scholarly journals Geographical Survey and Genetic Variation Studies of Few Chilly Varieties Collected from Different Regions of Karnataka, India

2021 ◽  
Vol 6 (04) ◽  
pp. 50-56
Author(s):  
Devi Shree ◽  
Pavitra B. S. Rao ◽  
Surendra H. Gowda ◽  
Shruthi S. Dakappa
Keyword(s):  
Genetic Variation ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Pcr Analysis ◽  
Local Alignment ◽  
Pair Group ◽  
Hybrid Variety ◽  
Search Tool ◽  
Genetic Level ◽  
The Relationship

Chillies are widely used throughout the world in the form of spice and are also used in making beverages and medicines. They are rich in vitamins, especially in vitamin A and C. Chillies contain lots of minerals like potassium, magnesium, and iron. They have been employed for pain relief as they are known to inhibit pain messengers and hence their extracts are used to alleviate the pain of arthritis, headaches, burns, and neuralgia. It is also claimed that they have the power to boost the immune system and lower cholesterol. They are also helpful in getting rid of gut parasites. In this regard we attempted to do a geographical survey about the chilly varieties and chilly growing states in India. We collected the local varieties of chillies available in Karnataka and performed genetic variation studies to understand their relationship at the genetic level. PCR analysis was done using the selected random amplified polymorphic DNA (RAPD) marker to identify the polymorphic loci between the genotypes taken. DNA Barcoding was done to validate the species using basic local alignment search tool (BLAST) and Clustal Omega, further dendrogram was constructed which guide the joining linkage rule of unweighted pair group average (UPGMA) and the genetic distance to compute from matrix table. The results obtained highlight the relationship between species of Capsicum annum, Capsicum frutescens which are closely related followed by Capsicum pubescens and Capsicum baccatum providing knowledge about its application in genetics and plant breeding in developing efficient hybrid variety.

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

scholarly journals Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

2016 ◽  
Vol 25 (2) ◽  
pp. 223-229 ◽  
Author(s):  
Kuasha Mahmud ◽  
KM Nasiruddin ◽  
MA Hossain ◽  
L Hassan
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Sugarcane Varieties ◽  
Main Cluster ◽  
Pair Group ◽  
The Relationship ◽  
Linkage Distance

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

scholarly journals Molecular characterization of onion (Allium cepa) using RAPD markers

1970 ◽  
Vol 35 (2) ◽  
pp. 313-322 ◽  
Author(s):  
M Maniruzzaman ◽  
ME Haque ◽  
MM Haque ◽  
MA Sayem ◽  
M Al-Amin
Keyword(s):  
Allium Cepa ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Group Method ◽  
Genetic Studies ◽  
Pair Group ◽  
Genetic Level ◽  
Polymerase Chain

A polymerase chain reaction (PCR) based approach, namely random amplified polymorphic DNA (RAPD) analysis was applied to l0 varieties of onion (Allium cepa) in order to assess the degree of polymorphism within the genes and to investigate if this approach was suitable for genetic studies of onion. For this study, ten cultivars of onion were evaluated for variability using a set of 15 random l0-mer primers. The polymorphisms in PCR amplification products were subjected to the unweighed pair group method for arithmetic averages (UPGMA) and plotted in a phenogram. The dendogram constructed from the similarity data showed that all the cultivars analyzed were related. Among them, 12 of the primers revealed scorable (168 bands) polymorphisms between cultivars of A. cepa and the rest did not show polymorphism in their genetic level. In this study, it was found that Bermis and India-2 were more dissimilar and on the other hand, Faridpuri and Bhati were the most similar in their genetic level. Keywords: RAPD; onion; genetic diversity; polymorphism. DOI: 10.3329/bjar.v35i2.5894Bangladesh J. Agril. Res. 35(2) : 313-322, June 2010

scholarly journals VARIASI GENETIK Lactobacillus fermentum Beijerink ASAL SAYUR ASIN BERDASARKAN ANALISIS RFLP 16S-23S rDNA ISR, RAPD-PCR DAN ERIC-PCR

2017 ◽  
Vol 16 (2) ◽  
Author(s):  
Sulistiani Sulistiani ◽  
Wibowo Mangunwardoyo ◽  
Abinawanto Abinawanto ◽  
Endang Sukara ◽  
Achmad Dinoto ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Molecular Techniques ◽  
Lactobacillus Fermentum ◽  
Pcr Analysis ◽  
Intergenic Spacer Region ◽  
Rapd Pcr ◽  
Upgma Cluster Analysis ◽  
Process Combination

Molecular analysis of Lactobacillus fermentum isolates is essential to understand their genetic variation in relations to their roles in sayur asin fermentation process. Combination of three molecular techniques which is restriction fragment length polymorphism (RFLP) of 16S23S rDNA intergenic spacer region (ISR), random amplified polymorphic DNA (RAPD-PCR) and an enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis were performed to discriminate 19 representative isolates of L. fermentum isolated from sayur asin. The result showed that L. fermentum strain D11 is distantly related to other isolates based on RFLP using HhaI restriction enzyme and RAPDPCR analyses. In addition, both of RAPD-PCR and ERIC-PCR successfully determined the genetic variation among L. fermentum strains by exhibiting distinct 4-8 bands (800-2080 bp) and 4-10 bands (280-3050 bp), respectively. A dendogram generated from UPGMA cluster analysis of both RAPD-PCR and ERIC-PCR data showed two distinct genotypic groups exist among L. fermentum isolated from sayur asin in Indonesia.

scholarly journals Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

Genetic Variability and Relationships among Seventeen Trichoderma Isolates to Control Dry Root Rot Disease Using RAPD Markers

2008 ◽  
Vol 63 (9-10) ◽  
pp. 740-746 ◽  
Author(s):  
Kuruba Gopal ◽  
Yasodam Sreenivasulu ◽  
Venati Gopi ◽  
Gundala Prasadbabu ◽  
Teruvai Bharat Kumar ◽  
...  
Keyword(s):  
Root Rot ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Trichoderma Spp ◽  
Major Cluster ◽  
Rot Disease ◽  
And Cluster Analysis ◽  
The Relationship ◽  
Potential Antagonist

Trichoderma spp. has been identified as potential antagonist of Fusarium solani, which is causing dry root rot of Citrus. A random amplified polymorphic DNA (RAPD) marker was used to estimate the genetic variation among 17 isolates of Trichoderma. These isolates were characterized using 20 random primers of the OPM series, out of which 16 primers gave a total of 145 DNA fragments, showing 91.8% polymorphism. The genetic distance between each isolate was calculated, and cluster analysis was used to generate a dendrogram showing the relationship among them. The isolates grouped into two major clusters, the first major cluster consisted of TCT14, TCT17, TCT13, TCT12 and TCT16. The remaining isolates in the second major cluster separated in two sub-clusters; the first cluster consisted of TCT4, TCT10, TCT2, TCT3, TCT8, TCT6, TCT9, and the second sub-cluster consisted of TCT1 TCT15 TCT5, TCT11, and TCT7. The similarity matrix indicated that TCT6 and TCT13 were genetically distinct as they showed only 22.6% similarity followed by TCT5 and TCT16; TCT6 and TCT16 (25%), while the isolates TCT4 and TCT10 were found to be genetically similar, as 66.7% similarity was observed between the isolates followed by 61.3% similarity between the TCT2 and TCT4 isolates.

scholarly journals ANALISIS KEKERABATAN GENETIK TANAMAN PADI (Oryza sativa L.) DI KABUPATEN KAMPAR DENGAN MENGGUNAKAN PENANDA Random Amplified Polymorphic DNA (RAPD)

2021 ◽  
Vol 11 (2) ◽  
pp. 75
Author(s):  
Rita Elfianis ◽  
Joko Warino ◽  
Rosmaina Rosmaina ◽  
Suherman Suherman ◽  
Zulfahmi Zulfahmi
Keyword(s):  
Genetic Distance ◽  
Oryza Sativa L ◽  
Polymorphic Locus ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Economic Value ◽  
Molecular Data ◽  
Polymorphic Loci ◽  
Average Percentage ◽  
The Relationship

Rice is a cereal crop that belongs to the graminae family of high economic value, and is the main food for more than a portion of the world's population. This study aims to determine the relationship genetic of rice in Kampar by RAPD marker. Eight genotypes of rice from district in Kampar were amplified using eight primers (OPA 5, OPB 7, OPC 19, OPD 2, OPD 3, OPD 8, OPD 11, and OPD 13). The analysis of molecular data was performed by using NTSys pc -2.02 and GenAlex 6.1 . The results of the amplification of rice produced 48 loci with DNA band sizes obtained ranging from 350-1700 bp. The average percentage of polymorphic loci of the eight primers was 49.80%, where the highest percentage of polymorphic loci produced by OPA-7 primer was 75%, while the lowest polymorphic locus percentage was observed in OPD-13 primer which was 14.28%. The value of genetic distance between rice from Kampar in this study is in the range of 0.06 - 0.37. At a genetic distance of 0.79, rice plants can be grouped into two groups, namely the first group consisting of sokan and coku. The second group consisted of suntiong, korean , cupak putio, kuniong, jangguik, and cupak tenggi. The results of this study are expected to be taken into consideration in developing rice breeding strategies in the future.

scholarly journals Genetic Variability Assay of Different Strains of Catla catla

2015 ◽  
Vol 9 (1) ◽  
pp. 37-42
Author(s):  
Md. Rayhan Ali ◽  
Md. Lifat Rahi ◽  
Shikder Saiful Islam ◽  
Md. Saifuddin Shah ◽  
Foyez Ibn Shams
Keyword(s):  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Marker ◽  
Group Method ◽  
Catla Catla ◽  
Breeding Programs ◽  
Pair Group ◽  
Commercially Important ◽  
Different Populations ◽  
Different Strains

Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) marker was used to assay genetic variation in two river populations (Halda and Padma) as well as in three hatchery populations of the commercially important Indian major carp, C. catla. Five specimens of each population were collected from each location. Genomic DNA was isolated from the muscle tissue. Five primers were used and in total, 117 bands were obtained of which 51.57% bands were polymorphic. Overall proportions of polymorphism obtained from different populations were found to be 75%, 62%, 50%, 37.5% and 33.33% for BoluharBaor hatchery, Halda and Padma River, Kapotakkha hatchery, and Ma-Fatema hatchery respectively. The highest percentage of intrapopulation genetic similarity was found to be 61.81% in case of Baluhar Baor hatchery and the lowest was found to be 25.63% in case of Kapathakha hatchery. The highest percentage of interpopulation genetic similarity was found to be 85.21% between Kapathakha and Ma-Fatema hatchery population; and the lowest was found to be 46.00% in case of Kapathakha and BaluharBaor hatchery population.  The dendrogram on Average Unweighted Pair Group Method of Arithmatic Mean (UPGMA) showed two clusters, the Halda River and BaluharBaor hatchery population forming one cluster and the other populations the second cluster. Genetic variation obtained in different population of C.catla in the present study is highly satisfactory and indicates that the species can be very easily employed for exploitation for genetic improvement through selection.DOI: http://dx.doi.org/10.3126/10.3126/ijls.v9i1.11924 International Journal of Life Sciences Vol.9(1) 2015 37-42

scholarly journals Discrimination and Genetic Diversity among Cultivated Olives of Greece Using RAPD Markers

2003 ◽  
Vol 128 (5) ◽  
pp. 741-746 ◽  
Author(s):  
N. Nikoloudakis ◽  
G. Banilas ◽  
F. Gazis ◽  
P. Hatzopoulos ◽  
J. Metzidakis
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Fruit Size ◽  
Similarity Index ◽  
Group Method ◽  
Poor Correlation ◽  
Pair Group ◽  
Electrophoretic Patterns

Random amplified polymorphic DNA (RAPD) markers were used to study the genetic diversity and to discriminate among 33 Greek olive (Olea europaea L.) cultivars. Three feral forms from Crete and five foreign cultivars recently introduced into Greece were also included. Nineteen primers were selected which produced 64 reproducible polymorphic bands in the 41 olive genotypes studied, with an average of 3.4 informative markers per primer. The RAPD markers resulted in 135 distinct electrophoretic patterns, with an average of 7.1 patterns per primer. Based on either unique or combined patterns, all genotypes could be identified. Genetic similarities between genotypes were estimated using the Dice similarity index and these indicated that a high degree of diversity exists within the Greek olive germplasm. Using the unweighted pair-group method (UPGMA) most cultivars were clustered into two main groups according to their fruit size or commercial use (table or olive oil). However, poor correlation was detected between clustering of cultivars and their principal area of cultivation. RAPD marker data were subjected to nonmetric multidimentional scaling (NMDS) which produced results similar to those of the UPGMA analysis. The results presented here contribute to a comprehensive understanding of cultivated Greek olive germplasm and provide information that could be important for cultural purposes and breeding programs.

scholarly journals Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

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