 S. scitamineum isolates into three main groups (G1, G2, and G3) based on a Jaccard’s similarity coefficient of 0.74. The S. scitamineum isolates collected from the same province tended to cluster in the same main groups. This study showed that the genetic diversity of the 90 S. scitamineum isolates was associated with their geographic origin, with no evidence of coevolution between the host and S. scitamineum. The knowledge of genetic diversity of S. scitamineum is useful in breeding programs for development of smut-resistant sugarcane genotypes. The results of this study demonstrate that SCoT markers are informative and can be used to evaluate the genetic diversity of S. scitamineum.

Black nightshades are a group of species best known for their ‘poisonous' or noxious weedy reputation. It is not so well known that species of this group serve as emerging food source in many countries worldwide especially in the African continent. Despite the fact that the section has recently been studied extensively, taxonomy is still unsettled and debated because of inter- and intraspecific hybridization, phenotypic plasticity and polyploidization. In this study we analyze the genetic relationships among diploid, tetraploid and hexaploid species of sect. Solanum, which have possibly taken part in the formation of Solanum nigrum, utilizing multi-locus (SCoT, ISSR) markers combined with chloroplast trnL-F sequence data and morphological characters. We scored 51 morphological characters united with SCoT (171), ISSR (224) and trnL-F (1042), for simultaneous analysis of 49 terminals and 1488 characters. The topology of the tree is concordant with the results of the network analysis. In the phylogenetic networks, all the accessions of the diploid species shared a split with all of the polyploid species. This reflected a high portion of shared ISSR and SCoT bands between diploids and polyploids. In addition, a strong split divided the diploid species. The history of S. nigrum might be reticulate with hybrid speciation playing an important rule. Genetically differentiated diploids in few combinations have created a series of genetically distinct polyploid populations. The insufficient isolation that permitted further recombination between ancient polyploids and diploids have resulted in high level of genotypic and phenotypic polymorphism. This high level of novel genomic variability obviously enabled species to succeed in their new environment.

The current study explores the impact of gamma radiation on the in vitro morphogenesis of Moringa concanensis . In vitro regenerated shoots were exposed to 133 Barium and 57 Cobalt gamma radiation sources for varying lengths of time (3, 6, 9, and 15 min). All the treated shoots survived with 100% regeneration frequency. The number of regenerated shoots was increased to 4.33 ± 1.57/inoculum in cobalt radiation-treated shoots. The field survival rate was increased, and 70% of plantlets from gamma radiation-treated shoots were successfully transferred to polybags. The multiple layers of epidermis, elongated cortical cells, pericycle cells, and increased content of vascular elements were observed in the anatomical assessment of regenerated shoots after treatment. The variations and altered responses of the treated shoots were further evaluated through CBDP (CAAT Box Derived Polymorphism), SCoT (Start Codon Targeted) gene-based, and ISSR (Inter Simple Sequence Repeat) intergenic sequence-based markers. An effective range of polymorphism of 75.00%, 77.77%, and 80.76% was observed from all the employed primers. A total of 0.2 PIC value was obtained from all used 6 primers that represent their informativeness in evaluating diversity among genotypes. The given minimum dose influenced the in vitro growth, anatomical development, and variations in genomic sequences, proving gamma radiation as an effective mutagen for Moringa concanensis . The gamma radiation source 133 Ba and 57 Co would be further used as a physical mutagen for developing efficient varieties of Moringa concanensis for the Moringa breeding program.

Ashwagandha ( Withania somnifera L. Dunal) is a highly acclaimed medicinal herb belonging to the family Solanaceae. The plant has been rendered an essential component of the Indian medicinal system due to its high therapeutic potential, attributed to its rich profile of secondary metabolites, namely withanolides. Widespread cultivation of the herb across diverse agroclimatic conditions has resulted in the development of numerous varieties and landraces, making it very difficult to discriminate the elite germplasm using conventional approaches. To overcome these, we use two molecular marker systems, SCoT and EST-SSR, to study the genetic variation and population structure of 32 Withania accessions. A total of 113 and 26 reproducible bands were generated using 10 SCoT and 17 EST-SSR markers, respectively, of which 100 and 20 were polymorphic, with an average polymorphism rate of 88 and 85.3%. The mean polymorphism information content (PIC), Marker Index (MI), and Resolving Power (Rp) for SCoT and EST-SSR markers were 0.327 and 0.172, 2.98 and 0.282, and 7.24 and 1.14, respectively, indicating that SCoT markers are more informative than EST-SSR markers for genetic diversity assessment. Cluster analysis using Jaccard similarity coefficients revealed distinct genetic groupings: SCoT markers formed two clusters, and EST-SSR markers formed two main clusters, with some outliers. Population structure analysis using Bayesian clustering revealed two ancestral populations with high admixture. This is the first time SCoT markers were used to assess genetic diversity in Withania somnifera . Quantitative real-time (qRT-PCR) expression analysis of six withanolide biosynthetic pathway genes (GT, CAS, FPPS, HMGR, SE, SS) across four genotypes of Withania somnifera reveals genotype-specific differential expression, further supporting the diversity observed by molecular markers. Our results indicate that both markers are informative and can be used to detect distinct genetic variations within Withania genotypes, providing valuable insights for breeding and conservation efforts and enabling the development of improved cultivars suited to various agroclimatic conditions.