Assessment of polymorphism using RAPD in the generalized hemiparasitic plant Helicanthes elasticus (Desv.)Danser collected from six different hosts

2021 ◽  
Vol 16 (7) ◽  
pp. 141-149
Author(s):  
T.G. Ajithkumar ◽  
Mathew Lizzy ◽  
K.N. Sunil Kumar
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Anacardium Occidentale ◽  
Random Primers ◽  
Citrus Maxima ◽  
Polymorphic Bands

RAPD analysis was carried out to determine genetic diversity that occurred among the selected accessions of H.elasticus obtained from six different hosts. All together 10 random primers were used for the RAPD assay, of which primer S11 produced 12 amplified bands in which 10 are polymorphic. Primer S9 produced the least number of amplified fragments. 10 primers together resulted in 88 amplified fragments, of which 26 are found to be polymorphic. Considerable polymorphism was shown by 3 primers that can be represented in a descending order S11>S79>S10. Accessions of H.elasticus obtained from Anacardium occidentale and Citrus maxima produced more polymorphic bands with S11. The overall polymorphism obtained in the selected samples of this hemiparasite was 29.54 indicating that genetic similarity was more among these samples rather than genetic diversity.

scholarly journals IDENTIFIKASI KERAGAMAN GENETIK KENTANG SUPEJOHN TRANSGENIK (Solanum tuberosum L. var supejohn)

EUGENIA ◽  
2012 ◽  
Vol 18 (3) ◽  
Author(s):  
Christine L.W. Lengkong ◽  
Jeany Polii-Mandang ◽  
Edy F. Lengkong
Keyword(s):  
Genetic Diversity ◽  
Dna Isolation ◽  
Rapd Analysis ◽  
Solanum Tuberosum L ◽  
Similarity Coefficient ◽  
Agarose Gel ◽  
Buffer Solution ◽  
Random Primers ◽  
Average Similarity ◽  
Polymorphic Bands

ABSTRACT   The aim of this study was to determine the genetic diversity of potato Supejohn transgenic that had been twenty-five times subcultured with exploration  method. The genetic variability was calculated using molecular marker Polimorphic Random Amplified DNA (RAPD) analysis of ten samples from four weeks planlets of Supejohn transgenic plants using ten random primers. DNA isolation of 10 samples using CTAB buffer  then measurement of the DNA qualification and quantification,  afterwards amplification of DNA by PCR using 10 random primers followed by electrophoresis on a 1% agarose gel with TAE 1x electrode buffer solution. Visualisation  the results used UV Transluminator to see DNA bands and the data of  polymorphic bands had been analized used the NTSYS-pc version of 1.07 program to obtain the similarity coefficient  and the dendrogram.The results showed that five random primers produced polymorphic DNA bands with 0.39 - 0.88 similarity coefficient  and the average similarity coefficient is 0.63 (63%) or the genetic diversity of the samples as many as 37%. Dendrogram formed eight distinct clusters corresponding similarity coefficient, the formation of clusters means that there is genetic diversity among the DNA samples. Keywords: potato Supejohn transgenic, RAPD, genetic diversity ABSTRAK Penelitian ini bertujuan untuk  menentukan keragaman genetik kentang Supejohn transgenik yang telah dua puluh lima kali disubkultur dengan menggunakan metode penelitian eksplorasi dengan penanda molekuler  Random Amplified Polimorphic DNA (RAPD) terhadap 10 sampel tanaman Supejohn transgenik, berumur empat minggu dan  menggunakan  10 primer random.  Isolasi DNA dari 10 sampel menggunakan buffer CTAB sesudah itu dilakukan pengukuran kualitas dan kuantitas  DNA, kemudian dilanjutkan dengan amplifikasi DNA secara PCR menggunakan 10 primer random diikuti dengan  elektroforesis pada gel agarose 1% dengan larutan penyanggah elektroda TAE 1x. Visualisasi hasil elektroforesis  menggunakan UV Transluminator untuk melihat pita DNA  dan analisis  data pita polimorfik  menggunakan program NTSYS-pc versi 1.07 sehingga didapatkan koefisien kesamaan dan dendrogram. Hasil penelitian menunjukkan bahwa lima primer random menghasilkan pita DNA polimorfik dengan koefisien kesamaan 0.39 – 0.88 dan rata-rata koefisien kesamaan yaitu 0.63 (63%) atau  keragaman  genetik sampel sebesar 37%.  Dendrogram  membentuk delapan cluster yang berbeda sesuai koefisien kesamaan,terbentuknya clusters mengartikan bahwa ada keragaman genetik antar sampel DNA. Eugenia Volume 18 No. 3  Desember 2012 Kata kunci : kentang Supejohn transgenik , RAPD, keragaman genetik

Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

2011 ◽  
Vol 343-344 ◽  
pp. 981-987
Author(s):  
Feng Juan Li ◽  
Chang Lu Wang ◽  
Dong He ◽  
Ya Qiong Liu ◽  
Mian Hua Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Oil Content ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Ricinus Communis ◽  
Major Group ◽  
Ricinus Communis L ◽  
Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

scholarly journals Genetic Diversity in Muscadine and Bunch Grapes Based on RAPD Analysis

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 877A-877
Author(s):  
Jiang Lu ◽  
Xianping Qu ◽  
Olusola Lamikanra
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Separate Study ◽  
Random Primers ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically very distinct grapevines belonging to the subgenera Euvitis and Muscadinia of the genus Vitis are cultivated in the United States. The former is commonly called “bunch” grape, while the latter is usually called “muscadine.” Genetic diversity among these grapes was investigated based on random amplified polymorphic DNAs (RAPDs). Sixteen grape cultivars, with their parentage including V. rotundifolia, V. vinifera, and several American Vitis species, were used for the RAPD analysis. More than 200 RAPDs were produced from 20 random primers. More than 90% of which were polymorphic between the muscadine and the bunch grapes, while polymorphism was considerably low within the muscadine and the bunch grapes. The relationships of grapes between these two subgenera were estimated based on bandsharing and cluster analysis. The result based on the DNA analysis agrees with the isozyme data obtained from a separate study, which demonstrated that the muscadine grape shares very low common alleles with the American bunch grapes and the European grapes.

scholarly journals Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 571-580
Author(s):  
Vladan Popovic ◽  
Aleksandar Lucic ◽  
Danijela Ristic ◽  
Ljubinko Rakonjac ◽  
Sabahudin Hadrovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Bald Cypress ◽  
Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

scholarly journals Diversitatea moleculară a două ecotipuri de Datura inoxia provenite din vestul şi estul României

2020 ◽  
Author(s):  
Cristina Chelu ◽  
◽  
Carmen Varlam ◽  
Gheorghe Titescu ◽  
Gallia Butnaru ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Genetic Similarity ◽  
Molecular Diversity ◽  
Rapd Analysis ◽  
Genomic Variation ◽  
Origin And Evolution ◽  
Random Primers ◽  
Datura Inoxia

Molecular Diversity of two Ecotypes of Datura inoxia Originating from Western and Eastern Romania. To characterize genomic variation among genotypes, we have performed RAPD analysis using ten random primers. The results yielded 88 bands out of which 39 were polymorphic. The primers US1 and US7 showed 87.71% and 72.72% polymorphism respectively. The least polymorphism was shown by primer US9 (12.50%). The primer US15 did not produce any bands suggesting the absence of matching sequences in the genomic DNA. The dendrogram classified ecotypes into two clusters (A and B); cluster B possess three sub-clusters: B1 - Socodor 2; B2 - Flamura 1 and Flamura 2, and B3 - Flamura 3. Overall, the values of genetic similarity between ecotypes were low pointing out their particular origin and “evolution”.

Population genetic diversity of Phytophthora infestans from China as revealed by SSRs and RAPDs

2009 ◽  
Vol 6 (2) ◽  
pp. 161-170 ◽  
Author(s):  
Li Ben-Jin ◽  
Lv Xin ◽  
Chen Qing-He ◽  
Lan Cheng-Zhong ◽  
Zhao Jian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phytophthora Infestans ◽  
Inner Mongolia ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
The North ◽  
Random Amplification ◽  
Ssr Primers ◽  
Polymorphic Bands ◽  
Simple Sequence

AbstractSimple sequence repeats (SSR) and random amplification of polymorphic DNA (RAPD) molecular markers were used to assess the genetic diversity of 80 isolates of Phytophthora infestans in potato (Solanum tuberosum) from Fujian, Heilongjiang, Hebei and Inner Mongolia Provinces in China. Polymorphism was identified by 13 SSR primers and 14 RAPD primers in the isolates of P. infestans in potato. A total of 76 bands were amplified by SSRs, with the percentage of polymorphic bands (PPB) being 78.9% and the similarity coefficient ranging between 0.00 and 0.42. A total of 189 bands were amplified by RAPDs, with the percentage of polymorphic bands being 95.2% and the similarity coefficient ranging between 0.04 and 0.66. Analysis of genetic diversity showed that there exists higher genetic variation in the Fujian population in comparison to the populations of Heilongjiang, Hebei and Inner Mongolia. Nei's genetic identity analysis indicates that the genetic similarity between populations of Heilongjiang and Inner Mongolia is the highest and that between Fujian and Hebei is the lowest. A cluster analysis revealed that isolates from Fujian, in the south of China, are distantly related to those from Heilongjiang, Hebei and Inner Mongolia in the north, and the Fujian population is distributed among more groups than the other three, exhibiting a higher genetic diversity.

scholarly journals Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 457
Author(s):  
HyokChol Kim ◽  
Pei Lei ◽  
Aizhi Wang ◽  
Shuo Liu ◽  
Yong Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Castor Bean ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Ricinus Communis ◽  
Similarity Coefficient ◽  
Morphological Data ◽  
Oilseed Crop ◽  
Ricinus Communis L ◽  
Polymorphic Bands

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

scholarly journals Genetic diversity of Falcataria moluccana and its relationship to the resistance of gall rust disease

2018 ◽  
Vol 19 (1) ◽  
pp. 12-17
Author(s):  
NEO ENDRA LELANA ◽  
SURYO WIYONO ◽  
GIYANTO GIYANTO ◽  
ISKANDAR Z. SIREGAR
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Disease Resistance ◽  
Rapd Analysis ◽  
Principal Component ◽  
Rust Disease ◽  
Preliminary Information ◽  
Rapd Primer ◽  
Polymorphic Bands ◽  
Disease Severity Level

Lelana Ne, Wiyono S, Giyanto, Siregar IZ. 2018. Genetic diversity of Falcataria moluccana and its relationship to the resistance of gall rust disease. Biodiversitas 19: 12-17. The use of cultivars that are resistant to a particular disease is one strategy that could mitigate the incidence of gall rust disease on Falcataria moluccana. Previous studies on the genetic diversity of F. moluccana did not attempt to link that genetic diversity to gall rust disease resistance. This research was carried out using RAPD analysis to determine the preliminary information on the association between different markers and the resistance to gall rust disease. The analysis evaluated a total of 20 pairs of healthy and infected F. moluccana trees that were classified based on their disease severity level. The RAPD primers used in this study were as follows: OPA-05, OPA-08, OPA-10, OPA-13, OPA-18, OPB-07, OPD-13, OPF-02, and OPG-05. The results showed that each RAPD primer produced a varying number of polymorphic bands, ranging from 3 to 12 bands, with a total of 80 polymorphic bands. Despite the number of loci analyzed, however, no specific polymorphic bands were found that could distinguish between healthy and diseased trees. This was supported by principal component analysis, which showed that healthy and diseased populations were not distributed separately. The structure analysis also showed that the healthy and diseased populations were not different.

scholarly journals INTER- AND INTRA-SPECIFIC VARIATION AMONG FOUR IPOMOEA SPECIES AS DETECTED BY RAPD ANALYSIS

HortScience ◽  
1995 ◽  
Vol 30 (3) ◽  
pp. 442e-442
Author(s):  
Dapeng Zhang ◽  
Wanda Collins
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Analysis ◽  
Preliminary Assessment ◽  
Separate Species ◽  
Cluster Procedure ◽  
Specific Variation ◽  
Polymorphic Bands ◽  
Genebank Collections ◽  
Ipomoea Species

To understand the prospects of applying the RAPD technique to assay genetic diversity in Ipomoea, four species (I. batatas, I. trifida, I. triloba, and I. ×leucantha) were analyzed for RAPD molecular markers. Six accessions of each species were used. Significant RAPD polymorphisms were detected within each species. Of 20 primers used, nine produced clear scorable polymorphic bands. The number of polymorphic bands produced per primer ranged from two to nine. Pair-wide genetic distance was calculated based on “band sharing”. The SAS-CLUSTER procedure was used to build a hierarchical species dendrogram. The four species were clearly separated by the clustering, which agrees with their existing taxonomic relationship. This study shows that RAPD analysis can be a powerful tool for identifying duplicates of germplasm acessions and for assessing genetic diversity. The procedures are relatively inexpensive and easy to perform and could be valuable in preliminary assessment of field genebank collections to separate species and indicate duplications in collected material.

scholarly journals DETERMINATION GENETIC DIVERSITY OF INBRED LINES AND HYBRIDS OF MAIZE USING ISSR TECHNIC

2020 ◽  
Vol 51 (1) ◽  
Author(s):  
Amoon & Abdul -Hamed
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Genetic Similarity ◽  
Inbred Lines ◽  
Marker Data ◽  
Molecular Length ◽  
Polymorphic Bands ◽  
Degree Of Similarity

This study was carried out in the biotechnology laboratories of the Seed Inspection and Certification Department - Ministry of Agriculture during 2019, to study the relation among molecular five inbred lines with hybrid crosses of maize. to estimate the genetic diversity and determine the degree of genetic similarity among them using the ISSR based on PCR technic with 6 primers. All primers produced 79 bands at a rate of 13.2 bands per primer. The number of amplified bands ranged from 10 to the primer UBC 835 and 16 in the UBC 897, with a molecular length ranged between 100 - 1700 bp. The total number and percentage of polymorphic bands was 71 and 90% respectively. The primers UBC 856 and UBC 866 the highest percentage of had polymorphic bands of 100%. While the UBC 835 showed the lowest (70%). The highest efficiency and specificity were 12.7% and 9.9% respectively in UBC835. Based on molecular marker data and genetic similarity using the UPGMA method in establishing the dendrogram, the study showed that genetic similarity between the inbred lines ranged from 0.105 to 0.40, the highest (0.40) between the two strains  BK121 and Zm6 , While the lowest degree of similarity (0.105) was between the two strains  BK121 and ART-817 .

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