scholarly journals Diversity analysis of Rhacophorus margaritifer (Schlegel, 1837) in Baturraden based on RAPD markers

2020 ◽  
Vol 5 (1) ◽  
pp. 44
Author(s):  
Fajar Nur Sulistyahadi ◽  
I Gusti Agung Ayu Ratna Puspitasari ◽  
Agus Nuryanto
Keyword(s):  
Binary Data ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Genetic Difference ◽  
Rapd Marker ◽  
Botanical Garden ◽  
Primary Forest ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Marker Band

Rhacophorus margaritifer is an endemic species of arboreal frog in Java. Previous studies found this frog in several locations of Baturraden, namely in primary forest of Ketenger area, along Pancuran Pitu tourism track, and Baturraden Botanical Garden. There were still limited studies of molecular diversity of R. margaritifer and no prior data from population in the southern slope of Mount Slamet. This study aimed to look at the genetic polymorphism and determine the locus diversity of R.margaritifer population in Baturraden by using the PCR-RAPD technique.  Frog tissue samples were taken from three populations in Kalipagu hiking trail (HPK 01), Baturraden hiking trail (HPK 02), and Baturraden Botanical Garden (KRB). DNA was extracted using the Chelex method. Molecular characterization was performed based on RAPD markers. The RAPD marker band pattern was changed to binary data 0-1 and analysed using Arlequin software ver.3.5. A total of 19 frog individuals were obtained during sampling at three locations. High genetic diversity had been observed in all populations with gene diversity range from 0.9643 in HPK 01 population to 1.0000 in both KRB and HPK 02 populations. A high locus variation was also observed for all populations with values of 0.159524 in KRB; 0.165816 in HPK 01; 0.192857 in HPK 02, respectively. AMOVA indicated no genetic difference among populations of R. margaritifer (p=0.50244). 

Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

2021 ◽  
Vol 43 (1) ◽  
pp. 38-42
Author(s):  
Kavungal Priya ◽  
◽  
Indira . ◽  
Vadakkethil Balakrishnan Sreekumar ◽  
Renuka . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Ghats ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Western Ghats Of India ◽  
The Mean ◽  
Two Parameters ◽  
Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

scholarly journals RAPD ANALYSIS OF GENETIC VARIATION IN NATURAL POPULATIONS OF AEGILOPS SP. FROM SOUTH ADRIATIC

AGROFOR ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Miodrag DIMITRIJEVIĆ ◽  
Sofija PETROVIĆ ◽  
Borislav BANJAC ◽  
Goran BARAĆ
Keyword(s):  
Genetic Variation ◽  
Food Production ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Gene Diversity ◽  
Rapd Marker ◽  
Natural Populations ◽  
Genetic Structuring ◽  
Potential Source ◽  
Novel Approach

New challenges that food production is facing, requires novel approach inagricultural strategy. The scissors of growing demand for food and the limits of theEarth's resources are forcing plant breeders to run for the new borders, utilizing allthe available genetic variation in order to create fruitful and economically soundcultivars. Aegilops sp. (Poaceae) is a potential source of genetic variation for wheatimprovement. RAPD marker analysis was used in order to distinguish and evaluatedifferent genotypes of Aegilops sp. population samples from the collectiongathered during few years’ expeditions in South Adriatic, along the coastal, littoraland the inland parts of Montenegro. Ten randomly amplified polymorphic DNAmarkers (RAPDs) were tested: OPA-05, OPA-08, OPB-06, OPA-02, OPA-07,OPA-25, OPB-07, OPB-18, OPC-06, OPC-10 to examine genetic structuring on 18samples of 6 populations of different Aegilops sp. According to global AMOVA,75% of total gene diversity was attributable mostly to diversity within population(ΦPT =0.205 p=0.001), indicating that the groups of studied goat grass populationswere seemingly to differing genetically. In contrast, 25% of the variation camefrom variation among populations. According to PCoA, the distribution of 18 goatgrass accessions by Principal Coordinate Analysis shows 3 distinct groups. PCoaxis 1, PCo axis 2, and PCo axis 3 account for 20.8%, 18.2% and 14.1% of thevariation, respectively. The results showed that RAPD markers could be aconvenient tool for investigating genetic variation and for detecting geneticstructuring of populations. Genetic variability formed under natural selection wasentrenched.

scholarly journals Assessment of genetic diversity in bread wheat (Triticum aestivum L.) using RAPD markers

2017 ◽  
Vol 9 (3) ◽  
pp. 1751-1755
Author(s):  
Amit Kumar ◽  
R. S. Sengar ◽  
Vivekanand Pratap Rao ◽  
Gyanika Shukla ◽  
Rekha Dixit ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genomic Dna ◽  
Core Collection ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Triticum Aestivum L ◽  
Wheat Cultivars ◽  
High Genetic Diversity ◽  
Wheat Genotypes

The present study aimed to evaluate the genetic diversity of 10 wheat cultivars by Random Amplified Pol-ymorphic DNA (RAPD) marker. The genomic DNA of 10 wheat genotypes were amplified with 10 RAPD primers that produced 53 amplified band, out of which 23 band were polymorphic (43.39%). The number of fragment amplified per primer ranged from 4 to 9. Primer A01 generated maximum number of amplified band, out of which 5 band were polymorphic. Cluster analysis of wheat genotypes were based on UPGMA method. Cluster analysis of 10 wheat genotypes were classified in to two main group; single variety AKW 1071 was placed in first group and rest 9 variety were placed in second group. The pair wise similarity values ranged from 0.58% to 100% and showed that cultivars Raj-3765 and K-7903 were the closest with highest similarity value (100%), while genotypes AKW 1071 and K9006 showed minimum similarity value (62%). The present study indicated the presence of high genetic diversity among wheat cultivars, which could be used for the developing core collection of wheat germplasm for breeding purpose.

Detection and Mapping of RAPD Markers Associated with QTL Affecting Seed Size and Shape in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547b-547
Author(s):  
Soon O. Park ◽  
Dermot P. Coyne ◽  
Geunhwa Jung ◽  
E. Arnaud-Santana ◽  
H. Ariyarathne
Keyword(s):  
Linkage Group ◽  
Common Bean ◽  
Seed Size ◽  
Phenotypic Variation ◽  
Seed Weight ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Seed Shape ◽  
Seed Length ◽  
Ri Lines

Seed size is an important trait in common bean. The objective was to identify RAPD markers associated with QTL for seed weight, seed length, and seed height in a molecular marker-based linkage map in a recombinant inbred (RI) population from the common bean cross of the larger seeded (100 seed/39 to 47 g) PC-50 (ovate seed shape) × smaller seeded (100 seed/26 to 35 g) XAN-159 (flat rhomboidal seed shape). The parents and RI lines were grown in two separate greenhouse and two field (Wisconsin, Dominican Republic) experiments using a RCBD. Continuous distributions for seed weight, seed length, and seed height were observed for RI lines indicating quantitative inheritance. One to three QTLs affecting seed weight explained 17% to 41% of the phenotypic variation. Two to three QTLs for seed length explained 23% to 45% of the phenotypic variation. One to four QTL associated with seed height explained 17% to 39% of the phenotypic variation. A RAPD marker M5.850 in linkage group 3 was consistently associated with seed weight, seed length, and seed height in all experiments and explained 7% to 13% of the phenotypic variation for these traits. A seedcoat pattern morphological marker (C) in linkage group 1 was associated with seed weight and seed height in two greenhouse experiments.

Randomly amplified polymorphic DNA linkage relationships in different Norway spruce populations

2001 ◽  
Vol 31 (8) ◽  
pp. 1456-1461
Author(s):  
M Troggio ◽  
T L Kubisiak ◽  
G Bucci ◽  
P Menozzi
Keyword(s):  
Rapd Markers ◽  
Rapd Marker ◽  
Population Based ◽  
Italian Population ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Consensus Map ◽  
Norwegian Population ◽  
Marker Loci ◽  
Linkage Relationships

We tested the constancy of linkage relationships of randomly amplified polymorphic DNA (RAPD) marker loci used to construct a population-based consensus map in material from an Italian stand of Picea abies (L.) Karst. in 29 individuals from three Norwegian populations. Thirteen marker loci linked in the Italian stand did show a consistent locus ordering in the Norwegian population. The remaining 16 unlinked marker loci were spread over different linkage groups and (or) too far apart both in the population map and in this study. The limited validity of RAPD markers as genomic "hallmarks" resilient across populations is discussed. We also investigated the reliability of RAPD markers; only 58% of the RAPD markers previously used to construct the consensus map in the Italian population were repeatable in the same material. Of the repeatable ones 76.3% were amplified and found polymorphic in 29 megagametophyte sibships from three Norwegian populations.

Genetic Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

2021 ◽  
Vol 1 (01) ◽  
pp. 9-14
Author(s):  
SAILA KABIR ◽  
MD ABUL KASHEM ◽  
MOHAMMAD ZABED HOSSAIN
Keyword(s):  
Genetic Diversity ◽  
Alien Species ◽  
Invasive Alien Species ◽  
Gene Diversity ◽  
Lantana Camara ◽  
Native Plant ◽  
High Genetic Diversity ◽  
Native Plant Species ◽  
Information Index ◽  
Genetic Clustering

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

scholarly journals Segregation for Resistance to Eastern Filbert Blight in Progeny of `Zimmerman' Hazelnut

2006 ◽  
Vol 131 (6) ◽  
pp. 731-737 ◽  
Author(s):  
China F. Lunde ◽  
Shawn A. Mehlenbacher ◽  
David C. Smith
Keyword(s):  
Rapd Markers ◽  
Chromosome Region ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Segregation Ratio ◽  
Enzyme Linked Immunosorbent Assay ◽  
Resistance Locus ◽  
Resistance Allele ◽  
Reciprocal Translocations ◽  
Eastern Filbert Blight

Eastern filbert blight (EFB), caused by the fungus Anisogramma anomala (Peck) E. Müller, is an important disease of european hazelnut (Corylus avellana L.) in the Pacific northwestern United States. In 1989, a chance seedling free of EFB was discovered adjacent to a severely diseased orchard near Troutdale, Ore. This selection, subsequently named `Zimmerman', was crossed with three susceptible selections. Based on morphological characters and incompatibility alleles, we speculated that `Zimmerman' (S1 S3) was a hybrid between `Barcelona' (S1 S2) and `Gasaway' (S3 S26). The three seedling populations were inoculated with spores of the pathogen in a greenhouse test and assayed by indirect enzyme-linked immunosorbent assay (ELISA) and by observation of canker incidence. The observed segregation fit a 3 resistant : 1 susceptible ratio in all three progenies, in contrast to the 1 : 1 ratio found when the resistant pollinizer `Gasaway' was crossed to susceptible genotypes. Random amplified polymorphic DNA (RAPD) marker UBC 152800 linked to the resistance gene in `Gasaway' co-segregated with the resistant phenotype in all three populations with 2%, 4%, and 6% recombination, respectively. Seed germination and transplanting records did not provide evidence of selection in favor of resistant seedlings. Pollen germination was 71% in `Gasaway', 29% in `Zimmerman', and 18% in `Barcelona', indicating possible selection at the gametophytic level. Subsequently 16 resistant seedlings of `Zimmerman' were crossed with the highly susceptible selection OSU 313.078. Segregation fit a 3 : 1 ratio in 14 of the 16 progenies, and showed a surplus of resistant seedlings in the other two. None showed a 1 : 1 segregation. Resistance co-segregated with two RAPD markers that flank the `Gasaway' resistance allele. To test allelism of resistance from `Gasaway' and `Zimmerman', VR 6-28 with resistance from `Gasaway' was crossed with `Zimmerman'. Eight resistant selections from this progeny were crossed with OSU 313.078. Five of the eight progenies segregated 3 : 1, two progenies segregated 1 : 1, and OSU 313.078 × OSU 720.056 gave only resistant offspring. The ratios indicate that OSU 720.056 is homozygous resistant and that `Zimmerman' and `Gasaway' share a common resistance allele. Reciprocal translocations have been reported in hazelnut cultivars, including `Barcelona', the leading cultivar in Oregon. `Zimmerman' appears to be a hybrid of `Barcelona' and `Gasaway', but because of cytogenetic abnormalities, `Zimmerman' may have inherited two copies of the chromosome region that contain the resistance locus and flanking RAPD markers. If the region containing the resistance were attached to two independent centromeres, a 3 : 1 segregation ratio for disease response and flanking markers would be expected, and we propose this as the most likely explanation. Resistance from `Gasaway' and `Zimmerman' has been called “immunity” or “complete resistance.” However, we noted a few seedlings with small cankers, nearly all of which lacked sporulating stromata. Flanking RAPD markers indicate that the resistance allele is present in these seedlings. Although not “immune” or “completely resistant,” `Gasaway' and `Zimmerman' transmit a very high level of resistance.

scholarly journals Regression Analysis for the Identification of RAPD Markers Linked To Drought Tolerance in Sorghum

2015 ◽  
Vol 17 (1) ◽  
pp. 61
Author(s):  
Paramita Cahyaningrum ◽  
T. Taryono ◽  
Anto Rimbawanto
Keyword(s):  
Regression Analysis ◽  
Drought Tolerance ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Pcr Amplification ◽  
Raw Material ◽  
Vegetative Stage ◽  
Severe Condition ◽  
Logistic Analysis ◽  
Logistic Method

Sorghum (Sorghum bicolor) can actually withstand in dry or drought condition better than other crops,therefore it can be grown at different agroclimatic conditions and its product can be used for different purposessuch as food, feed and industrial raw material. However at severe condition, the productivity will also dropdrastically. The aim of this research was to identify RAPD marker linked to the drought tolerance. In thisresearch, varieties of sorghum used as research materials were Durra, Zhengzu, the mutants of Durra andZhengzu (from 300 Gy gamma radiation) B-100 and Zh-30, and the F2 seeds from Zh-30 x B-100 and B-100 xZh-30. Drought screening was carried out using 0.3 % KI during sorghum vegetative stage. DNA extractionwas done using a modified CTAB method. PCR was carried out for RAPD analysis. PCR amplification productswere scored and analyzed using SAS program. The result showed that potassium iodide can be used fordrought screening during the vegetative stage and regression analysis using the logistic method can be usedto identify RAPD markers that is linked to drought tolerance in sorghum. The logistic analysis showed thatband A8-480 was linked to drought tolerance in sorghum.

Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 844-851 ◽  
Author(s):  
K. F. Yu ◽  
K. P. Pauls
Keyword(s):  
Chromosome Segregation ◽  
Dna Markers ◽  
Rapd Markers ◽  
Molecular Mapping ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Female Parent ◽  
Linkage Groups ◽  
Double Reduction ◽  
Chromatid Segregation

An F1 population was used to analyze the inheritance of random amplified polymorphic DNA (RAPD) markers in tetraploid alfalfa. Of the 32 RAPD markers that were used for a segregation analysis in this study, 27 gave ratios that are consistent with random chromosome and random chromatid segregation at meiosis. However, among all of the RAPD markers (121) that were screened in this study, only one example of a double reduction, that is typical of chromatid segregation, was observed. These results indicate that random chromosome segregation is likely the predominant but not the exclusive mode of inheritance for tetraploid alfalfa. χ2 analyses of cosegregation for RAPD marker pairs derived from the female parent revealed nine linkages that fell into four linkage groups. The recombination fractions among linked marker pairs ranged from 1 to 37%. These are the first molecular linkage groups reported in tetraploid alfalfa. In addition, various strategies for molecular mapping in the tetraploid alfalfa genome are proposed that should be of interest to plant breeders who are planning to use molecular markers for alfalfa or other tetraploid species.Key words: RAPD markers, tetraploid alfalfa, segregation, linkage groups.

scholarly journals Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment

2018 ◽  
Vol 16 (1) ◽  
pp. 1 ◽  
Author(s):  
Yong Li ◽  
Jianqiang Zhang ◽  
Zhiliang Gong ◽  
Wenlai Xu ◽  
Zishen Mou
Keyword(s):  
Correlation Analysis ◽  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Pearson Correlation ◽  
Glucose Dehydrogenase ◽  
Sampling Site ◽  
Soluble Phosphate ◽  
High Genetic Diversity ◽  
Alpha And Beta Diversity ◽  
Insoluble Phosphate

Quinoprotein glucose dehydrogenase (GDH) is the most important enzyme of inorganic phosphorus-dissolving metabolism, catalyzing the oxidation of glucose to gluconic acid. The insoluble phosphate in the sediment is converted into soluble phosphate, facilitating mass reproduction of algae. Therefore, studying the diversity of gcd genes which encode GDH is beneficial to reveal the microbial group that has a significant influence on the eutrophication of water. Taking the eutrophic Sancha Lake sediments as the research object, we acquired samples from six sites in the spring and autumn. A total of 219,778 high-quality sequences were obtained by DNA extraction of microbial groups in sediments, PCR amplification of the gcd gene, and high-throughput sequencing. Six phyla, nine classes, 15 orders, 29 families, 46 genera, and 610 operational taxonomic units (OTUs) were determined, suggesting the high genetic diversity of gcd. Gcd genes came mainly from the genera of Rhizobium (1.63–77.99%), Ensifer (0.13–56.95%), Shinella (0.32–25.49%), and Sinorhizobium (0.16–11.88%) in the phylum of Proteobacteria (25.10–98.85%). The abundance of these dominant gcd-harboring bacteria was higher in the spring than in autumn, suggesting that they have an important effect on the eutrophication of the Sancha Lake. The alpha and beta diversity of gcd genes presented spatial and temporal differences due to different sampling site types and sampling seasons. Pearson correlation analysis and canonical correlation analysis (CCA) showed that the diversity and abundance of gcd genes were significantly correlated with environmental factors such as dissolved oxygen (DO), phosphorus hydrochloride (HCl–P), and dissolved total phosphorus (DTP). OTU composition was significantly correlated with DO, total organic carbon (TOC), and DTP. GDH encoded by gcd genes transformed insoluble phosphate into dissolved phosphate, resulting in the eutrophication of Sancha Lake. The results suggest that gcd genes encoding GDH may play an important role in lake eutrophication.

Sign in / Sign up

Export Citation Format

Share Document