Genetic profiles of three Cinchona species in Junghuhn Natural Reserve, Indonesia

Cinchona species were widely used as ancient medicines for different diseases because they contain the active component quinine and its derivatives. However, studies on the molecular aspects of cinchona, including its genetic diversity, have not been reported because most previous works focused on the administration of the antimalarial cinchona alkaloid. Quinine is also being tested as alternative compound for the treatment of Covid-19. The Junghuhn Natural Reserve in Indonesia contains three different types of cinchona plants, namely, Cinchona calisaya, Cinchona pubescens, and Cinchona sp. Given that the genetic diversity and kinship of these species have never been studied, collecting data on the cinchona gene pool has become imperative. This study analyzed the genetic diversity of the cinchona species in the Junghuhn Natural Reserve, Indonesia, by using eight RAPD markers, i.e., OPA-2, OPA-9, OPB-02, OPB-03, OPB-04, OPB-05, OPB-7, and OPJ-07, during 2020 at the University of Jenderal Soedirman, Purwokerto-Indonesia. Polymorphic band data were obtained. Then, phenogram analysis was conducted by using UPGMA and maximum parsimony with MEGA7. The RAPD profiles of Cinchona species (C. calisaya, C. pubescent, and Cinchona sp.) revealed polymorphism with different markers, i.e., OPA-2 (90%), OPB-2 (75%), OPB-5 (75%), OPB-3 (66.66%), OPB-4 (66.66%), OPB-7 (66.66%), OPJ-7 (66.66%), and OPA-9 (58.33%) sequentially with total polymorphism (70.62%). C. calisaya was identified as the most distinctive species. UPGMA yielded a coefficient of 0.200 and two distinctive groups: Group I, which comprised C. pubescens and Cinchona sp. with the p-distance value of 0.333, and Group II, which contained C. calisaya. Ixora sp. was treated as an outgroup plant. The topology of the dendrogram was consistent with that of the UPGMA dendrogram. Results may be used for the further exploration of the genetic diversity of cinchona species.

Investigation of modified WPM medium for the best meristem proliferation of Corylus avellana L.

Cultivation of Corylus avellana L. in Turkey is performed generally in the northern regions where it is an important source of livelihood for the local farmers. More than 70% of world hazelnut production is supplied by Turkey, but compared with other countries, Turkey’s hazelnut production area is quite narrow. In this study was aimed to develop an effective in vitro production for seven local cultivars of C. avellana. Therefore, WPM medium supplemented with 6-Benzylaminopurine (BAP) was modified by using single or in combination of Fe-EDDHA, AgNO3, H3BO3, charcoal and gibberellic acid. In all varieties, the best regeneration rates varying between 68% and 94% were obtained from WPM medium supplemented with 4.4 µM BAP, 27.8 µM Fe-EDDHA and 10g/L Charcoal. Genetic stability of shoots derived from meristem culture using the best medium was analysed using ISSR primers, when the gel images of the PCR products were examined, no polymorphic band was observed in samples collected from seven provinces, and the genetic stability was determined as 100%.

The cytological and molecular investigation of the toxic effects of the herbicide Roundup on Cucumis sativus

In the current study, it is aimed to investigate the toxic effects of a widely used herbicide Roundup containing active ingredient glyphosate on cucumber (Cucumis sativus) by cytological and molecular investigation. Three different concentrations (0.6%, 1.2% and 2.4%) of Roundup were applied to cucumber for 48 and 72 hours. At the end of the application procedure, the germination percentage, mean root length, mitotic frequency and mitotic abnormalities, RAPD profiles and Genomic template stability (GTS) were determined in root apical meristematic cells. For RAPD PCR analysis 10 RAPD primers were used, 8 of them produced band patterns and it was found that 5 RAPD primers among them produced unique polymorphic band patterns and subsequently were used to produce a total of 24 bands. Observed percentage of polymorphism was 26%. The changes in RAPD profiles after Roundup treatment was included variations as gain and/or loss of bands compared with the control group. Genomic template stability changed in RAPD profiles at various Roundup concentrations.

ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon’s information index, polymorphism percentage, effective allele number, Nei’s genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei’s unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.

Genetic Relationship of Four Strains of Guppy (Poeciliareticulata Peters, 1859) Using RAPD-PCR Method

This study aims to determine the genetic relationship between four strains of guppy, albino full platinum (AFP), albino german yellow (AGY), top sword (TS) and guppy yellow cobra (GYC) using the RAPD-PCR method. This study used explorative method without experimental design and analyzed by descriptive qualitative and quantitative. The obtained genetic relationship data could be used as data reference for hybridization between strains of guppy fish that have been researched. The research was conducted in October 2020-April 2021. The three fish samples (AFP, TS and GYC) obtained from fish breeder in Cilengkrang-Bandung and AGY sample obtained from fish breeder in Tanggerang-Banten. Based on the results of amplification using OPA-03 primer (AGTCAGCCAC), four strains of guppy fish showed 30 DNA bands that included polymorphic and monomorphic bands. The AFP strains had 19 monomorphic bands, AGY had 21 DNA bands (20 monomorphic bands and one polymorphic bands), TS had 19 DNA bands (17 monomorphic bands and two polymorphic bands) and GYC had 15 DNA bands (14 monomorphic bands and one polymorphic band). Phylogenetic tree analyzed by NTSys program. It is shown between AFP and AGY strains had 95% relationship index, then between TS and GYC strains had 82% relationship index and between AFP-AGY and TS-GYC had 50% relationship index.

Genetic variability and relationship among different accessions of Froriepia subpinata Bail (Gijavash) an endangered medicinal plant from Iran revealed by ISSR and IRAP markers

The genetic variability of Froriepia subpinata Ledeb. Bail., an endangered Iranian endemic species, has been estimated with a total of 52 accessions using 20 markers including ISSR and IRAP. The results showed the polymorphic band produced by primers was 82.3%. The best mean values of genetic diversity parameters observed in ISSRs markers, being UBC873, UBC811, and UBC873 the best primers tested. The similarity range among accessions was 34.45% to 93.3%. The cluster analysis classified the accessions into five main groups that in totally, accessions with similarity in region generally were clustered in the same group. Overall, present study could provide elementary information for formulation of conservation strategies and invaluable elementary genetic information for next breeding or designing conservation programs.

Exploitation of the genetic variability in the genotype of Egyptian Wheat by studding Molecular Markers, Molecular Docking, and Nano Composites. Regulation of leaf and stem rust.

Puccinia graminis f. sp. tritici (Pgt) and P. triticina (Pt), the causal agents of stem rust and leaf rust, respectively form new physiological races that significantly reduce growth and yield of wheat cultivars. Therefore, seeking for resistant cultivars and exploring it to continuously produce new wheat cultivars resistant to stem and leaf rust through breeding programs is urgent. The aim of the present study was to assess 18 Egyptian wheat genotypes for resistance to stem and leaf rust. The 18 genotypes were also analyzed for polymorphism using 20 SCoT and SRAP primers. Furthermore, the activity of chitosan-cupper composite nanoparticle in controlling stem rust is examined and its mode of action is studied using molecular docking analysis. In seedling stage, the genotypes were tested against 20 stem rust races, and the host reaction types were noticed. The lowest host reaction types (It = 0; to 2++) were recorded for Sakha 94, Sakha 95, Beni Sweif 4, Beni Sweif 7, Sohag 4, Sohag 5 and Gemmeiza 12. These genotypes except Gemmeiza 12 were resistant to all races. The remaining genotypes were susceptable to most races, but Giza 160 was highly susceptible to all races. In adult stage, the 18 genotypes were evaluated for resistant to stem rust and leaf rust in two different location, i.e. Giza and sids. The evaluation was expressed as percentage of final rust severity (FRS%), Area under disease progress curve (AUDPC) and rate of rust disease increase (r-value). SCoT and SRAP analysis generated 140 and 121 polymorphic band with 97 and 99% polymorphism, respectively. Among them, 71 and 73 were unique loci for SCoT and SRAP, respectively. The 18 genotypes were divided into two main groups depending on the similarity matrix. The first cluster consists of the most resistant genotypes to leaf rust (Giza 171, Sakha 94, Misr 1, Misr 2, Misr 3, Giza 168, Gemmeiza 12 and Sids 12) in addition to two cultivars susceptible to leaf and stem rust (Beni Sweif 7, Gemmeiza 11). Meanwhile, the second ones consists of the most susceptible genotypes to stem and leaf rust (Giza 164, Sakha 69, Giza 160, Beni Sweif 4, Sohag 5 and Sohag 4) in addition to Sakha 95 (resistant to leaf rust but susceptible to stem rust) and Shandaweel 1 (resistant to stem rust but susceptible to leaf rust). Moreover, the 18 genotypes were sprayed with Cu-chitosan composite nanoparticle either before or before and after inoculation with uridiospores of stem rust to determine the effect of this solution and its application method in controlling the disease. The infection was reduced when the plant sprayed 24 h before and 24 h before and after inoculation. Incubation and latent periods were increased in treated plant genotypes. Besides, the treatment gave the lowest infection type compared to the control. The foliar spray application did not affect the efficacy of the tested treatment. Keywords: Molecular markers, Genetic diversity, stem rust, leaf rust, nanoparticle.

Keragaman genetik Anggrek Grammatophyllum scriptum asal biji dari hasil Kultur In Vitro berdasarkan penanda RAPD

Propagation through tissue culture by using orchid seed as explants will produce a lot of orchid plants. This study aims to measure the genetic character of orchid plantlets that were regenerated from seeds which have been resulted from in vitro culture. The genetic character of the original orchid plants produced from in vitro culture was determined using Random Amplified Polymorphic DNA (RAPD) molecular markers. The results showed that the primers used in the RAPD analysis showed a polymorphic band pattern of 14 DNA bands, with sizes between 500 bp - 8000 bp. The genetic distance of Grammatophyllum scriptum orchids that was regenerated from seeds is between 0.229 and 0.649. The progenis produced from in vitro culture were clustered into seven groups at a dissimilarity coefficient of 45%.

Çerezlik Kabak (Cucurbita pepo L.) popülasyonlarında yeni SSR markörlerinin geliştirilmesi ile genetik çeşitlilik analizi

Cucurbitaceae family, contain lots of important species in terms of worldwide nutritional and economical value. Despite the molecular genetic researches conducted in recent years, genome data is quite limited for C. pepo which is agriculturally important. The main motivation of this work is to develop new and numerous SSR markers (Simple Sequence Repetitions) that is unique to Cucurbita genome which has extremely small number of genome-specific markers. The reference genome was scanned with bioinformatic tools in terms of repetitive motifs and 76744 genome-specific SSR loci were found. In this scope, 52303 SSR markers were developed for the first time by containing 20 chromosomes in C. pepo L. genotype and the data that belongs to the developed markers is saved in a database. The majority of the most common SSR motifs were detected as di-nucleotide repeats which was rich in terms of AT/AT. To evaluate the amplification efficiency and polymorphic band producing capability of newly developed SSR markers, a collection which contains 39 Cucurbita pepo L. genotypes is characterized and the SSR alleles are scored as 0/1, so that the data file was subjected to the analysis of genetic diversity in DARwin6 software program. The results of this study were evaluated as obtaining important molecular genetic markers of the pumpkin and using them in the future studies of molecular breeding and mapping to obtain important information.

Identification of Races of Fusarium oxysporum f.sp. ciceris, Inciting Wilt of Chickpea in Andhra Pradesh and Parts of Telangana

Background: Fusarium oxysporum f.sp. ciceris (Foc) is one of the most important pathogen, causing wilt of chickpea. It is soil and seed borne pathogen. A serious threat in Foc is the evolution of new races, which reduces exploitation of wilt resistance in the crop in a particular area. Eight races (race 0, 1A, 1B/C, 2, 3, 4, 5 and 6) were reported in the world and among them four races (race 1, 2, 3, 4) were from India. Race 1 was reported from Andhra Pradesh. It is very important to monitor the variation regularly in new isolates collected from different varieties or genotypes and different geographical regions to identify the racial pattern. Development of SCAR markers for identification of Foc isolates is also important as they are highly reliable. Methods: Twenty isolates of Fusarium oxysporum f.sp. ciceris were obtained from wilt infected plants of chickpea covering different places of Andhra Pradesh including two isolates from Telangana and confirmed the pathogen based on pathogenicity test. They were tested on host differentials of chickpea for races identification. Among these twenty isolates five most virulent isolates (Foc-6, Foc-10, Foc-12, Foc-17 and Foc-24) were selected for RAPD based on pathogenicity test and SCAR marker was developed based on DNA banding pattern during RAPD for one isolate.Result: Based on the disease reaction on differentials, concluded that 17 of them out of 20 were matched with race-1 reaction. Two isolates were matched with race-6 reaction and one is not matched with none of the races. An amplified product of polymorphic band of approximately 700 bp in the isolate Foc-12, obtained during RAPD analysis was selected for SCAR marker development and two SCAR markers were developed and validated. Identification of races mainly helps in development of resistant cultivars to specific races and might be contributed to development of integrated disease management practices for Fusarium wilt.