Random Amplified Polymorphic DNA Markers Research Articles

Assessment of Genomic Integrity of Vitex negundoL., An Important Indian Medicinal Plant, Using RAPD Markers

Vitex negundo is an Indian medicinal plant containing steroids, flavonoids, lignans and terpenoids that can be used as a precursor for commercial production. An efficient marker system such as Random Amplified Polymorphic DNA (RAPD) was used to assess the genetic integrity of V. negundo. The straightforward method RAPD can be used to evaluate genomic integrity because it uses a small amount of DNA for PCR amplification. Six out of thirteen RAPD primers generated 150 distinct bands, of which 31 were polymorphic, with an average of 5.16 polymorphic bands per primer. A maximum of up to 32 fragments were amplified, and an average of 25 per primer, and the amplicons varied in size between 100 and 2000bp. The percentage of polymorphism ranges from 12.9 to 22.5, with an average of 16.6. The PIC values ranged from 0.11 to 0.63 for RAPD primers. The study pointed out that RAPD markers evaluate the genetic fidelity in Vitex negundo. The UPGMA cluster analysis grouped all in vitro raised plantlets treated with different growth regulators such as BAP, DPU, TDZ, and mT. The principal component analysis also substantiates this clustering pattern. Thus, the phylogenetic relationship and a high genetic variation revealed in the present study could provide baseline data for the conservation and improvement of this plant in future. Also, the molecular marker identified in this study will be helpful in the authentication of this species to prevent adulteration in herbal medicine.

Phenotypic and Molecular-Markers-Based Assessment of Jamun (Syzygium cumini) Genotypes from Pakistan

Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs.

Unveiling Genetic Variation in Garlic Genotypes in Response to Rust Disease Using RAPD Markers

Garlic (<em>Allium sativum</em>), cultivated worldwide for its medicinal and nutritional value, faces challenges due to diseases caused by various pathogens. In this study, eleven garlic genotypes from Iran and one from China were selected and sown under natural infection rendered by the rust fungus (<em>Puccinia alli</em>) over two consecutive years. Subsequently, disease distribution and severity, percentage of infection and susceptibility of different garlic genotypes to rust disease were investigated. The results showed that genotype Solan was the most susceptible, with disease severity of 30.81%. In comparison, genotypes Aliabad and Bahar were resistant against rust disease with the lowest infection percentages of 13% and 16.37%, respectively. Further, genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) markers. Out of 10 primers used, 95 scorable bands were generated, of which 66 (69.48%) were found to be polymorphic. A dendrogram was constructed based on RAPD polymorphism using the UPGMA method, and the genotypes were separated into six distinct clusters based on Jaccard's coefficient of similarity. Additionally, it was observed that there is no genetic differentiation among the genotypes based on their geographical origin. This study highlights the significant diversity in resistance and susceptibility among garlic genotypes, which can be harnessed in plant breeding programs.

Phenotypic and Molecular Diversity of Wild Populations of Acca sellowiana (Berg.) Burret in the Southern Area of Natural Distribution

Acca sellowiana is a subtropical tree in the myrtle family (Myrtaceae) native to southern Brazil and northeastern Uruguay. It is recognized for its value as a fruit-bearing, ornamental, and medicinal species. Based on distinctive characteristics of fruits, seeds, and leaves, as well as its geographical distribution pattern, two variants of the species are distinguished: the “Brazilian type” and the “Uruguayan type”. The objective of this study was to characterize, for the first time, the diversity of 202 individuals from four wild populations in Uruguay, representative of the species’ most southern natural distribution. Twenty-three morphological descriptors (leaf, flower, and fruit) and 204 RAPD (Random Amplified Polymorphic DNA) markers were used. The morphological data collected validated the main criteria that distinguish “Uruguayan type” populations from “Brazilian type” populations, such as lower seed weight and fruit size, thin and slightly rough skin, high pulp percentage, and hairy white abaxial leaf surfaces. Analyses of both morphological and molecular data indicated wide diversity and strong population structuring, which is relevant information for designing conservation plans, sustainable utilization, and genetic improvement of the plant genetic resources of this species.

Genetic variability analysis of tomato varieties using rapd markers under heat stress

Heat stress threatens agricultural and food security by reducing yield and causing plant death. The use of intra-genetic diversity in heat stress responses is a potential avenue for harnessing tolerance to climate change circumstances. This study investigated the genetic diversity of twelve tomato genotypes in Bangladesh, focusing on their suitability for summer cultivation using seven Random Amplified Polymorphic DNA (RAPD) markers. The banding patterns obtained from the PCR results were used to identify genetic differences between individuals. The RAPD markers were found to show their effectiveness in discriminating the studied lines through the computation of average Polymorphism Information Content (PIC) values, particularly focusing on dominant markers with PIC values ranging from 0 to 0.5, emphasizing the informative nature of the employed primers. Cluster analysis grouped several genotypes with possible common ancestry. Overall, BARI Hybrid Tomato 4, BARI Hybrid Tomato 8, A12, D13, and RHS1 emerged as promising candidates for further genetic research and breeding programs, particularly in the context of heat-stress conditions during summer tomato cultivation in Bangladesh. Bangladesh J. Bot. 53(1): 91-100, 2024 (March)

Genetic diversity of maize resources revealed by different molecular markers

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.

Screening of among seventeen sunflowers (Helianthus annuus L.) genotypes for oil content and the first flowering day using random amplified polymorphic DNA markers

Background Sunflower refers to the tribe Helianthus, subtribe Helianthinae, and family Asteraceae, which collectively contains 20 genera and 400 species. An important oilseed crop that yields edible oil is Helianthus annuus L. Objective The primary goal of the current study was to assess the genetic diversity of 17 genotypes of sunflower (Helianthus annuus L) To measure the oil content during the initial flowering period and to reach the highest percentage of oil can be obtained from the first flowering day. Materials and methods Five RAPD (random amplified polymorphic DNA) primers were used to detect the genetic diversity of the 17 sunflower hybrid genotypes obtained from Spain. Phylogenetic relationships of 17 sunflower genotypes were determined using three replications and 6 m lines on August 15, 2019, at the National Research Centre farm in Nubaria as part of a donation from the German corporation (strobe), Spain. To analyze the genetic diversity and phylogenetic linkages in sunflower germplasm, DNA fingerprinting and the Random Amplified Polymorphic DNA (RAPD) molecular marker approach were also used. Results and conclusion The oil content of 17 sunflower genotypes (Helianthus annuus L.) was assessed, with values ranging from 46 to 50%, with the highest values falling into five genotypes. However, the two genotypes were found to have the lowest oil percentage (46%). The early age and oil percentage differed among the varieties. In the Tornado and Elves genotypes, the longest and shortest days were 59 and 47, respectively. The means and standard errors for all statistical data are reported. Statistical significance was evaluated using the LSD. P values were considered statistically significant at P less than or equal to 0.05. According to the findings, RAPD primers generated 49 bands with a size range of 0.1–3 kb and an 87.75% polymorphism percentage. For RAPD, 43 polymorphic bands with distinct bands were observed. Morphological features and RAPD analysis separated the UPGMA Dendrogram into three groups. Jaccard’s coefficient was used to analyze the genetic similarity matrix, and a morphological study revealed that Tornado and Elvas, both from Spain, shared the most genetic similarity (0.970). RAPD analysis and morphological features are useful in identifying genetic variants. Conclusion, according to our findings, Helianthus annuus L. has a significant variation ratio. Indicating substantial diversity across the 17 sunflower genotypes, the genetic similarity index calculated using pooled data from RAPD markers showed an extensive range from 0.645 to 0.986. This study may be a reference for future research on Helianthus annuus L. and may support breeding initiatives and species concepts.

Using RAPD and ISSR markers to assess genetic diversity and conservation of Bruguiera gymnorrhiza (L.) Lam. for sustainable management on Kerala's West Coast

In this genetic study focusing on Kerala’s west coast, particularly the southern region with diverse demographics and fluctuating salinity, we utilized random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) molecular markers to assess the genetic variation of the plant species Bruguiera gymnorrhiza, which is facing habitat loss in the region. The ISSR marker demonstrated a higher degree of polymorphism (13.6%) compared with RAPD (3.5%). The polymorphic information content averaged 0.484 for ISSR and 0.354 for RAPD. The B. gymnorrhiza samples from Alappuzha and Thrissur clustered together in both markers. Nei’s genetic diversity index (h) was determined to be 0.430 for RAPD and 0.453 for ISSR. The unweighted pair group with the arithmetic mean dendrogram, reflecting a greater degree of polymorphism, supports the conservation of B. gymnorrhiza throughout Kerala’s west coast. Additionally, the marker index was calculated as 0.506 for ISSR and 0.392 for RAPD, highlighting the efficacy of ISSR markers in assessing the genetic diversity of B. gymnorrhiza.

Genetic Diversity of West African Honey Bee (Apis ‎mellifera adansonii Latreille, 1804) from Rural and Urban ‎Areas of ‎Kwara State, North-Central Nigeria

Over one third of the world’s crops– including fruits, vegetables, nuts, spices, and oilseed–‎require insect pollination, and human reliance on ‎pollination services by honey bees (Apis ‎mellifera) to promote these crops continues to rise due to increasing demands from growing ‎human ‎populations. Identifying the effects of urbanization on genetic diversity on this ‎pollinating insect is important in the field of bioscience. This study aimed to investigate genetic diversity of A. mellifera in Kwara State, Nigeria, using the random amplified polymorphic DNA (RAPD) marker. ‎Thirty honey bees ‎were simultaneously collected from both rural and urban regions in ‎Kwara state, Nigeria. Samples were morphologically identified using ‎standard methods, ‎genomic DNA isolated and amplified using five RAPD primers. Data collected were ‎analysed using PyElph, ‎ARLEQUIN, and GeneAlEx version 6.501 software. The results ‎showed that the DNA fragment sizes produced per primer varied from 200 to ‎‎3000 bp. Percentages of polymorphic loci amplified by each primer varied from 17.33 to 33.33%. ‎Analysis of unbiased Nei genetic ‎distance values showed that Agbede (rural) and Adewole ‎‎(urban) showed the highest value of unbiased genetic distance (0.073), while ‎Amoyo ‎‎(rural) to Idofian (urban) exhibited the lowest value (0.027). Dendrogram analysis revealed ‎genetically close relationships among the sampled ‎A. mellifera‎ populations. The low level of genetic ‎polymorphisms observed among the honey bee populations in the two ‎regions ‎indicated that there is genetic relatedness among them. This study concluded that RAPD ‎marker is a useful method for ‎understanding population genetic structure of the African honey ‎bees. These results can be used as baseline information for future genetic ‎diversity ‎assessment of honey bees in Nigeria with larger samples. It is therefore recommended that ‎there is a need to safeguard the genetic ‎diversity of A. mellifera‎ to prevent extinction or ‎gradual loss of diversity‎‎‎.

Genetic Diversity Analysis of Bitter Gourd (Momordica charantia L.) Germplasm using Molecular Markers

Bitter gourd [Momordica charantia L.] is an important cucurbitaceous crop of medicinal and nutraceutical value. The present study was conducted to compare the efficacy of random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) molecular markers for genetic diversity analysis of bitter gourd. Twenty-one genotypes of bitter gourd, collected from different parts of India, were used for diversity analysis using two different types of markers. RAPD and ISSR markers yielded an average of 7.16 and 5.73 amplicon per primer, respectively. In the present study, RAPD and ISSR showed 89 and 63% polymorphic bands, respectively. Combined data analysis of RAPD and ISSR markers provided 73.66% polymorphism with 5.33 polymorphic amplicons per primer. The better discriminatory power of ISSR markers over RAPD markers may be due to comparatively higher values of average polymorphic information content (0.175) as well as the diverse nature of the genotypes. The information generated in this study would be helpful in designing breeding strategies for bitter gourd improvement.

Improve Abiotic Stress Tolerance in Crops by Molecular Markers: A Review

Abiotic stressors include things like heat, cold, drought, and salt that plants have to withstand. These are the main and ongoing agricultural challenges that lower crop production. In the end, modifications to components, nutrient control, and biosynthetic ability hinder or even stop plant development. Stress is an environmental factor that, in terms of genetics, prevents full genetic expression. These markers are divided into many types based on their intended use: Simple sequence repeat (SSR) markers are a great tool for determining stress tolerance, but RAPD (random amplified polymorphic DNA) markers are useful for identifying and screening hybrids based on salinity and drought stress resistance. These markers are also necessary for the QTL (Quantitative Trait Loci) mapping of genes linked to stress. These ancestor genes control the production of dehydrins and saltol in response to dryness and salinity, respectively. DNA markers enable the use of innovative approaches and marker modification in marker-assisted breeding to increase tolerance to abiotic stress.

Evaluation of Biological Control of Sorghum Strains Using Bacillus Thuringiensis and Pseudomonas Aeruginosa Under Drought Stress

Background: Sorghum is an economically significant staple food crop for more than half a billion people in developing nations, especially in arid and semi-arid locations where drought stress is a significant limiting factor. Despite usually being regarded as tolerant, sorghum suffers severely from drought stress, which lowers its productivity and nutritional quality throughout its principal cultivation areas. Objective: Improvements in DNA fingerprinting by ISSRs, SSRs, and RAPD markers have also been employed in sorghum genetic modification (GMOs) to enhance the economic characteristics of this crop. Materials and methods: To provide a natural defence against pests, the most tolerant plants among the seven varieties of sorghum bicolour were selected and planted in the second season of 2020–2021 under treatment with two microorganisms, B. thuringiensis and P. aeruginosa. This study considered seven varieties of sorghum bicolour planted under 50% water deficiency in 2019–2020. Genetic variability analysis of sorghum genotypes was performed using seven Inter-Simple Sequence Repeat (ISSR) primers, six Simple Sequence Repeat (SSR) primers, and five Random Amplified Polymorphic DNA (RAPD) primers. Seven Sorghum bicolour accessions were collected from various regions of Egypt and their phylogenetic relationships were evaluated. Additionally, DNA fingerprinting and analyses of the genetic diversity and evolutionary linkages in the sorghum germplasm employed the (ISSR) molecular marker technique. Results and conclusion: The Fisher Least Significant difference test (LSD) at P < 0.05, based on RAPD, ISSR, and SSR markers demonstrated a significant connection. The findings demonstrated that 51 bands with a size range of 100–1500 bp and polymorphism percentage of 72.5% were created using five RAPD primers. Seven ISSR primers generated 45 bands With a 57.8(%) polymorphism percentage, ranging in size from 100 to 3000 bp. six SSR primers generated 28 bands with (67.86%) polymorphism percentage of 67.86 %, ranging in size from 100 to 1500 bp. Morphological characteristics and ISSR, SSR, and RAPD analyses were used to group the UPGMA Dendrogram into groups. Jaccard's coefficient was used to analyse the genetic similarity matrix. The maximum similarity was observed for ISSR between Hybrid Sh1 and Hybrid Sh306 (0.984%), SSR between Hybrid Sh306 and Sudan grass (0.964%), and RAPD between Giza 15 and Indian Millet (0.706%). The classification of sorghum germplasm, breeding initiatives, and conservation efforts rely heavily on the determination of the genetic diversity among sorghum species. Identification of genetic variants, morphological features, and genetic analysis of ISSR, SSR, and RAPD are useful techniques. These findings demonstrate a large ratio of variation in sorghum. This work could serve as a guide for future research on sorghum and aid in the understanding of species and breeding initiatives.

Detected Genetic Markers for Three Varieties of Rice (Oryza sativa L.) under Nano- Particles

Despite the enormous advancements in breeding, fresh and accessible methods of plant development are preferred. Many research have been done to determine the impact of zinc oxide nanoparticles (ZnO NPs) and magnesium nanoparticles (MgONPs) on plant growth. ZnO NPs and MgONPs have been used extensively in agriculture. Few research have looked into the potential impact of ZnO NPs on grain Zn content or cereal yield formation to date. The goal of the study was to demonstrate how varied concentrations of nanoparticles affected root germination in three different rice types (Giza 177, Sakha super 300, and Sakha 108) and the fungus Fusariummoniliforme, which causes foot rot in rice. Here, we performed a pot experiment to assess the effects that ZnO nanoparticles and MgONPs had on the shoot length, root length, and germination of rice. The experiment involved three dosages of Zn and Mg nanoparticle solution at varying concentrations of 10, 20, and 100 ppm. The outcomes showed that, when compared to the control treatment, ZnO NPs and MgONPs increased the length of the shoot, the length of the roots, and the rate of germination. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers, the genetic makeup of plants treated with 10, 20, and 100 ppm AgNPs was also examined. In vitro rooted shoots were acclimated in a greenhouse before being tested for biochemical stability and phenotypic stability. In vitro, callogenesis and caulogenesis were both reduced by AgNPs at the greatest dose (100 ppm). In order to maximise genome coverage, three rice cultivars from distinct origins were chosen, and they were tested using three RAPD markers and seven selected ISSR markers. AgNPs-treated plants using ISSR markers produced 87 amplified bands in total, 45 polymorphic allelic variants, and 36 monomorphic allelic variations. The Pearson correlation coefficient was used in the Mantel test to determine whether there was a significant association between the Jaccard's dissimilarity matrices based on ISSR and RAPD markers (r = 0.69; P 0.05). Morphological characteristics, ISSR, and RAPD analysis were used to partition the UPGMA Dendrogram into two groupings. Jaccard's coefficient was used to analyse the genetic similarity matrix. Sakha Super 300 and Giza 177 had the most genetic similarity (95%) while Sakha 108 and Giza 177 had the lowest genetic similarity (90%) according to ISSR and RAPD study. The classification of rice germplasm, breeding initiatives, and conservation efforts all heavily rely on the determination of genetic diversity within the rice species. To find genetic variations, morphological characteristics, ISSR, and RAPD analysis are useful techniques. The findings demonstrated the large ratio of variation in rice. This work successfully established the possibility of using MgONPs and ZnO NPs as high-performing fertilisers to improve rice output and quality.This study could serve as a guide for future research on rice and could support efforts to understand the species and improve breeding stock.

Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Chilli Pepper Cultivar: Physiology and Molecular Approach

The fruit color of chili pepper is an important characteristic in identification and classification and is often used as the basis for determining consumer preferences. Information on the relationship between chili fruit color and its molecular profile is very important in supporting selection activities in plant breeding. This study aims to identify genetic diversity associated with the fruit color of three genotypes of chili (Capsicum frutescens L.): Cakra Hijau, HV-149 and G1/M8, using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). Morphological confirmation was carried out according to Capsicum descriptors. Nineteen RAPD markers and six SSR markers were used for genetic variability assessment. Genetic variation was analyzed using the unweighted pair group method with the arithmetic mean and the Jaccard similarity index. The three chili genotypes had different fruit colors at each maturation stage. The immature Cakra Hijau fruit is dark green and turns dark red as it ripens. The immature fruits of the G1/M8 line are light green and turn red when ripe. Finally, immature HV-149 fruits are dark green and yellow when ripe. The SSR markers used in this study were unable to show polymorphism. On the other hand, the RAPD marker successfully detected genetic variation in the three chili genotypes and resulted in a total of 49 alleles. The average value of polymorphic information content of the RAPD primers used ranged from 0 to 0.296, with the highest index indicated by OPA-1. The dendrogram shows the separation of the three genotypes into two main clusters, with the first cluster consisting of the HV-149 variety and the second cluster consisting of Cakra Hijau and G1/M8 lines. This study revealed that there are genetic variations based on the morphological characteristics of fruit color at each ripening stage and RAPD band profile. The RAPD marker was more effective than the SSR marker for identifying the genetic diversity of fruit color in the three chilies studied.

Association between quantitative morphological traits and RAPD molecular markers in pomegranate (Punica granatum L.).

Pomegranate (Punica granatum L.) is very important in terms of horticulture and food around the world. The present research aimed to identify the random amplified polymorphic DNA (RAPD) markers associated with morphological traits in pomegranate genotypes. Significant differences were observed among the studied genotypes based on the recorded traits. The 18 RAPD primers produced a total of 154 polymorphic fragments among genotypes. Using multiple regression analysis between each of the morphological traits and 154 RAPD polymorphic bands, RAPD markers associated with each of the morphological traits were identified. In total, 11 markers showed significant correlations with fruit weight, 9 markers with 100-aril weight, 11 markers with anthocyanin, and 8 markers with total soluble solids. Some markers were associated with more than one morphological trait, showing that the association of a marker with more than one trait can be caused by the pleiotropic effects of quantitative trait loci related to each other in different traits. For instance, the BA6-1 marker showed positive correlations with fruit weight, fruit crown width, and leaf length. Also, OPG13-3 and BA6-10 markers showed positive correlations with total soluble solids and anthocyanin content. The informative markers identified related to morphological characteristics in pomegranate can be a suitable guide to identify the genotypes with valuable fruit traits. Also, these markers can be used in selecting suitable parents for population generation for mapping purposes.

The potential of gamma irradiation on antioxidant capacity and genomic alterations in Calendula officinalis

There are lines of evidence that ionizing radiations such as gamma rays can cause different biological effects on plants. Marigold (Calendula officinalis L.) is a member of the family Asteraceae. It possesses profound amounts of active ingredients. The aim of this study was to evaluate the changes imposed upon different dose levels of gamma radiation on some features of Calendula officinalis such as antioxidant activity, total phenolic compounds and flavonoid contents, antibacterial activity and genomic alterations. Calendula officinalis seeds were exposed to different doses of Gamma radiation (0, 10, 15, 20 and 25 GY). Total phenolics, flavonoids, antioxidant activity (measured by DPPH assay) using methanolic extracts of plants and antibacterial activity measured by the disc diffusion assay showed significant differences to the control samples. The samples treated with 10 GY gamma rays showed the highest total phenol and flavonoid contents. Antioxidant activity significantly differed between Gamma rays dose levels and it was the highest at 25 GY. Four bacterial strains including E. coli, Bacillus subtilis and Pseudomonas aeroginosa were used for the antibacterial assay. Extracts from plants treated with 25 GY gamma rays showed the highest antibacterial activity against the 4 bacterial strains. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the genetic variation. The polymorphism information content (PIC) for RAPD primers ranged from 3% to 13% and ranged from 6 to 13% for ISSR primers. Results indicated that ISSR markers were more efficient than RAPD markers, as they detected 25.57% polymorphic DNA bands compared to 21.31% polymorphism for RAPD markers.

DNA barcodes, ISSR, RAPD and SCAR markers as potential quality control tools for molecular authentication of black and white mulberry

Morus species, especially black mulberry (Morus nigra L.), are well known for their nutritive and economic values. Black mulberry is often a subject for deliberate and undeliberate substitution with the morphologically similar white mulberry (Morus alba L.). In the current study, the genetic diversity of Morus nigra L. and Morus alba L. was assessed using different genetic profiling and fingerprinting techniques namely namely DNA barcoding, Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR). DNA barcoding was implemented using 2 plastid loci (matK, and rbcL-1) and 2 nuclear spacers (ITS and ITS2) aiming at accurate authentication of the studied species. DNA barcoding, targeting the selected loci succeeded to identify and authenticate the studies Morus species but failed to differentiate them, owing to their close genetic resemblance. Out of 52 screened RAPD primers, 27 were able to produce reproducible and clear profiles with 115 amplified fragments of which 37 were polymorphic accounting for 32.17% polymorphism. The number of amplified bands varied from 2 to 7 ranging in size from 100 to 700 bp. Moreover, 55 ISSR primers were evaluated, 108 fragments were produced, using 20 primers, of which 28 were polymorphic accounting for 25.92% polymorphism with size range of 200–800 bp. Sequence Characterized Amplified Region (SCAR) marker was developed based on reproducible banding pattern obtained by RAPD primer (OPG-03), for the purpose of accelerating the initial screening of Morus batches and enabling the preventative rejection of adulterated samples. The polymorphic band obtained was sequenced and specific primers were designed to develop a SCAR marker of approximately 558 bp exclusively for M. nigra, allowing detection of down to 1 ng, of M. nigra. The SCAR marker showed 100% success in differentiating authentic M. nigra and M. alba samples. In addition, the application of the developed SCAR marker was extended to distinguish M. nigra from its four common adulterants namely Ficus carica L., Fragaria vesca L., Ficus racemosa L. and Vitis vinifera L.. The proposed protocol was successfully implemented for the evaluation of 47 commercial M. nigra samples collected from different Egyptian locations.

Comparative Assessment of SSR and RAPD markers for genetic diversity in some Mango cultivars.

Genetic improvement mainly depends on the level of genetic variability present in the population, and the degree of genetic diversity in a population largely determines the rate of genetic advancement. For analyzing genetic diversity and determining cultivar identities, a molecular marker is a useful tool. Using 30 SSR (simple sequence repeat) and 30 RAPD (randomly amplified polymorphic DNA) markers, this study evaluated the genetic divergence of 17 mango cultivars. The effectiveness of the two marker systems was evaluated using their genetic diversity characteristics. Additionally, the effects of SM (simple matching) and Dice similarity coefficients and their effects on mango clustering were evaluated. The findings showed that SSR markers generated 192 alleles, all of which were polymorphic (100%). With RAPD markers, 434 bands were obtained, 361 of which were polymorphic (83%). The average polymorphic information content (PIC) for RAPD and SSR was 0.378 and 0.735, respectively. Using SSR markers resulted in much higher values for other genetic diversity parameters compared to RAPD markers. Furthermore, grouping the genotypes according to the two similarity coefficients without detailed consideration of these coefficients could not influence the study results. The RAPD markers OPA_01, OPM_12 followed by OPO_12 and SSR markers MIAC_4, MIAC_5 followed by mMiCIR_21 were the most informative in terms of describing genetic variability among the cultivars under study; they can be used in further investigations such as genetic mapping or marker-assisted selection. Overall, 'Zebda' cultivar was the most diverse of the studied cultivars.

Evaluation of the Genetic Stability of Amaranthus viridis L. Species in Selected Regions of Western Ghats using Random Amplified Polymorphic DNA (RAPD)

Random Amplified Polymorphic DNA is cheap and fast molecular technique to identify the genetic resemblances or variations in DNA in various plants. The proposed research work wasintendedto compare the genetic diversification of Amaranthus viridis species in selected regions of Western Ghats in Tamilnadu and Kerala by RAPD analysis.The biometric morphological data among the five A. viridis accessions were compared. Their genomic DNA was isolated and finger prints were obtained using three RAPD markers. The percentage polymorphism, polymorphism information content, effective multiplex ration and resolving power were calculated. UPGMA dendrogram was constructed and their genetic relatedness was compared using Jaccard coefficient.Upon finger printing, 66 bands were counted for the three RAPD primers used,among which 46 bands were polymorphic band numbers from 8 to 21. Percentage of polymorphic bands ranged between 44.44% and 80.77%. EMRvalues for 66 polymorphic loci ranged between 3.56 and 17.01. The UPGMA dendrogram comparing the genomic profiles of the 5 A. viridis accessions using Jaccard coefficient revealed their genetic distances where the maximum Jaccard’s coefficient value observed was 0.96 between AVKATN and AVNEK. Among the 5 selections the peak similarity index (0.9565) was witnessed between AVKATN and AVNEK. The cuurent study revealed that AVKATN and AVNEK had the highest their genetic distances, whereas AVKATN and AVNEK were genetically similar among the 5 A. viridis accessions. Several polymorphic bands which ranged up to 80.77% have proved their genetic variations.

Genetic Variation of Ceiba pentandra (L.) Gaertn. from Three Populations in West Sumatra, Indonesia Based on RAPD Markers

Ceiba pentandra (L.) Gaertn. is one of the cotton-producing plants. However, there is a population decline in some areas, resulting in a decrease in genetic variation. This study aims to determine intrapopulation and interpopulation genetic variation and genetic differentiation of C. pentandra in three populations in West Sumatra. The research was conducted with the descriptive method using molecular data and sample collection with the survey method. Analysis of genetic variation using RAPD (Random Amplified Polymorphic DNA) markers on 15 individual plants collected from three populations, namely Solok, Pesisir Selatan, and Padang Pariaman. The results showed that primers OPA-01, OPA-02, and OPB-10 could detect polymorphism. The value of intrapopulation genetic variation was highest in the South Coastal population (H = 0.1857) and lowest in the Solok population (H = 0.1228). Interpopulation genetic variation (DST = 0.0326) was lower than intrapopulation genetic variation (Hs = 0.1607), with a low genetic differentiation value (GST = 0.1686) and a high gene flow value (Nm = 2.4660). Cluster analysis showed that the Pesisir Selatan and Solok populations had the farthest genetic distances (0.0580). UPGMA analysis shows that accessions do not cluster specifically based on their population.