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.

Fingerprinting Indian potato cultivars by random amplified polymorphic DNA (RAPD) markers

2001 ◽  
Vol 44 (4) ◽  
pp. 375-387 ◽  
Author(s):  
S. K. Chakrabarti ◽  
D. Pattanayak ◽  
P. S. Naik
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Potato Cultivars ◽  
Indian Potato Cultivars

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.

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 Molecular characterization and genetic diversity of potato cultivars using SSR and RAPD markers

2010 ◽  
Vol 10 (3) ◽  
pp. 204-210 ◽  
Author(s):  
Elizângela Almeida Rocha ◽  
Luciano Vilela Paiva ◽  
Humberto Henrique de Carvalho ◽  
Claudia Teixeira Guimarães
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Ssr Markers ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Potato Cultivars ◽  
High Information Content ◽  
Commercial Potato ◽  
Polymorphic Bands ◽  
High Information

This study aimed to evaluate the genetic diversity and identify potato cultivars by RAPD and SSR markers. The genomic DNA of 16 potato cultivars was amplified with 25 RAPD primers that generated 92 polymorphic bands and 20 SSR primer pairs that produced 136 polymorphic bands. The dendrograms generated by cluster analysis distinguished the cultivars genetically although the dendrograms were not correlated in the comparison of the two markers used. The PIC values demonstrated the high information content of the primers used and 16 potato varieties were identified based on six RAPD primers and three SSR primer pairs. Thus, by means of RAPD and SSR markers the genetic diversity was assessed and the 16 commercial potato cultivars analyzed in this study were identified.

scholarly journals Assessment of genetic diversity and relationship among some commercial cucumber varieties and genotypes using RAPD markers

2013 ◽  
Vol 6 (1-2) ◽  
pp. 51-63
Author(s):  
SM Faisal ◽  
MS Haque ◽  
KM Nasiruddin ◽  
MM Islam ◽  
MA Shrafuzzaman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Upgma Dendrogram ◽  
Cluster 2

Genetic variability among the genotypes of any species could be utilized for its improvement. PCR-based Random Amplified Polymorphic DNA (RAPD) technique was used to determine the genetic diversity and relationship among 10 cucumber varieties and genotypes. Five decamer primers were used to amplify genomic DNA and the primers yielded a total of 54 bands of which 36 bands were polymorphic and 18 bands were monomorphic. The UPGMA dendrogram based on Nei’s (1972) genetic distance indicated segregation of 10 cucumber varieties and genotypes into two main clusters. Variety Joti alone grouped in cluster 1 while variety Green Master, Shahi-50, Shikha, Shila, Shital, Naogaon-5, Shohag-50, Giant Long and genotype CS-043 grouped in cluster 2. Variety Shila was very close to variety Shital with the least genetic distance (0.1712). The highest genetic distance (0.5352) was found between Joti and Naogaon-5. DOI: http://dx.doi.org/10.3329/cujbs.v6i1-2.17081 The Chittagong Univ. J. B. Sci.,Vol. 6(1&2):51-63, 2011

scholarly journals Anatomical profile and genetic variability of sweet potato (Ipomoea batatas) cultivars in Banyumas, Central Java, based on RAPD markers

2020 ◽  
Vol 21 (4) ◽  
Author(s):  
SITI SAMIYARSIH ◽  
Nur Fitrianto ◽  
ENUR AZIZAH ◽  
WIWIK HERAWATI ◽  
ROCHMATINO
Keyword(s):  
Genetic Variability ◽  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Anatomical Study ◽  
Wide Distribution ◽  
Potato Cultivars ◽  
Central Java

Abstract. Samiyarsih S, Fitrianto N, Azizah E, Herawati W, Rochmatino. 2020. Anatomical profile and genetic variability of sweet potato (Ipomoea batatas) cultivars in Banyumas, Central Java, based on RAPD markers. Biodiversitas 21: 1755-1766. Indonesia has developed a food consumption diversification based on local sources. Sweet potato (Ipomoea batatas) is one of the tubers of carbohydrate sources in addition to wheat, rice, corn, potatoes, and cassava. It has a wide distribution, and high cultivars diversity produces a high variation on its morphology, anatomy, and genetic modification. The objectives of this research were to investigate the anatomical profile and genetic variability of eight sweet potatoes (Ipomoea batatas) cultivars found in Banyumas, Central Java, Indonesia. Anatomical profile was observed by the embedding method and subjected to analysis of variance. DNA amplification using Random Amplified Polymorphic DNA (RAPD) method with 10 primers, namely OPA-1, OPA-2, OPA-3, OPA-4, OPA-9, OPA-11, OPA-13, OPA-15, OPA-16, and OPA-18. The result of the anatomical study showed that eight sweet potato cultivars have significantly different (p<0.05) variation in leaf anatomical profile. RAPD primers produced 52 amplified fragments varying from 100 to 1300 bp in size, and 90.40% of the amplification bands were polymorphic. The genetic similarity level is ranged from 0.37 to 0.93. Two unspecific groups were forming at a coefficient of 55% from the dendrogram. The first group consisted of one cultivar, Cangkuang, and the second group consisted of seven cultivars Antin, Ungu Tua, Borobudur, Sukuh, Sari, Beta, and Kidal. The nearest relationships cultivars were Borobudur, and Ungu Tua had the highest similarity coefficient of 93%, and the lowest similarity found in Cangkuang and Antin with a coefficient of 37%. The range of genetic distance of eight cultivars was from 0.37-0.93. Implementation of the research would particularly useful for the identification and evaluation of the genetic improvement of sweet potato cultivars.

scholarly journals OPTIMIZING RAPD MARKERS FOR ONION GENOMIC DNA ANALYSIS

HortScience ◽  
1995 ◽  
Vol 30 (3) ◽  
pp. 435a-435
Author(s):  
Ruwanthi C. Wettashinghe ◽  
Ellen B. Peffley
Keyword(s):  
Cost Effectiveness ◽  
Plant Breeding ◽  
Dna Extraction ◽  
Genetic Markers ◽  
Plant Tissue ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Dna Isolation ◽  
Random Amplified Polymorphic Dna

Random amplified polymorphic DNA (RAPD) are genetic markers that facilitate selection in plant breeding. To obtain clear reproducible, and repeatable RAPD bands, four DNA extraction protocols and two Taq polymerases were compared using thirteen TG1015Y (Allium cepa) genotypes. Protocols for DNA extraction followed those of a modified Tai and Tanksley, 1989 (PMBR); a modified Dellaporta et al., 1983 (PMBR); a modified Guillemunt et al., 1992 (PMBR); and extracted with a plant tissue DNA isolation kit from Gentra System (Minneapolis). The modified Guillemunt protocol was selected due to ease of extraction and cost effectiveness. Polymerases compared were Taq and Taq Stoffel fragment. Results are based on three separate amplifications and electrophoretic assays. PCR amplifications of Stoffel fragment produced more scorable and reproducible RAPD bands compared to bands produced using Taq polymerase.

Genomic Relations among 31 Species of Mammillaria Haworth (Cactaceae) Using Random Amplified Polymorphic DNA

2006 ◽  
Vol 61 (7-8) ◽  
pp. 583-591 ◽  
Author(s):  
Ilwola Mattagajasingh ◽  
Arup Kumar Mukherjee ◽  
Premananda Das
Keyword(s):  
Genomic Dna ◽  
Rapd Markers ◽  
Cetyl Trimethyl Ammonium Bromide ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Ammonium Bromide ◽  
Phylogenetic Relations ◽  
Pair Group ◽  
Wide Variability ◽  
Cetyl Trimethyl Ammonium

Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.

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.

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