RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress

Association between molecular markers and resistance to bacterial blight using binary logistic analysis

The most effective strategy for managing wheat bacterial blight caused by Pseudomonas syringae pv. syringae is believed to be the use of resistant cultivars. Researching the correlation between molecular markers and stress resistance can expedite the plant breeding process. The current study aims to evaluate the response of 27 bread wheat cultivars to bacterial blight disease in order to identify resistant and susceptible cultivars and to pinpoint ISSR molecular markers associated with bacterial blight resistance genes. ISSR markers are recommended for assessing a plant's disease resistance. This experiment is focused on identifying ISSR molecular markers linked to bacterial blight resistance. After applying the bacterial solution to the leaves, we performed sampling to determine the infection percentage in the leaves at different intervals (7, 14, and 18 days after spraying). In most cultivars, the average leaf infection percentage decreased 18 days after spraying on young leaves. However, in some cultivars such as Niknegad, Darab2, and Zarin, leaf infection increased in older leaves and reached up to 100% necrosis. In our study, 12 ISSR primers generated a total of 170 bands, with 156 being polymorphic. The primers F10 and F5 showed the highest polymorphism, while the F7 primer exhibited the lowest polymorphism. Cluster analysis grouped these cultivars into four categories. The resistant group included Qods, Omid, and Atrak cultivars, while the semi-resistant and susceptible groups comprised the rest of the cultivars. Through binary logistic analysis, we identified three Super oxide dismutase-related genes that contribute to plant resistance to bacterial blight. These genes were linked to the F3, F5, and F12 primers in regions I (1500 bp), T (1000 bp), and G (850 bp), respectively. We also identified seven susceptibility-associated genes. Atrak, Omid, and Qods cultivars exhibited resistance against bacterial blight, and three genes associated with this resistance were linked to the F3, F5, and F12 primers. These markers can be used for screening or transferring tolerance to other wheat cultivars in breeding programs.

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.

Exploring the impact of nano-Se and nano-clay feed supplements on interleukin genes, immunity and growth rate in European Sea Bass (Dicentrarchus labrax)

This study aimed to investigate the effects of adding Nano-Selenium (NSe) and Nano-clay (NC) as feed supplements on European Sea Bass (Dicentrarchus labrax). Two separate experiments were conducted, one with NC and the other with NSe. Each experiment consisted of four sub-groups with varying concentrations of NC or NSe. The expression levels of five immune-related genes (TNF-α, TNF-β, IL-2, IL-6 and IL-12) were measured using Real-time Quantitative PCR (Rt-PCR) Assay. The results showed an increase in the expression of interleukins (IL-2, IL-6 and IL-12) and pro-inflammatory cytokines (TNF-α and TNF-β) after exposure to NC and NSe. TNF-α gene expression was significantly higher with both 1 mg and 10 mg concentrations of NC and NSe. TNF-β gene expression was highest with the 5 mg concentration of NC. The concentrations of 1 mg and 10 mg for NC, and 1 mg, 5 mg, and 10 mg for NSe, led to the highest (p < 0.05) levels of IL-2 expression compared to the control. Similar trends were observed for IL-6 and IL-12 gene expression. Understanding the impact of these concentrations on gene expression, growth rate, biochemical indices, and antioxidant status can provide valuable insights into the potential applications of NC and NSe supplements on European Sea Bass.

Synergistic effect of cucurbitacin E and myricetin on Anti-Non-Small cell lung cancer: Molecular mechanism and therapeutic potential

BACKGROUND

Non-small cell lung cancer (NSCLC) is associated with extremely high morbidity and mortality rates worldwide. Citrullus colocynthis (L.) Schrad, widely distributed in Asian and African countries, is used to treat cancers in traditional Uyghur medicine.

HYPOTHESIS/PURPOSE

The combination of Cucurbitacin E (CuE) and Myricetin (Myr) of C. colocynthis could treat NSCLC by targeting autophagy.

STUDY DESIGN

The potential anti-cancer components (CuE and Myr) of C. colocynthis were identified using in-silico methods and further in vitro explored the anti-NSCLC properties of the combination of CuE and Myr.

METHODS

Network pharmacology and molecular docking were used to identify potential therapeutic compounds of C. colocynthis for the treatment of NSCLC. In A549 cells, the anti-cancer activities and synergy of CuE and Myr were studied using CompuSyn, their mechanism behind autophagy regulation was determined by western blotting and immunofluorescence staining.

RESULTS

CuMy-12 (CuE: 0.5 µM, Myr: 20 µM), a combination of CuE and Myr from C. colocynthis, inhibited A549 cell proliferation and colony formation, and induced apoptosis and cell cycle arrest in the G0/G1 phase, exhibiting a synergistic effect. Furthermore, CuMy-12 inhibited autophagy and activation of the PI3K/AKT/mTOR signaling pathway, which was characterized by a decrease in Beclin 1, AKT, and phospho-AKT proteins.

CONCLUSION

CuMy-12 can be considered a natural candidate with anticancer activity for autophagy-based regulation, but mechanistic and clinical studies are required to validate its potential.

Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

Background

Capsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers.

Results

Out of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index (I), expected heterozygosity (He), Nei’s gene diversity, total diversity among species (Ht), diversity within species (Hs), respectively. Further, the coefficients of gene differentiation (Gst) and gene flow (Nm) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA).

Conclusion

ISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.

Morpho-Physiological and Molecular Characterization Reveal Low Genetic Variation for Conservation of Endangered Iranian Moshgak (Ducrosia anethifolia Boiss)

Ducrosia anethifolia Boiss is an aromatic vegetable and medicinal plant of Apiaceae family. In this study, morphological and essential oil studies as well as ISSR analyses were employed to investigate genetic diversity in 120 Moshgak accessions of 24 Iranian populations. High variations were observed in morpho-physiological traits (morphological and essential oil contents) of the populations in 2 consecutive agronomic years. In both studied years, the highest leaf (1% and 1.2%) and seed (2.46% and 2.9%) essential oil contents were recorded for the Abarkuh population. For ISSR analysis, 15 primer combinations were employed that produced 120 polymorphic bands. Dendrogram and STRUCTURE software grouped the accessions into four clusters although such grouping did not fit the geographic regions perfectly. Among the populations, Abarkuh and Kerman exhibited the highest genetic distance. Based on analysis of molecular variance (AMOVA), only 4.32% of the total genetic diversity was observed among the populations, while 95.68% was detected within the populations. Moreover, the studied populations exhibited a low genetic differentiation (Gst = 0.13) but a high gene flow (Nm = 3.26). It may be concluded that the results of the study provide new insights regarding the genetic diversity of Moshgak germplasm that will be useful for its conservation management and breeding programs for oil- and yield-related traits.

Genetic Analysis of Prunus salicina L. by Random Amplified Polymorphic DNA (RAPD) and Intersimple Sequence Repeat (ISSR)

Background

Prunus salicina L. is an important fruit tree species of great economic value which is mainly distributed in the northern hemisphere.

Methods

25 samples of Prunus salicina L. were collected from 8 provinces in China, Japan, USA, and New Zealand. The genetic variations of these samples were characterized by the random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) technique, respectively, and in combination.

Results

Totally, 257 RAPD bands ranging 200∼2300 bp was found, and 81.59% of these bands were polymorphic. ISSR analysis identified 179 bands ranging 300∼2500 bp, and 87.74% of the bands were polymorphic. ISSR results showed that the similarity coefficient index between samples P10 (Maihuangli in Anhui, Chin) and P13 (Longyuanqiuli in Heilongjiang, China) was lowest, while that between samples P10 (Maihuangli in Anhui, Chin) and P15 (Baili in Japan) was highest. Combined analysis of RAPD and ISSR demonstrated that the similarity coefficient index between samples P4 (Qiepili in Ningbo, Zhejiang, China) and P13 (Longyuanqiuli in Heilongjiang, China) was lowest, while that between samples P19 (Laroda in USA) and P20 (Red heart in USA) was highest.

Conclusion

RAPD combined with ISSR analysis can be used for genetic characterization of Prunus L. species.

Impact of Limited Dispersion Capacity and Natural Barriers on the Population Structure of the Grasshopper Ommexecha virens (Orthoptera: Ommexechidae)

The grasshopper Ommexecha virens Serville has low dispersion capacity, and it is regarded as a specialist, only being found in sandy, dry environments with high incidence of sunlight. Considering these aspects, we evaluated the diversity and genetic structure of O. virens natural populations using ISSR (Inter Simple Sequence Repeat) markers. The data pointed to low expected heterozygosity for some populations (H_E = 0.06-0.09), probably a consequence of positive inbreeding, which is typical of species showing low or null dispersion indices. Moreover, significant genetic differentiation was observed (F_ST = 0.50 and G_ST = 0.51), as well as low number of migrants (N_m = 0.47), indicating that the populations are genetically differentiated. This is likely related to the limitation in dispersing and fragmentation of suitable environment localities colonized by O. virens. The populations of O. virens were structured in three genetic groups associated to different landscapes, revealing the presence of a secondary contact zone, possibly arisen from isolation followed by genetic divergence among populations and subsequent gene flow of divergent individuals of O. virens. At last, we found positive isolation by distance (IBD; r: 0.427; P: 0.025) which is an important factor, since it may be adding to the emergence of reproductive barriers among individuals of O. virens that have been experiencing isolation.

Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: an endangered medicinal plant

Gloriosa superba L., an endangered medicinal plant with global interest due to presence of colchicine, an important alkaloid used in formulations of Indian and Traditional medicine. The plant has become endangered due to its unscientifically exploitation and high medicinal values. In the Present study 10 randomly amplified polymorphic DNA (RAPD) and 6 ISSR markers were employed to assess genetic divergence among micro propagated, wild and field cultivated plants of Gloriosa superba collected from different parts of India. In RAPD analysis, all the 10 accession with 10 RAPD primers amplified 466 fragments, with 96.43 % polymorphism and with an average of 46.6 bands per primer. The size of amplicons varied from 1656 to 100 bp. While, ISSR primers produced 328 fragments of which 298 were polymorphic with an average of 49.7 bands per primer with 91.83% polymorphism. The size of amplicons ranges from 2395 to 181 bp. RAPD, ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes, Average PIC value for RAPD, ISSR and combined RAPD + ISSR markers obtained was ≤ 0.50 suggesting the informativeness of markers. Jaccard's coefficient ranges from 0.18 to 0.75 (RAPD) and 0.17 to 0.61 (ISSR) and 0.21-0.52 for pooled ISSR and RAPD markers. The clustering pattern based on UPGMA analysis of the genotypes in the combined analysis revealed that the majority of the genotypes remained similar to the ISSR dendrogram, while the RAPD-based dendrogram showed some variation in the clustering of genotypes. The result of PCA scattered plot obtained were in agreement with the UPGMA dendrogram, which further confirms the genetic relationships explain by cluster analysis. Results confirmed that the genotype studied had good genetic diversity and can be used for identification, conservation, and future breeding program of Gloriosa species and consequently for the benefit of the pharmaceutical industries.

Comparative assessment of ISSR, RAPD, and SCoT markers for genetic diversity in Clerodendrum species of North East India

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.

Genetic relations among and within wild and cultivated Thymus species based on morphological and molecular markers

In the present study, the diversity of 11 Thymus species was assessed using molecular and morphological markers. Essential oil content and morphological traits were also investigated during two agronomic years. The result of the analysis of variance showed considerable differences among morphological traits. In the first and second years, the essential oil content of the species varied from 0.63 to 1.94% and 0.86 to 2.34%, respectively. T. vulgaris and T. migricus showed the highest essential oil content in two agronomic years. In this research, nine ISSR primers were also used to amplify 151 polymorphic bands in 77 accessions belonging to 11 Thymus species. Cluster and principal component (PCA) analyses classified the species in three major groups. Among the species, T. vulgaris and T. fedtschenkoi presented relatively higher genetic distance in comparison with other species. Analysis of molecular variance (AMOVA) revealed that 72.34% of the total variation was belonged to within-species variation, while 27.66% was associated among the species. High gene flow (Nm = 1.11) and genetic differentiation (Gst = 0.31) were also observed among the species. T. transcaspicus exhibited the highest genetic variation (0.19), polymorphism % (57.69%), and Shannon index (0.29). The STRUCTURE analysis also showed a high admixture of Thymus species that might be originated from a high rate of natural hybridization. Finally, based on molecular and morphological information, T. vulgaris and T. carmanicus can be suggested as good candidate species for further breeding programs in Thymus species.

Foliar application of elicitors enhanced the yield of withanolide contents in Withania somnifera (L.) Dunal (variety, Poshita)

This study involves a detailed investigation about the effect of three elicitors, such as chitosan, jasmonic acid and salicylic acid (SA) on withaferin A and withanolide A contents of Withania somnifera (L.) Dunal (Poshita variety). Moreover, the different environmental regimes were also studied to assess and optimise the accumulation of withaferin A and Withanolide A contents. In an open environment, the total withaferin A content was found to be increased 6.3 and 5.8 times when sprayed with chitosan, 10 ppm and 50 ppm, respectively, as compared to control. Similarly, the total withanolide A content was found to be increased 4.5 and 3.6 times when sprayed with jasmonic acid (400 ppm and 200 ppm, respectively) with respect to control. In a controlled condition, the total withaferin A content was found to be increased 6 and 4.5 times when sprayed with jasmonic acid (400 ppm and 200 ppm, respectively) as compared to control. On the other hand, the total withanolide A content was found to be enhanced by 7 and 4.3 times when sprayed with jasmonic acid (400 ppm) and SA (1 ppm), respectively, as compared to control. Therefore, this study was focussed on the optimisation of enhanced accumulation of withaferin A and withanolide A contents in the aerial parts of the plant in open and controlled environment by foliar application of elicitors in minimal concentrations.

Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt

BACKGROUND

Silybum marianum L. Gaertn is a medicinal plant of unique pharmaceutical properties in the treatment of liver disorders and diabetic nephropathy. Biochemical (SDS-PAGE) and molecular markers such as randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) technologies were used in this work to detect genetic diversity of 14 collections of Silybum marianum population in Egypt.

RESULTS

The electrophoretic pattern of seed protein gave different molecular weight bands, ranging from 24 to 111 KDa with the presence of unique bands. RAPD results revealed a high level of polymorphism (73.2%) using 12 RAPD primers, but only eight of them gave reproducible polymorphic DNA pattern. Sixteen primers were used in the ISSR method; only ten of them yielded clearly identifiable bands. The percentage of polymorphism is about 80% of the studied samples.

CONCLUSION

The obtained data confirmed that SDS-protein, RAPD, and ISSR markers are important tools for genetic analysis for Silybum marianum and recommended to give accurate results.

Isolation-by-environment as a driver of genetic differentiation among populations of the only broad-leaved evergreen shrub Ammopiptanthus mongolicus in Asian temperate deserts

Whether the effect of migration-selection-drift equilibrium on population structure is governed by spatial or environmental differences is usually elucidated by isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-resistance (IBR) tests. The population structure of Ammopiptanthus mongolicus, a broad-leaved evergreen psammophyte in eastern Central Asia, was previously thought to follow an isolation by distance pattern. However, recent studies have emphasized the effects of environmental factors on its growth and distribution, suggesting an important influence of local adaptation on the genetic structure of the species. Using inter-simple sequence repeat (ISSR) markers, we verified the previously inferred low intra-population variation and high inter-population differentiation. However, in contrast to previous studies, the results of partial Mantel tests and a maximum likelihood population effects mixed model (MLPE) suggested that local climate differences, rather than geographic distances or resistance distances, are the main factor affecting population differentiation. Further analysis with removal of multicollinear climatic variables and univariate MLPE found that summer and winter precipitation were crucial for shaping the current population genetic structure. Since local precipitation is related to the regeneration, colonization, and overwintering survival of A. mongolicus, its influence on demographic change may explain its effect on the population genetic structure. In addition, precipitation is related to terrain despite westward decreases, which explains the independence of genetic difference and geographic distance. The identified role of IBE suggests that collecting germplasm resources from genetically differentiated populations could be a more effective strategy to preserve the overall genetic diversity of the species than the establishment of corridors to enhance gene flow among populations.

Intra-population genetic diversity of Buchloe dactyloides (Nutt.) Engelm (buffalograss) determined using morphological traits and sequence-related amplified polymorphism markers

Genetic variation and diversity are prerequisites for improvement of buffalograss breeding. To assess the within-population genetic diversity of buffalograss, seven morphological traits were evaluated to confirm the variations at the morphological level. The principal component analysis revealed that leaf length, leaf width and stolon branches had a significant contribution to the total variation. The first three principle components showed 72.55% variation. The DNA analysis performed using SRAP primers was used for deducing the diversity at the DNA level. A total of 125 bands were obtained with 8 selected SRAP primer pairs, of which 119 (95.2%) were polymorphic. The polymorphic information content ranged from 0.94 to 0.97 with a mean of 0.96; the marker index ranged from 10.34 to 18.43 with an average value of 14.28. The individuals were successfully assigned to two major groups according to sex in the PCoA and UPGMA dendrogram based on SRAP data, while the individuals could not be grouped based on morphological traits, and the two markers were not significantly correlated (r = 0.0753, P = 0.8489 > 0.05). The molecular data revealed that sex is a critical factor and that female and monoecious plants could be chosen as parents to breed new varieties.