scholarly journals KARAKTERISASI BEBERAPA STRAIN GURAMI Osphronemus gouramy Lac. MENGGUNAKAN MARKA RAPD

2014 ◽  
Vol 1 (1) ◽  
pp. 109
Author(s):  
Anisa Kartika Sari ◽  
Agus Nuryanto ◽  
Agus Hery Susanto
Keyword(s):  
Fish Species ◽  
Genetic Relationship ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Dna Marker ◽  
Random Amplified Polymorphic Dna ◽  
Economic Value ◽  
Pcr Amplification ◽  
Sampling Technique ◽  
Survey Method

Giant gouramy, Osphronemus gouramy Lac. is a popular fish species in Indonesia, especially in Java and Sumatera as this freshwater fish species has a high economic value of stable price. Fish farmers in Bogor divide giant gouramy into six strains based on egg productivity, growth rate, and maximum weight of the adult. They are soang, jepang, blue saphire, paris, bastar, and porselin. These various strains lead to the need of study on the genetic relationship among them, which can be performed by the use of RAPD (Random Amplified Polymorphic DNA) marker. This study aims to determine primers producing consistent and polymorphic RAPD markers, determine specific RAPD markers, and know the genetic relationship among several giant gouramy strains. The strains used in this study are soang, jepang, and blue saphire. Survey method was applied employing purposive random sampling technique. Total genomic DNA was isolated using Genjettm genomic DNA purification kit (Fermentas), which was then used as template to amplify RAPD markers with primers OPA-07, OPA-09, OPA-11, OPA-20, OPAH-01, OPAH-08, OPAH-09, and OPAC-14. The variables examined were patterns and numbers of specific DNA fragments as the PCR amplification products. Selected primers were determined descriptively on the basis of specific DNA bands appearing on the agarose gel. Genetic diversity was predetermined by changing qualitative band pattern into quantitative binnary data. Genetic relationship was analyzed using cladistic method with PAUP software. The results showed that only five of the eight primers produce consistent and polymorphic RAPD markers, i.e. OPA-11, OPA-20, OPAH-1, OPAH-8, and OPAH-9. Specific RAPD markers which can be used to distinguish several gouramy strains are those amplified with OPA-20 of 786 bp, OPA-20 of 1,176 bp, OPAH-8 of 1,000 bp and OPAC-14 of 1,607 bp. Nervertheless, it was found that RAPD markers cannot be used to clearly determine genetic relationship among gouramy strains.

scholarly journals Genetic diversity among forty coffee varieties assessed by RAPD markers associated with restriction digestion

2005 ◽  
Vol 48 (4) ◽  
pp. 511-521 ◽  
Author(s):  
Leandro Eugênio Cardamoni Diniz ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Fabrício Medeiros Torres ◽  
Eduardo Augusto Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Clustering Analysis ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Restriction Digestion ◽  
Agronomic Features

The genetic variability of 40 accessions of_C. arabica was evaluated using a combination of the random amplified polymorphic DNA (RAPD) technique and restriction digestion of genomic DNA. The genetic variability and the relatedness among all accessions were initially evaluated using 195 RAPD primers which revealed a very low level of genetic variation. To improve the efficiency in the detection of polymorphism, the genomic DNA of all accessions were submitted to digestion with restriction endonucleases prior to PCR amplification. A total of 24 primers combined with restriction digestion of DNA rendered 318 bands, of which 266 (83.65%) were polymorphic. The associations among genotypes were estimated using UPGMA-clustering analysis. The accessions were properly clustered according to pedigree and agronomic features. The ability to distinguish among coffee accessions was greater for RAPD plus restriction digestion than for RAPD alone, providing evidences that the combination of the techniques was very efficient for the estimation of genetic relationship among_C. arabica genotypes.

scholarly journals Genetic Diversity Among Three Cultivars Of Peanut (Arachis hypogaea L.) Based On Rapd Markers

2019 ◽  
Vol 1 (2) ◽  
pp. 22
Author(s):  
Suryadi Suryadi ◽  
Alice Yuniaty ◽  
Agus Hery Susanto
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Economic Value ◽  
Morphological Data ◽  
Survey Method ◽  
Polymorphic Band ◽  
Tropical Regions ◽  
Arachis Hypogea ◽  
Increasing Demand

Peanut (Arachis hypogea) is a typical plant species of tropical regions that has high economic value. The plantation is widely spread over many areas and the production is being pushed to meet the increasing demand. Peanut breeding program is aimed to improve genetic quality, mainly with resepct of production and thus information on genetic diversity is necessary as a basis for consideration in breeding, management and sustainable utilization. One approach to analyse genetic diversity of peanut is by using molecular markers. Random Amplified Polymorphic DNA (RAPD) is a widely used molecular marker for genetic diversity analysis. Therefore, the aim of this study was to assess genetic diversity of peanut cultivars, i.e. Jerapah, Kancil, and Hypoma 2, based on RAPD markers. The study was conducted in a survey method, in which three individuals of each cultivar were analyzed using PCR-RAPD technique employing twelve primers, i.e. OPA-1, OPA-2, OPA-9, OPA-13, OPB-2, OPB-3, OPB-4, OPB-5, OPB-7, OPB-11, OPB-12 and OPJ-07. Data analysis based on morphological data is also included. Molecular analysis revealed that only 7.55% polymorphic band was obtained, while most of the bands were monomorphic, indicating very low variation among the cultivars. The phenogram that constructed based on literature showed that Kancil was closer to Jerapah cultivar, while RAPD-based dendogram showed that Hypoma 2 was closer to Kancil cultivar.

RAPD and Protein Analyses Revealed Polymorphism in Mutated Potato Cultivars

2013 ◽  
Vol 64 (2) ◽  
Author(s):  
Irshad Ahmad ◽  
Samiullah Khan ◽  
Muhammad Arshad Javed ◽  
Fahrul Zaman Huyop ◽  
Muhammad Tariq ◽  
...  
Keyword(s):  
Banding Pattern ◽  
Total Protein ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Potato Cultivars ◽  
Polymorphic Behavior ◽  
Mutant Lines

Genomic DNA of the mutant lines of the three potato cultivars, Cardinal, Diamant and Desiree, with respect to controls were isolated and analyzed for polymorphisms by using random amplified polymorphic DNA (RAPD) markers. Four 10 bp random fragment primers, S-13, S-18, S-19 and R-17 were studied and all of them gave the amplification of genomic DNA. All of the mutant lines gave different banding pattern against different primers with respect to control plants of the three varieties, and bands are present at 50 bp to 1500 bp. All these primers with specific banding pattern were unique in their polymorphic behavior. Different banding pattern of total protein contents were also observed by PAGE analysis of all the mutant lines as compared with the control plants. It is therefore suggested that RAPD and protein analyses would be important tools to detect the polymorphism in mutated lines of potato.

Relationships among 3 Kochia species based on PCR-generated molecular sequences and molecular cytogenetics

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1104-1115 ◽  
Author(s):  
B S Lee ◽  
M Y Kim ◽  
R R.-C Wang ◽  
B L Waldron
Keyword(s):  
United States ◽  
In Situ Hybridization ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
5S Rdna ◽  
The United States ◽  
Cross Hybridization ◽  
Forage Kochia

Forage kochia (Kochia prostrata ssp. virescens 'Immigrant' is native to the arid and semiarid regions of central Eurasia. It was introduced into the United States in 1966 as PI 314929 and released as a perennial forage shrub in 1984. Kochia americana is a perennial native to the United States, whereas Kochia scorparia is an introduced annual species that became a weed. To assess both the breeding potential and the possibility of genetic contamination, relationships among the 3 Kochia species were analyzed using random amplified polymorphic DNA (RAPD) markers, sequence tagged site (STS) marker sequences of the chloroplast NADH dehydrogenase gene (ndhF), genomic in situ hybridization (GISH), and multicolor fluorescence in situ hybridization (MC-FISH). Seventy decamer random primers yielded 458 polymorphic bands from 9 plants of K. americana, 20 plants of K. prostrata, and 7 plants of K. scoparia. Fifty-four and 55 species-specific RAPD markers were identified for K. americana and K. prostrata, whereas 80 RAPD markers were specific to K. scoparia. Based on the presence or absence of informative RAPD markers, the 3 species always grouped into 3 distinct clusters in a NTSYSpc2.01b-generated dendrogram. The same relationships were found among the 3 Kochia species based on ndhF DNA sequence divergence. Using a set of 7 STS markers that can identify each Kochia species, we did not find a single interspecific hybrid from artificial hybridizations among the 3 Kochia species. In GISH studies, chromosomes of 1 species fluoresced in green only when they were probed by genomic DNA of the same species. Cross-hybridization by genomic DNA of another species was not observed. In FISH studies using pTa71 (for 18S–5.8S–26S rDNAs) and pScT7 (for 5S rDNA) as probes, there were 1, 1 and 3 pTa71 sites and 2, 1, and 1 pScT7 sites in each haplome of K. prostrata, K. americana, and K. scoparia, respectively. It is concluded that these 3 Kochia species are so genomically distinct that gene introgression among them would be extremely rare.Key words: RAPD, STS, ndhF, GISH, FISH, mixoploidy, forage kochia.

Development of random amplified polymorphic DNA markers for genetic mapping in Pacific yew (Taxusbrevifolia)

1996 ◽  
Vol 26 (3) ◽  
pp. 497-503 ◽  
Author(s):  
B. Göçmen ◽  
Z. Kaya ◽  
K.D. Jermstad ◽  
D.B. Neale
Keyword(s):  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Polymorphic Locus ◽  
Single Mother ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Arbitrary Sequence ◽  
Linkage Groups ◽  
Polymerase Chain

A genetic linkage map was constructed for Pacific yew (Taxusbrevifolia Nutt.) based on random amplified polymorphic DNA (RAPD) markers. A series of optimization experiments were conducted to develop a highly repeatable protocol for Pacific yew. In these experiments, a high MgCl2 concentration (5.5 mM) together with a low primer concentration (0.2 μm) in the polymerase chain reaction (PCR) mixture yielded the best amplification products. PCR amplification products were further improved by treating the template DNAs with RNase. Experiments showed that bovine serum albumine had the same effect as RNase on PCR amplification. The segregating mapping population consisted of 39 haploid megagametophytes from a single mother tree. DNA extracted from a subset of 6 megagametophytes was screened with 345 ten-base oligonucleotide primers of arbitrary sequence. Of the screened primers, 28% revealed at least one polymorphic locus. Eighty-six of these primers revealed at least one polymorphic locus and were used with the entire set of megagametophyte DNAs. One-hundred-two loci were scored and segregated in the expected 1:1 ratio (1.19 locus per primer). Linkage analysis was conducted using MAPMAKER. Forty-one of 102 markers were distributed into 17 linkage groups and covered 305.8 centimorgans. The remaining 61 unlinked markers should be assigned to linkage groups as more markers are added to the map.

scholarly journals Random Amplified Polymorphic DNA Analysis of Garlic (Allium sativum L.) Germplasm Collection

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 452F-452
Author(s):  
M.M. Jenderek ◽  
K.A. Schierenbeck ◽  
R.M. Hannan
Keyword(s):  
Rapd Markers ◽  
Allium Sativum ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Pcr Amplification ◽  
Germplasm Collection ◽  
Plant Introduction ◽  
Germplasm Collections ◽  
Dna Template

Maintenance of garlic (A. sativum L.) germplasm collections is based on year-to-year vegetative propagation of individual accessions. Several accessions are phenotypically similar, often originating from the same region of the world, but have been collected by different people at different times. These accessions are currently maintained as separate and unique samples, but may represent genetic duplication in the collection. In order to identify genetic duplication in the USDA collection, 45 garlic Plant Introduction accessions from the garlic USDA germplasm collection were analyzed for RAPD marker polymorphism. The samples originated from 20 countries worldwide. RAPD bands were generated by 20 decamer primers, using 100-ng DNA template, and 38 PCR amplification cycles. Polymorphism between accessions was defined as presence or absence of particular bands at given loci. However, a few distinguishing RAPD markers were established for selected accessions, identifying additional molecular markers to wholly assess the similarities or polymorphism of the garlic collection units is necessary.

scholarly journals Inheritance of Random Amplified Polymorphic DNA (RAPD) Markers in Theobroma cacao L.

1995 ◽  
Vol 120 (4) ◽  
pp. 681-686 ◽  
Author(s):  
C.M. Ronning ◽  
R.J. Schnell ◽  
D.N. Kuhn
Keyword(s):  
Genetic Analysis ◽  
Theobroma Cacao ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Polymorphic Locus ◽  
Random Amplified Polymorphic Dna ◽  
Phenotypic Expression ◽  
Backcross Population ◽  
Backcross Family ◽  
Theobroma Cacao L

RAPD markers have been used successfully in genetic analysis of several crop plants. This method poses difficulties with a highly heterozygous species such as Theobroma cacao because of the dominant phenotypic expression of bands. A backcross family derived from ctultivars Catongo and Pound 12 was analyzed to determine the efficacy of RAPD markers in analyzing cacao populations. A preliminary screen of the parents and the F1 plant used as the backcross parent was conducted with 180 RAPD primers; of these, 26% were polymorphic and reproducible and produced 104 storable loci. Genomic DNA from 54 individuals of the backcross population was then amplified with these primers; 68.3 % of the loci segregated as expected in a Mendelian fashion. Separation of RAPD fragments on acrylamide revealed an additional polymorphic locus from one primer that was indistinguishable on agarose. The results demonstrated that RAPD markers can be used to study the cacao genome.

DNA FINGERINTS OF TILAPIA SPECIES IN SHATT AL-AREB RIVER USING RAPD MARKERS

2020 ◽  
Vol 51 (4) ◽  
pp. 1082-1087
Author(s):  
Faddagh & et al.
Keyword(s):  
Fish Species ◽  
Rapd Markers ◽  
Pcr Amplification ◽  
Dna Fingerprint ◽  
Species Discrimination ◽  
Oreochromis Aureus ◽  
Rapd Pcr ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Blue Tilapia ◽  
Dna Profiles

In the last decade, tilapia fish species distributed in the Iraqi inland waters. Three species; Nile tilapia Oreochromis niloticus (Linnaeus, 1758), Blue tilapia Oreochromis aureus (Steindachner, 1864) and Redbelly tilapia Coptedon zillii (Gervais, 1848) inhibiting Shatt Al-Arab River. They belong to family Cichlidae. They are very similar to differentiate among them using biometry. So, genetic markers used for species discrimination. Randomly amplified polymorphic DNA (RAPD) protocol used to examine genetic variation and to generate DNA fingerprints of tilapia fish species in Shatt Al-Arab River. Sixty-two specimens of tilapia fish collected from Shatt Al-Arab River at the governorate of Basrah. Seven universal decamer primers selected (OPA08, OPA10, OPA13, OPA17, OPA19, OPB08 and OPC02) to create RAPD DNA fingerprint. RAPD-PCR amplification carried out and electrophoresed with 100 bp ladder. DNA bands scored and molecular weight was calculated using PhotocaptMW software. Analog histogram drew using MS-Excel. The three RAPD DNA profiles apparently were different. DNA bands scored in the three species were 67 bands. The size of DNA bands was ranged from 64 bp to 2344 bp. RAPD fingerprints were efficient to distinguish the three species of tilapia fish.  DNA markers of the three species of tilapia fish can use to achieve conservation programs of fish species in the future.

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

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