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Background: Pseudomonas aeruginosa is a major cause of healthcare-associated infections (HAIs), particularly in immunocompromised patients, leading to high morbidity and mortality rates. This study aimed to investigate the antimicrobial resistance patterns, virulence gene profiles, and genetic diversity among P. aeruginosa isolates from hospitalized patients in Mazandaran, Iran., Methods: From September 2021 to April 2022, 82 non-duplicate P. aeruginosa isolates were collected from diverse clinical sources. Identification was confirmed using API 20 NE (bioMérieux, Marcy l'Etoile, France). Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method according to CLSI guidelines to assess resistance to a range of antibiotics. The virulence profile (exoT, exoY, exoU, toxA, plcH, plcN, algD, aprA, lasB and exoS) of each P. aeruginosa isolate was determined by PCR. The genetic diversity among the strains was evaluated using the random amplification of polymorphic DNA (RAPD) technique. Clustering was based on a Dice similarity coefficient of ≥ 85%., Results: Of the 82 total strains, P. aeruginosa exhibited the highest and lowest resistance toward ticarcillin-clavulanate (98.78%) and colistin (0%), respectively. Moreover, 100% of the P. aeruginosa isolates were MDR. The following prevalence of virulence factor genes was observed: aprA, lasB, algD, toxA, plcH, exoY, and exoT in 100% of isolates. The plcN, exoS, and exoU were identified 98.78%, 67.07%, and 45.12%, respectively. The RAPD patterns obtained with primers 272 and 208 had respectively 2-19 and 6-17 bands. According to the Dice similarity coefficient of higher than 85%, 56 and 39 clusters were recognized., Conclusion: The high rate of multidrug resistance combined with the widespread presence of virulence genes in P. aeruginosa isolates highlights the potential for increased infection severity, morbidity, and mortality in hospitalized patients. The substantial genetic diversity observed among isolates suggests that P. aeruginosa in this region may rapidly evolve, necessitating ongoing surveillance and more targeted antimicrobial strategies., Clinical Trial Number: Not applicable., Competing Interests: Declarations. Ethics approval and consent to participate: This study was performed in agreement with the Declaration of Helsinki. This study was also approved by the Iran National Committee for Ethics in Biomedical Research with the national ethical code (ref number: IR.MAZUMS.REC.1399.901) and informed consent was obtained from all participants and/or their guardian. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

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., Competing Interests: Diaa Abd El-Moneim is an Academic Editor for PeerJ., (©2023 A. A. Hussein et al.)

Background: Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD., Methods: RAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics., Results: The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein., Conclusions: The RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions.

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.

10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision., Competing Interests: Declaration of competing interest The authors declare that the research is pure and there is no conflict of interest., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Aflatoxins (AF) are highly toxic compounds produced by Aspergillus section Flavi . They spoil food crops and present a serious global health hazard to humans and livestock. The aim of this study was to examine the phylogenetic relationships among aflatoxigenic and non-aflatoxigenic Aspergillus isolates. A polyphasic approach combining phylogenetic, sequence, and toxin analyses was applied to 40 Aspergillus section Flavi isolates collected from eight countries around the world (USA, Philippines, Egypt, India, Australia, Indonesia, China, and Uganda). This allows one to pinpoint the key genomic features that distinguish AF producing and non-producing isolates. Based on molecular identification, 32 (80%) were identified as A. flavus, three (7.5%) as A. parasiticus, three (7.5%) as A. nomius and one (2.5%) as A. tamarii. Toxin analysis showed that 22 (55%) Aspergillus isolates were aflatoxigenic. The majority of the toxic isolates (62.5%) originated from Egypt. The highest aflatoxin production potential was observed in an A. nomius isolate which is originally isolated from the Philippines. DNA-based molecular markers such as random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) were used to evaluate the genetic diversity and phylogenetic relationships among these 40 Aspergillus isolates, which were originally selected from 80 isolates. The percentage of polymorphic bands in three RAPD and three ISSR primers was 81.9% and 79.37%, respectively. Analysis of molecular variance showed significant diversity within the populations, 92% for RAPD and 85% for ISSR primers. The average of Polymorphism Information Content (PIC), Marker Index (MI), Nei's gene diversity (H) and Shannon's diversity index (I) in ISSR markers are higher than those in RAPD markers. Based on banding patterns and gene diversities values, we observed that the ISSR-PCR provides clearer data and is more successful in genetic diversity analyses than RAPD-PCR. Dendrograms generated from UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analyses for RAPD and ISSR markers were related to the geographic origin.

Objective: The increase in Escherichia coli bloodstream infections mandates better characterisation of the relationship between commensal and invasive isolates. This study adopted a simple approach to characterize E. coli in the gut reservoir from patients with either E. coli or other Gram-negative bacteraemia, or those without bacteraemia, establishing strain collections suitable for genomic investigation. Enteric samples from patients in the three groups were cultured on selective chromogenic agar. Genetic diversity of prevailing E. coli strains in gut microbiota was estimated by RAPD-PCR., Results: Enteric samples from E. coli bacteraemia patients yielded a median of one E. coli RAPD pattern (range 1-4) compared with two (range 1-5) from groups without E. coli bacteraemia. Of relevance to large-scale clinical studies, observed diversity of E. coli among hospitalised patients was not altered by sample type (rectal swab or stool), nor by increasing the colonies tested from 10 to 20. Hospitalised patients demonstrated an apparently limited diversity of E. coli in the enteric microbiota and this was further reduced in those with E. coli bacteraemia. The reduced diversity of E. coli within the gut during E. coli bacteraemia raises the possibility that dominant strains may outcompete other lineages in patients with bloodstream infection.

Genetic diversity between two ecotypes of Egyptian clover varieties, namely Fahl (mono-cut) and Helaly (multi-cut) have been assessed based on forage yield and yield components as well as molecular marker systems. The two parental genotypes were crossed to produce seeds of F 1 and F 2 progenies. Analyses of variance indicated significant differences between four populations (P 1 (Fahl), P 2 (Helaly), F 1 and F 2 ) for fresh forage yield, number of florets/inflorescence, number of seeds/inflorescence and 1000 seed weight. The mean of F 1 hybrid indicated over-dominance of the higher performance. The phenotypic and genotypic coefficients of variation were high for fresh forage yield, intermediate for 1000-seed weight and low for number of florets/inflorescence and number of seeds/inflorescence. Four molecular marker systems with 80 primers, 30 RAPD, 10 ISSR, 10 SRAP and 30 SSR were used for studying the genetic diversity between the two parents, out of which 64 primers (26 RAPD, 7 ISSR, 7 SRAP and 24 SSR) were polymorphic between the parents. The four molecular marker systems generated unique DNA bands for each parent. Twenty-one primers which produced higher unique bands in both parents were surveyed on bulked DNA from the extremes of four agro-morphological traits within and between the two ecotypes in F 2 generations. Twenty-one primers produced bands distinguish between the bulked extremes for at least one trait within each ecotype or between the two ecotypes. All polymorphic primers were subjected to QTL analysis, out of them 23 only were mapped on three linkage groups with four agro-morphological traits and showed 24 putative QTLs.

Finger millet (Eleusine coracana L. Gaertn., 2n=36) is one of the most important minor crops, commonly known as 'ragi' and used as a staple food grain in more than 25 countries including Africa and south Asia. Twenty-seven accessions of ragi were collected from different parts of India and were evaluated for morpho-genetic diversity studies. Simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers were used for assessment of genetic diversity among 27 genotypes of E. coracana. High degree of similarity (90%) was obtained between 'IC49979A' and 'IC49974B' genotypes, whereas low level of similarity (9.09%) was found between 'IC204141' and 'IC49985' as evident in morphological and DNA markers. A total of 64 SSR and 301 RAPD amplicons were produced, out of which 87.50% and 77.20% DNA fragments showed polymorphism, respectively. The clustering pattern obtained among the genotypes corresponded well with their morphological and cytological data with a monophyletic origin of this species which was further supported by high bootstrap values and principal component analysis. Cluster analysis showed that ragi accessions were categorised into three distinct groups. Genotypes IC344761, IC340116, IC340127, IC49965 and IC49985 found accession specific in RAPD and SSR markers. The variation among ragi accessions might be used as potential source of germplasm for crop improvement.

In this study, the genetic diversity and structure of 13 natural locations of Salix purpurea were determined with the use of AFLP (amplified length polymorphism), RAPD (randomly amplified polymorphic DNA) and ISSR (inter-simple sequence repeats). The genetic relationships between 91 examined S. purpurea genotypes were evaluated by analyses of molecular variance (AMOVA), principal coordinates analyses (PCoA) and UPGMA (unweighted pair group method with arithmetic mean) dendrograms for both single marker types and a combination of all marker systems. The locations were assigned to distinct regions and the analysis of AMOVA (analysis of molecular variance) revealed a high genetic diversity within locations. The genetic diversity between both regions and locations was relatively low, but typical for many woody plant species. The results noted for the analyzed marker types were generally comparable with few differences in the genetic relationships among S. purpurea locations. A combination of several marker systems could thus be ideally suited to understand genetic diversity patterns of the species. This study makes the first attempt to broaden our knowledge of the genetic parameters of the purple willow ( S. purpurea ) from natural location for research and several applications, inter alia breeding purposes., Competing Interests: The authors declare no conflict of interest.

To lay the foundation of the classification of Canarium album (C. album), and C. album from Terminalia Chebula (T. chebula) in different areas of China, improved RAPD and ISSR analysis were performed to analyze polymorphism and genetic relationship. Ten samples were collected from different locations in China. A total of 221 fragments were detected by improved RAPD, out of which polymorphic fragments accounted for 82.3% with average amplification bands of 10.05 per primer. ISSR markers revealed a total of 147 alleles, where polymorphic fragments accounted for 83.5%, with average amplification bands of 7.35 per primer. The sizes of fragments ranged from 200 to 2500bp and from 150 to 2000bp in RAPD and ISSR markers, respectively. The similarity coefficient ranged from 0.46 to 0.86 with RAPD markers and 0.36 to 0.89 with ISSR markers. The results indicated that improved RAPD and ISSR methods are useful for genetic diversity study of C. album. Thus, this study provides us the theoretical basis for the breeding and classification of C. album in South and Southwest China., (Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.)

Increasing olive germplasm erosion in the coastline of Tunisia has required an imperious conservation of the traditional genotypes before an ultimate disappearance. This region has been relatively neglected in the literature sources of olive identification. In this context, a prospection effort and a preliminary selection of olive accessions belonging to Central-Eastern Tunisia was carried out. Twenty-seven ancient olive accessions were studied by combining molecular and morphological data in order to fingerprint them, and to evaluate their relationships with classical cultivars. Compared to known classic Tunisian olive cultivars, the new prospected olive accessions were well distinguished, presenting a potential use as promising genotypes. The morphological and molecular data showed a high diversity between genotypes. 92 and 63 polymorphic bands were scored using 10 RAPD and 9 SSR markers, respectively. Significant correlation coefficients were obtained among fruit and stone sizes (r=0.90) and among their shapes (r=0.73). The genetic distances obtained with the two DNA marker systems were significantly correlated (r=0.45) according to Mantel's test. No significant correlation was observed between distances based on molecular and morphological markers. UPGMA analysis based on molecular data showed no clear clustering trends according to morphological traits or fruit use. Despite the high genetic variation among accessions in each prospected area, geographical origin seemed to have significant impact on the observed variability. The relationship between morphological and molecular data has confirmed that each marker expressed different aspects of variability. Integration between all markers will be useful for distinguishing new accessions and genotyping local varieties., (Copyright © 2017. Published by Elsevier Masson SAS.)

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r=0.78) was better than that of the RAPD marker system (r=0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding., (Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.)

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) are PCR-based molecular techniques used for evaluation and characterization of date palm to find the best genotype and male/female identification at an early stage. Genetic fingerprinting using molecular markers is an important tool for the analysis of genetic diversity and cultivar identification. Here, we present an improved DNA extraction protocol using leaf tissue, based on the standard cetyltrimethyl ammonium bromide (CTAB) protocol, which yields large amounts of high-quality amplifiable DNA. RAPD and ISSR markers reveal sufficient genetic diversity as well as give some unique markers in some genotypes with a maximum number of bands.

Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.

Euryale ferox Salisbury is an important aquatic food plant cultivated largely in eastern India. E. ferox is a monotypic genus, and breeding programmes have mostly relied on the variability present in the primary gene pool. Knowledge of the genetic structure of the population is limited, and there are very few reports available on the genetic diversity of E. ferox. In this study, comprehensive research on the genetic diversity of 16 germplasms of E. ferox was carried out using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 320 RAPD and 95 ISSR primers screened initially, 61 primers (40 RAPD and 21 ISSR) gave reproducible bands and were selected for further work. Amplification of the 40 RAPD primers gave 533 polymorphic bands with an average of 13.32 polymorphic bands per primer. The percentage of polymorphism ranged from 37.5 to 100, with an average of 88.3 %. The 21 ISSR primers produced 259 bands, of which 214 were polymorphic, with an average of 10.19 polymorphic bands per primer. The percentage of polymorphism using ISSR primers ranged from 50 to 100, with a mean of 82.6 %. Jaccard's coefficient ranged from 0.45 to 0.69 (RAPD), 0.50 to 0.77 (ISSR) and 0.48 to 0.71 (RAPD and ISSR). Molecular characterization of different germplasms of E. ferox not only is essential for its conservation but also can be used in further breeding programmes.

Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in "reasonable polymorphism" among donor plant and its 18 clones. Mantel's test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

ITS, RAPD-PCR and ISSR-PCR are most popular DNA-based techniques that are extensively applied in the determination of the genetic diversity of species among populations. However, especially for organisms having high genetic polymorphism, phylogenetic trees drawn from the results of these techniques may be different. For finding a meaningful phylogenetic tree, it should be compared phylogenetic trees obtained from these different techniques with geographic locations of populations. Lichens have a high genetic polymorphism and tolerance against different environmental conditions. In this study, these three DNA-based genetic diversity techniques were compared, using different populations of a lichen species (Xanthoria parietina). X. parietina was especially chosen because of its high genetic diversity in narrow zones. Lichen samples were collected from ten different locations in a narrow transition climate zone Bilecik (Turkey). Statistical analyses of all results were calculated using UPGMA analysis. Phylogenic trees for each technique were drawn and transferred to the Bilecik map for comparative analysis. The results of three techniques allowed us to verify that populations of X. parietina have high genetic variety in a narrow zone. But phylogenetic trees obtained from these results were found to be very different. Our comparative analysis demonstrated that the results of these techniques are not similar and have critical differences. We observed that the ITS method provides more clear data and is more successful in genetic diversity analyses of more asunder populations, in contrast to ISSR-PCR and RAPD-PCR methods., (Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.)

In this study, Random amplified polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analysis were used to examine the genetic relationships among eight Aethionema species (Aethionema caespitosum, A. arabicum, A. cordatum, A. fimnraitum, A. armenum, A. speciosum supsp. speciosum, A. memraneceum, A. grandiflorum var. grandiflorum) growing in the wild in Eastern Anatolia, Turkey. Fourteen RAPD primers and 7 ISSR primers were used. The UPGMA cluster was constructed using a combination of data from RAPD and ISSR markers. The Aethionema species were classified into two major groups. The similarity matrix values of between 0.182 (A. cordatum, A. speciosum supsp. speciosum) and 0.927 (A. grandiflorum var. grandiflorum, A. cordatum). High genetic variations among Aethionema species growing in the wild in Eastern Anatolia, Turkey may reveal differences in their origin. The present study suggests that both RAPD and ISSR analysis are useful for the differentiation of the Aethionema species., (Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.)

Aibika (Abelmoschus manihot L.) is believed to be a good source of micronutrients. However, although many varieties of aibika are commonly consumed in Papua New Guinea, their micronutrient content is unknown. Therefore, the mineral (Ca, Fe, K, Mg, Mn, Na, Zn & Cu), folate composition and the genetic variation of 23 aibika accessions from the collection at the National Agricultural Research Institute were studied over a 3year period to provide data for nutritional studies and to inform breeding programs. The data showed that aibika is, potentially, a crop of high nutritional value with the potential to boost the micronutrient status of local PNG communities. However, there were substantial differences in the micronutrient concentrations of the accessions from year to year and accessions that had the highest concentration of a particular mineral in 1year did not have the high concentrations in other years. Clusters determined using unweighted pair group method with arithmetic mean analysis (UPGMA) of the micronutrient contents differed in each of the 3years. Genetic analysis made using random amplification of polymorphic DNA and directed amplification of mini satellite region DNA placed the accessions into five groups. There was no correlation between these groups and leaf morphology, nor were there correlations with the clusters determined from the UPGMA analyses. There appears to be considerable interaction between genotype and environmental factors determining micronutrient composition and environmental factors may play a greater role than genotype in influencing micronutrient composition., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and directed amplification of minisatellite-region DNA (DAMD). Totally 15 ISSR, 8 RAPD and 7 DAMD primers generated 263 amplification products, accounting for 84.6% polymorphism across all the genotypes. The Mantel's test of correlation revealed the best correlation between ISSR and cumulative data with a correlation coefficient (r) of 0.84. Assessment of population diversity indicated that the maximum intra population genetic diversity was recorded among high FeZn lines (HFL) having maximum values of Nei's genetic diversity (h) (0.244), Shannon information index (I) (0.368) and the percentage of polymorphic loci (Pp) (72.65%) while the corresponding lowest values of 0.074, 0.109 and 17.95% respectively were observed among the members of MDT subpopulation. The mean coefficient of gene differentiation (GST) and the gene flow (Nm) between populations were observed to be 0.396 and 0.7680 respectively. The analysis of molecular variance (AMOVA) suggested that maximum genetic variation exists within populations (95%) than among populations (5%). Thus the information obtained from this study could be utilized in sorghum breeding programmes for the development of varieties with improved nutrition and agronomic values in future., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease of many economically important crop species. A significant variation in wilt incidence and severity in eggplant and potato was observed among the growing areas surveyed. R. solanacearum isolates obtained both from eggplant and potato belong to biovar III, while isolates from eggplant belong to race 1 and isolates obtained from potato belong to race 3. Random amplified polymorphic DNA (RAPD) technique was used as a tool for assessing genetic variation and relationship among seven isolate groups of R. solanacearum viz., RsB-1, RsB-2, RsB-3, RsP-1, RsP-2, RsP-3 and RsP-4, consisting in a total of 28 isolates. Out of the RAPD markers used, amplification with four decamer primers produced 70 bands with sizes ranging from 100 to 1400 bp. Out of 70 bands, 68 bands (97.06%) were polymorphic and two bands (2.94%) were monomorphic amongst the seven R. solanacearum isolates group. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's genetic distance produced two main clusters of the seven isolates of R. solanacearum. The isolates RsB-1, RsB-2, RsB-3 and R-4 grouped in cluster І, while RsP-2, RsP-3 and RsP-4 grouped in cluster ІІ. The highest intra-variety similarity index (Si) was found in RsB-1 isolate (86.35%) and the lowest one in RsP-2 (56.59%). The results indicated that relatively higher and lower levels of genetic variation were found in RsP-3 and RsB-3, respectively. The coefficient of gene differentiation (G(st)) was 0.5487, reflecting the existence of a high level of genetic variations among seven isolates of R. solanacearum. Comparatively higher genetic distance (0.4293) and lower genetic identity (0.6510) were observed between RsB-2 and RsP-4 combinations. The lowest genetic distance (0.0357) and highest genetic identity (0.9650) were found in RsB-1 vs. RsB-2 pair. Thus, RAPD offers a potentially simple, rapid and reliable method to evaluate genetic diversity analysis in R. solanacearum., (Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.)

The application of commercial rhizobial inoculants to legume crops is proving to be an alternative to synthetic fertilizer use. The challenge for sustainable agriculture resides in the compatibility between crop, inoculants and environmental conditions. The evaluation of symbiotic efficiency and genetic diversity of indigenous rhizobial strains could lead to the development of better inoculants and increased crop production. The genetic variability of 32 wild indigenous rhizobial isolates was assessed by RAPD (Random Amplified Polymorphic DNA). The strains were isolated from red clover (Trifolium pratense L.) nodules from two distinct geographical regions of Northern and Eastern Romania. Three decamer primers were used to resolve the phylogenetic relationships between the investigated isolates. Cluster analysis revealed a high diversity; most strains clustered together based on their geographical location.

Background: Synthetic hexaploid wheats are artificially reconstituted hexaploid wheats that possess high genetic variation which could be utilized for the development of new improved wheat varieties. One such group of synthetic wheats is called the Elite-II set of synthetic wheats that are derived from crossing durum wheat with different Aegilops tauschii wheats., Materials and Methods: In the current study genetic diversity was investigated among 18 Elite-II synthetic hexaploid wheat lines at DNA level. Two types of molecular markers i.e. RAPD and SSR were used for this purpose., Results: Both types of markers proved useful in estimating the overall genetic diversity among these lines. Based on RAPD data range of genetic distances in these lines was from 0 to 100 percent. Seven D-genome specific SSRs were also used to get further estimation of the genetic diversity contributed by Aegilops tauschii parent. On the basis of results obtained it is inferred that the Aegilops tauschi accessions used in the production of these synthetic lines were genetically different and they contributed to the enhancement of genetic variation in the synthetic lines. These results could be helpful for future genome mapping programs., Conclusion: The overall extensive genitive diversity indicates that these lines are good candidates for development of improved wheat varieties by crossing with cultivated wheat varieties.

To ascertain the conservation priorities and strategies for Commiphora wightii, an endangered medicinal plant of Indian Thar Desert, genetic diversity was estimated within and among different populations. The total of 155 amplification products were scored using ten each of RAPD and ISSR primers, exhibiting an overall 86.72% polymorphism across 45 individuals representing eight populations. The cumulative data of two markers were used to compute pair-wise distances. The Neighbor-Joining tree revealed high genetic differentiation among populations except Kiradu population. Nei's gene diversity (h) ranged between 0.082 and 0.193 with total diversity at species level is 0.294. Shannon's information index (I) ranged between 0.118 and 0.275 with an overall diversity of 0.439. Analysis of molecular variance showed more diversity among population level (56.65%) than at within population level (43.35%). The low gene flow value (Nm=0.349) and high coefficient of genetic differentiation (GST=0.589) and high fixation index (FST=0.566) demonstrated elevated genetic differentiation among the population and can be predicted that these populations are not in Hardy-Weinberg proportions. Principal Co-ordinate Analysis confirms that Akal population has become phylogenetically more distinct and less diverse than the rest of the samples. Mantel's test revealed no correlation between genetic and geographical distances of populations (R(2)=0.122). Overall highest diversity was observed in the population of Machiya Safari Park and Kiradu, while lowest in Akal population, later may constitute an evolutionary significant unit, having merit for special management., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Isolates of Streptococcus suis from different Western countries as well as those from China and Vietnam have been previously well characterized. So far, the genetic characteristics and relationship between S. suis strains isolated from both humans and pigs in Thailand are unknown. In this study, a total of 245 S. suis isolates were collected from both human cases (epidemic and sporadic) and pigs (diseased and asymptomatic) in Thailand. Bacterial strains were identified by biochemical tests and PCR targeting both, the 16S rRNA and gdh genes. Thirty-six isolates were identified as serotype 2 based on serotyping and the cps2-PCR. These isolates were tested for the presence of six virulence-associated genes: an arginine deiminase (arcA), a 38-kDa protein and protective antigen (bay046), an extracellular factor (epf), an hyaluronidase (hyl), a muramidase-released protein (mrp) and a suilysin (sly). In addition, the genetic diversities of these isolates were studied by RAPD PCR and multilocus sequence typing (MLST) analysis. Four virulence-associated gene patterns (VAGP 1 to 4) were obtained, and the majority of isolates (32/36) carried all genes tested (VAGP1). Each of the three OPB primers used provided 4 patterns designated RAPD-A to RAPD-D. Furthermore, MLST analysis could also distinguish the 36 isolates into four sequence types (STs): ST1 (n = 32), ST104 (n = 2), ST233 (n = 1) and a newly identified ST, ST336 (n = 1). Dendrogram constructions based on RAPD patterns indicated that S. suis serotype 2 isolates from Thailand could be divided into four groups and that the characteristics of the individual groups were in complete agreement with the virulence gene profiles and STs. The majority (32/36) of isolates recovered from diseased pigs, slaughterhouse pigs or human patients could be classified into a single group (VAGP1, RAPD-A and ST1). This genetic information strongly suggests the transmission of S. suis isolates from pigs to humans in Thailand. Our findings are the first to report genetic characteristics of strains from Thailand and to elucidate the genetic relationship among S. suis isolates from human and pig origins., (© 2013 Blackwell Verlag GmbH.)

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

This study evaluated the genetic diversity of twenty-four Coffea arabica accessions being maintained at Western Highlands Agriculture and Forestry Science Institute (WASI), Vietnam using 18 RAPD and 14 DAMD markers. RAPD markers produced a total of 171 loci with 151 loci (86.82%) were polymorphic while DAMD primers detected a total of 125 loci with 101 loci (80.11%) were polymorphic. The RAPD makers showed a higher PIC (0.31) and Rp (4.56) values than those of DAMD markers (0.24 and 3.12, respectively). The similarity coefficient ranged from 0.536 to 0.854 based on the pooled data. These results indicate a high genetic diversity among C. arabica accessions. Correlation analysis using Mantel's test indicated a moderate correlation (r = 0.544) between RAPD vs DAMD matrices, but a strong correlation between RAPD (r = 0.903)/DAMD (r = 0.860) and pooled data were obtained. PCA revealed the distribution of the 24 C. arabica accessions aligning with UPGMA categorised them into four distinct clusters. In general, coffee varieties belonging to the same geographic origin were grouped into distinct clusters. A high level of genetic diversity among C. arabica varieties could be used for crossing programmes to develop hybrid coffee accessions with the desired traits in Vietnam. [ABSTRACT FROM AUTHOR]

Crop productivity is declining due to climate change, with sesame being particularly vulnerable due to its narrow genetic base. To address this, 28 advanced sesame lines were evaluated across 23 environments in Egypt over six growing seasons (2018-2023). The study aimed to identify stable and high-yielding genotypes for developing climate-ready cultivars. Additive main effects and multiplicative interaction analyses were employed to assess genotype stability and performance. Molecular markers (RAPD and ISSR) were used to characterize genetic variation and identify markers linked to yield and stability. The experiments were performed in a randomized complete block design (RCBD) with three replicates. The results showed that the genotypes had significant differences (p < 0.05) for seed yield. AMMI analysis identified C5.8, C3.8, C6.11, C6.2, and C9.6 as stable and high-yielding genotypes. RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat) markers revealed high levels of genetic variation; eight RAPD and ten ISSR primers amplified 78 and 84 bands with a mean polymorphism of 77.5% and 60.47%, respectively. In addition to seven markers associated with yield and stability. These findings highlight the potential of these advanced lines for developing climate-ready cultivars. [ABSTRACT FROM AUTHOR]

ttarakhand has a rich plant biodiversity, many of which have high medicinal properties. Medicinal plants have been used against insects, diseases, and herbivorous mammals through the production of chemical compounds. Various reasons like overexploitation, overgrazing, unsustainable development, etc. lead to their extinction and make them threatened species. The International Union for Conservation of Nature (IUCN) was established to prioritize species conservation, assess threat status, and develop suitable strategies due to the vast diversity of species. The genetic diversity of these threatened species can be determined using various markers. Molecular marker technology aids in analyzing genetic diversity, population structure, and species adaptation, enabling conservation measures and assessing genetic stability in conserved species. In this article, we have reviewed the genetic diversity of six threatened plants of Uttarakhand (Picrorhiza kurroa, Aconitum heterophyllum, Nardostachys jatamansi, Dactylorhiza hatagirea, Zanthoxylum armatum, Saussurea costus) in India as well as in other countries. A review highlighting the use of recent molecular markers like ISSR, SSR, RAPD, etc. to determine genetic diversity. Most of the medicinal plants show diversity less than 0.5, which indicates that the plants are at extreme risk of extinction. The diversity is calculated based on polymorphism percentage. The analysis of genetic diversity between species using ISSR, nextgeneration sequencing, AFLP, and microsatellite markers reveals low genetic diversity in A. heterophyllum, P. kurroa, N. jatamansi, Z. armatum, D. hatagirea, and S. costus. [ABSTRACT FROM AUTHOR]

Copyright of Acta Biologica Slovenica is the property of Drustvo Biologov Slovenije and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Genetic diversity in plant selection refers to varieties and differences in the genetic composition of plant species. In this article, the types of molecular markers most commonly used in determining genetic diversity in plants are examined and their advantages and application in various research fields are covered. Also, future perspectives on this technology and innovations created by them in plant research will be discussed. The development of PCR-based molecular marker techniques plays an important role in the evolution of plant selection programs. It enables faster and more effective access to information about the genetic characteristics of particular economically valuable plant species. In plant selection, more commonly RAPD, ISSR, SRAP, and AFLP scar, SSR markers are used in assessing the genetic diversity of plants and have some positive properties according to the purpose of the study. The use of these marker techniques ensures a grade and reasonable improvement in the selection of plant species. These technologies help to make progress by distinguishing existing variations more efficiently and efficiently to identify the most desirable forms in selection programs. A significant step toward more effective selection processes, growth in crop cultivation, and protection of genetic diversity. [ABSTRACT FROM AUTHOR]

The purpose of this study is to investigate the intra- and inter-specific genetic relationship of some strawberry- and orange-associated fungi based on DNA markers technique. Five fungal isolates belonging to three different genera were isolated from strawberry and orange samples. The isolates were morphologically characterized as Aspergillus fumigatus, which originated from orange samples; A. flavus and A. niger, both originated from strawberries; and Rhizopus stolonifer and Alternaria alternata, both originated from orange samples. The five fungal isolates were subjected to investigating intra- and inter-specific genetic relatedness, employing the technique of random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) marker using ten oligonucleotide primers. The RAPD-PCR analysis revealed a high interspecific relationship between the three Aspergillus species and Rhizopus stolonifer, as well as Alternaria alternata. It also revealed a high intraspecific genetic relationship between A. fumigatus and A. flavus, which were isolated from different environments, surpassing the observed relationships between A. flavus and A. niger, which were isolated from the same environment. This finding confirms genetic homogeneity within the studied Aspergillus species, suggesting a potential for molecular identification of genetic diversity among different individuals in the Aspergillus genus, taking into consideration their respective origins. [ABSTRACT FROM AUTHOR]

The East African Highland banana (Mutika/Lujugira subgroup) is composed of triploid (AAA) cooking and beer banana varieties that are adapted to the high-altitude region of the Great Lakes region of East Africa. Banana production is affected by several biotic and abiotic factors. Breeding opportunities in bananas are limited due to female sterility and parthenocarpy. The genetic diversity of crops enables breeders to develop new germplasm. Molecular markers have been used widely to dissect crop plants' genetic diversity. This study assessed the genetic variation in 27 varieties from the Mutika/Lujugira subgroup using random amplified polymorphic DNA (RAPD). No genetic variation was observed among the banana varieties, and the 18 ten-mer primers produced monomorphic banding profiles. The genetic homogeneity of this banana subgroup is not congruent with their extensive morphological variation. Domestication and the bottleneck effect are often cited as the cause of reduced diversity in crop plants. On the other hand, several mechanisms, including somatic mutations, transposable elements, polyploidy, genome plasticity, and epigenetic mechanisms, are known to increase plant phenotypic variability. Further in-depth research is needed to explain the puzzle between the genetic and morphological diversity in the Mutika/Lujugira subgroup. [ABSTRACT FROM AUTHOR]

Background: Moth bean is a very nutritive and hardy crop, especially for resource poor-arid agriculture. The limited use of cultivars in moth bean breeding resulted into narrow genetic base. This study aimed to diversify the conical genetic base and developimproved cultivars, through molecular (RAPD) and morpho-agronomic characterization of commercially elite moth bean cultivars. Methods: Elite moth bean cultivars (15) were evaluated for 11 morpho-agronomic traits. Eleven RAPD markers were used to amplify genomic DNA and perform molecular characterization. Clustering approach was used for grouping of the cultivars. Result: RAPD markers revealed high polymorphism in 15 elite moth bean cultivars. The polymorphism information content (PIC) values varied within the range of 0.45 to 0.88, with an average of 0.77. The number of alleles at different loci ranged from 4 to 16, with an average of 10 alleles per locus. When employing UPGMA-based cluster analysis, utilizing 11 morpho-agronomic traits, the cultivars were grouped into four clusters. However, when RAPD markers were used, the cultivars were grouped into five clusters. The Jaccard's similarity coefficient and Manhattan dissimilarity coefficient fell within the ranges of 0.18 to 0.70 and 0.02 to 0.42, respectively. These values signify the degree of genetic variability within the cultivars. Furthermore, a Mantel test was conducted to examine the correlation between agronomic traits and the RAPD-based matrix. The results showed a negative correlation, but it was not statistically significant.The high PIC values and the successful amplification of multiple loci demonstrate the efficacy of RAPD markers in assessing genetic diversity in moth beans. The study revealed enormous genetic variation among cultivars and crosses can be attempted between cultivars of different groups to create better recombinants in moth bean breeding programmes. [ABSTRACT FROM AUTHOR]

Bird of paradise plants belong to families Strelitziaceae and Heliconiaceae, two close-related families in the Zingiberales order. This study aimed to study the genetic diversity and relationship of species among and within Strelitziaceae and Heliconiaceae using molecular RAPD markers and compare them to morphological characters. Samples used comprised two species from Strelitziaceae and eight species from Heliconiaceae. Twenty OPA primers showed that 17 out of 20 OPA primers were successfully amplified. Primer OPA-10 was the most informative and recommended, followed by OPA-5, OPA-7, OPA-9, OPA-11, OPA-17, OPA-18, OPA-19, and OPA-20. Heliconiaceae and Strelitziaceae were high genetic diversity (P=100%, I=0.388±0.016, He=0.237±0.013) with low similarities (0.09-0.39). Heliconiaceae was more genetically diverse than Strelitziaceae. Heliconiaceae produced P=98.88%, I=0.409±0.017, and He=0.254±0.014. Strelitziaceae produced P=60.53%, I=0.366±0.049, and He=0.251±0.033. The tree topology based on the RAPD marker differs slightly from morphology. However, the morphological characteristics are important to support and complement it. Strelitziaceae was strongly separated from Heliconiaceae, which supports the monophyly of both families. Heliconiaceae was separated into two subclusters and paraphyletic. Subcluster 1 comprises subgenera Heliconia and Stenochlamys. Subcluster 2 comprises subgenera Griggsia and Stenochlamys. In conclusion, the molecular RAPD marker proved the powerful of classification at the family level but moderate at subgenus, section, and species levels. Nonetheless, it is considered a simple and valuable method to provide a primary reference for taxonomic delimitation, conservation and breeding efforts of the bird of paradise plants in the future. [ABSTRACT FROM AUTHOR]

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.

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The present study aimed to conduct genetic diversity of four native chicken genotypes (Naked neck, frizzled, naked neck-frizzled and normally feathered). Diversity was assessed based on morphological measurements and molecular markers. A total of 500 chickens were used in this study. Productive traits of four genotypes were measured. RAPD technique was used to access the genetic diversity using five RAPD molecular markers. Main results referred to that naked neck and naked neck-frizzled genotypes had higher significantly body weight and body weight gain than normal feathering (nana-ff) ones. Naked neckFrizzled (Nana-Ff) genotype had better carcass characteristics than other genotypes. Nana-Ff and Nana-ff genotypes were significantly higher than other genotypes in egg weight. The percentage of polymorphic bands ranged between 13.33 % and 40 % with a mean of 25.83 %. Genetic diversity ranged between 0.06 and 0.18 with a mean of 0.12. Constantly, the minimum values were scored to the genotype nana-Ff while the maximum values were scored to the genotype Nana-ff. Conclusion indicated that Na- allele is effective in improving meat and egg production traits than frizzle and normal feathering chicken. The Principal Component analysis in this study reflected that a similar results to that of the morphological values to four genetic groups. We provide fundamental evidence to genetic improvement programs by crossing or selection methods based on each productive performance and genetic analysis by modern techniques and software. [ABSTRACT FROM AUTHOR]

Thirty Egyptian date palm cultivars were collected from different locations in three governorates: Assiut, New Valley, and Aswan. Physical characteristics of the Fruit were studied, such as fruit dimensions, fruit weight, seed weight, and flesh weight. Moreover, genetic diversity among cultivars was studied using RAPD-PCR molecular marker. Physical characteristics results of the fruit showed significant differences among the tested cultivars. Samani and Magdool showed the highest values for both fruit dimensions and weight characteristics. All 5 tested RAPD primers were able to differentiate among the tested date palm cultivars and showed high polymorphism percentage ranging from 75-100%. Thirteen different specific positive and negative markers associated with some cultivars were obtained. The genetic similarity among cultivars ranged from 40% to 100% and the highest genetic similarity value was observed between Nawashf Red and Nawashf White. The results showed that the cultivars with the same name from different geographical locations are genetically different and showed significant differences in fruit physical characteristics. [ABSTRACT FROM AUTHOR]

In the present study, RAPD markers were used to evaluate five different accessions of Madhuca longifolia (Koen) Macbr that were gathered from the Pachamalai Hills in the Tiruchirappalli district of Tamil Nadu, India. The CTAB procedure was utilized in the isolation of DNA. Ten out of fifteen primers were determined to be informative during the screening process. These primers produced 275 amplification products, 261 of which were polymorphic (94.90%). All five accessions shared a polymorphism percentage that ranged from 88.23% to 100% of its total. Most of the investigated RAPD markers exhibited varying degrees of genetic variation. 275 RAPD bands were used to calculate Jaccard’s similarity coefficients and create a UPGMA dendrogram. According to the findings, M. longifoliahas genetic variation due to the many different ecological situations. This analysis obtained a better understanding of the genetic variance among the accessions. Breeders will also benefit from this information since it will provide crucial feedback that will be used in the determination of novel management techniques. [ABSTRACT FROM AUTHOR]

Somaclonal variation in micropropagated plants improves crops. Genetic transformation research relies on micropropagated plant genetic integrity. Somaclonal variation frequently occurs in micropropagation, prompting an investigation of plant genetic stability. The high number of shoot buds was seen when Decalepis hamiltonii shooting tip explants were inoculated with reversed polarity in Murashige and Skoog (MS) medium supplemented with 0.5 mg L-1 benzylaminopurine (BAP). The shoot buds increased in length on an MS medium supplemented with 0.5 mg L-1 Benzylaminopurine (BAP) and 0.1 mg L-1 indole-3-acetic acid (IAA). The lengthened shoots were established in Murashige and Skoog (MS) medium supplemented with 1 mg L-1 Indole-3-butyric Acid (IBA). Well-rooted plants underwent greenhouse hardening. Micropropagated and seedpropagated plants have similar physical features. Regenerated plant genetic stability was assessed using ten primers in a Random Amplified Polymorphic DNA (RAPD) assay. Eighty-five bands were identified. Monomorphic features and original-type clones were found in field-grown plants and bands. The regeneration approach might help study D. hamiltonii micropropagation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The aim of the present study was to use RAPD and ATPase markers to measure and analyze the level of genetic variation within farm cultured populations of introduced Pangas catfish Pangasius pangasius to evaluate their potential in ascertaining genetic differentiation. Hence, genetic diversity of farmed P.pangasius was carried out from five different sites by using RAPD primer. Primers showed 151 total amplified locus with an average of 37.75 loci. The highest number of bands were observed in P.pangasius from population 1, maximum no of bands was observed in OPA-02 (56 bands), while the minimum from OPA-05 (26 bands). Minimum polymorphism was observed in OPA-08 (10.71%), while maximum in OPA-01 (66.67%). The value of heterozygosity of P. pangasius ranged from 0.123 to 0.444.A cluster between population 1 and 2, 2nd population 3 and 4, and population 5 with all other as 3rd cluster. Distance found maximum in population 5 that showed heterozygosity. The genetic variations and polymorphism among populations showed the degree of intra and inter-population genetic diversity in P. pangasius populations. Study is also done to access the genetic diversity by ATPase 6/8 gene. ATPase 6/8 showed highest haplotype diversity (0.800) in the P. pangasius population of Tariq Khan Faheem Fish Farm, while the lowest (0.700) in Al-Raheem fish Farm. Highest nucleotide diversity (0.5703) in Tariq Khan Faheem Fish Farm, while lowest (0.5026) in Mirza Rizwan Ahmed Fish farm. Higher diversity is important for conservation and management of population. Random amplified polymorphic DNA (RAPD) and ATPase 6/8 markers were used to estimate the genetic diversity and population structure among the samples of farmed P. pangasius. Overall, RAPD and ATPase 6/8 proved as valuable tool for reliable and quick stock discrimination and provided information that might be useful regarding management and conservation of P. pangasius. The findings will be helpful in developing stock specific management measures for conservation and sustainable utilization of the species. [ABSTRACT FROM AUTHOR]

The genetic diversity assessment of agricultural crops is crucial for breeding programs aimed at enhancing crop yield, resistance to diseases, and adaptation to changing environmental conditions. In the present investigation, a comparative genetic relationship in sixteen onion genotypes was assessed utilizing dominant (RAPD) and co-dominant (SSR) marker systems. Ten RAPD and nine SSR markers showed genetic diversity remarkably and produced 503 and 107 amplicons respectively. Spearman rank correlation was used to compare the different efficiency parameters in two marker systems with respect to sixteen onion genotypes. The genetic relationship based on similarity matrix values between a pair of cultivars was higher for SSR markers than for the RAPD marker system. OPC-04 (RAPD primer) and ACM-004 (SSR primer) witnessed the highest poly-morphic bands along with other polymorphic markers that proved to be useful in grouping onion genotypes. Finally, dendrograms were constructed and compared following the mantel test to find out the genetic diversity among the germplasms. This study will be effective for a selection of efficient primers and suitable marker systems to distinguish the onion genotypes in the future. [ABSTRACT FROM AUTHOR]

Commiphora wightii has massive economic value and a wide array of medicinal uses in both ancient and modern therapeutics. It has been observed that the number of C. wightii populations in Rajasthan are declining substantially because of anthropogenic activities in the form of over-exploitation for resin and fuel. Very limited molecular studies have been reported on the molecular characterization of Commiphora wightii at national and international level. The present investigation aims to assess the genetic diversity within and among different populations to determine the relationship of genetic variability with geographical distribution of Rajasthan and to offer genetic resource information for future meaningful implementation of conservation programs applicable for C. wightii. The present study comprised of 11 RAPD markers generated 37 loci of which two were polymorphic with an average 4.85% DNA polymorphism. The maximum polymorphism (33.33%) was detected for OPU-8 marker. Similarly, 9 ISSR markers generated 47 loci of which 10 were polymorphic with an average 22.11% DNA polymorphism. The maximum polymorphism (33.33%) was observed for ISSR marker 811P, 814P and UBC857. Jaccard's similarity coefficient varied from 0.55-1.00 among the populations of Commiphora wightii using all the ISSR marker, while it ranges 0.20-0.95 for RAPD markers. The row dendrogram constructed using unweighted pair group method with arithmetic averages or UPGMA with a SAHN module of the NTSYS software which showed a phenetic representation of genetic relationships as revealed by the similarity coefficient for all the ISSR and RAPD profiles. [ABSTRACT FROM AUTHOR]

The in vitro cultures of Rindera graeca, a rare endemic plant, were developed as a sustainable source of phenolic acids. Various shoot and root cultures were established and scaled up in a sprinkle bioreactor. A multiplication rate of 7.2 shoots per explant was achieved. HPLC–PDA–ESI–HRMS analysis revealed the presence of rosmarinic acid (RA) and lithospermic acid B (LAB) as the main secondary metabolites in both the shoot and root cultures. The maximum RA (30.0 ± 3.2 mg/g DW) and LAB (49.3 ± 15.5 mg/g DW) yields were determined in root-regenerated shoots. The strongest free radical scavenging activity (87.4 ± 1.1%), according to 2,2-diphenyl-1-picrylhydrazyl-hydrate assay, was noted for roots cultivated in a DCR medium. The highest reducing power (2.3 µM ± 0.4 TE/g DW), determined by the ferric-reducing antioxidant power assay, was noted for shoots cultivated on an SH medium containing 0.5 mg/L 6-benzylaminopurine. A genetic analysis performed using random amplified polymorphic DNA and start codon targeted markers revealed genetic variation of 62.8% to 96.5% among the investigated shoots and roots. This variability reflects the capacity of cultivated shoots and roots to produce phenolic compounds. [ABSTRACT FROM AUTHOR]