scholarly journals Application of Random Amplified Polymorphic DNA Analysis in Identifying Phellinus Igniarius Strains

2007 ◽  
Vol 26 (4) ◽  
pp. 289-293
Author(s):  
Ping Du ◽  
Yan-Qiu Chen ◽  
Chang-Tian Li ◽  
Yu Li
Keyword(s):  
Cluster Analysis ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Fragments ◽  
Base Pairs ◽  
Phellinus Igniarius ◽  
Random Primers ◽  
Upgma Cluster Analysis ◽  
The Difference

Application of Random Amplified Polymorphic DNA Analysis in Identifying Phellinus Igniarius Strains Described in this paper, the random amplified polymorphic DNA (RAPD) analysis was conducted with 20 random primers in various strains of Phellinus igniarius collected from different localities. The results showed that 17 of the 20 random primers were polymorphic ones. The DNA bands derived from each primer amplifying in tested strains ranged from 10 to 33. The size of the amplified DNA fragments ranged from 250 to 2000 base pairs. Of each test primer, a wide variation in banding profiles was observed among the 7 strains of P. igniarius. A total of 377 band positions were scored for all of the tested strains, which differed significantly among the bands from different primers. UPGMA cluster analysis subdivided the tested strains into two groups, which was helpful to find out the difference among the tested strains and to distinguish them directly.

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.

Analysis of Heterodera avenae populations by the random amplified polymorphic DNA technique

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 118-122 ◽  
Author(s):  
I. López-Braña ◽  
A. Delibes ◽  
M. D. Romero
Keyword(s):  
Cluster Analysis ◽  
Key Words ◽  
Dna Analysis ◽  
Fragment Size ◽  
Random Amplified Polymorphic Dna ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Heterodera Avenae ◽  
Random Primers

Eleven populations of the Heterodera avenae complex (four Spanish, two British, two French, and three Swedish) were studied by random amplified polymorphic DNA analysis. From 5 to 11 fragments were obtained with each of 14 random primers, with fragment size ranging from 200 to 2200 bp. Cluster analysis of the 11 populations, using 108 scorable markers, separate these populations into two main groups. These groups coincide with what is known as the "true" H. avenae and the "Gotland strain" or "British pathotype 3" of H. avenae. The results also clarify the relationships among some members of the H. avenae complex established previously using morphological and biochemical criteria. Key words : cereal cyst nematode, CCN, Heterodera avenae, RAPD.

scholarly journals The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions

2000 ◽  
Vol 23 (1) ◽  
pp. 169-172 ◽  
Author(s):  
Helvécio Della Coletta Filho ◽  
Marcos Antonio Machado ◽  
M. Luiza P.N. Targon ◽  
Jorgino Pompeu Jr.
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
The Other ◽  
Citrus Reticulata ◽  
Random Primers ◽  
Citrus Reticulata Blanco ◽  
Ponkan Mandarin

RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

Comparison of repetitive-sequence-based polymerase chain reaction with random amplified polymorphic DNA analysis for rapid genotyping of nontuberculosis mycobacteria

2012 ◽  
Vol 58 (8) ◽  
pp. 953-964 ◽  
Author(s):  
Sara Christianson ◽  
Joyce Wolfe ◽  
Hafid Soualhine ◽  
Meenu K. Sharma
Keyword(s):  
Repetitive Sequence ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Gene Sequencing ◽  
Variable Number ◽  
Outbreak Investigations ◽  
Hsp65 Gene ◽  
Polymerase Chain ◽  
Clinically Significant

Nontuberculosis mycobacteria (NTM) are an important cause of human disease and infections. Though less notorious than tuberculosis, these infections are clinically significant and have been associated with outbreaks in various settings. To accommodate outbreak investigations for the numerous species of NTM, we evaluated a DiversiLab repetitive-sequence-based PCR (rep-PCR) kit for genotyping of mycobacteria. This kit was used to genotype both rapidly and slowly growing mycobacteria and was compared with other PCR-based genotyping methods, including random amplified polymorphic DNA (RAPD) analysis, hsp65 gene sequencing, and mycobacterial interspersed repetitive unit – variable number of tandem repeat (MIRU–VNTR) analysis. Compared with RAPD analysis, rep-PCR achieved better reproducibility in testing. When compared with hsp65 gene sequencing and MIRU–VNTR for Mycobacterium avium , rep-PCR provided results that agreed with these less discriminatory genotyping methods but provided a higher level of discrimination for situations such as outbreak investigations. We also evaluated the kit for its ability to identify closely related rapidly growing NTM. While rep-PCR was informative in some cases, a much larger library of isolates would be necessary to truly evaluate it as an identification tool. Overall, rep-PCR was able to provide improved reproducibility over RAPD and a discriminatory genotyping method for the isolates evaluated in this study.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

Isolation of Genotype- and Chromosome-specific DNA Markers in a Biotype of Colletotrichum gloeosporioides Using Random Amplified Polymorphic DNA Analysis

1998 ◽  
Vol 46 (1) ◽  
pp. 143
Author(s):  
Agnieszka M. Poplawski ◽  
John A. G. Irwin ◽  
John M. Manners
Keyword(s):  
Dna Sequences ◽  
Fungal Pathogen ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Colletotrichum Gloeosporioides ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Probes ◽  
Race 2 ◽  
Biotype B

Genetic markers that distinguish fungal genotypes are important tools for genetic analysis of heterokaryosis and parasexual recombination in fungi. Random amplified polymorphic DNA (RAPD) markers that distinguish two races of biotype B of Colletotrichum gloeosporioides infecting the legume Stylosanthes guianensis were sought. Eighty-five arbitrary oligonucleotide primers were used to generate 895 RAPD bands but only two bands were found to be specifically amplified from DNA of the race 3 isolate. These two RAPD bands were used as DNA probes and hybridised only to DNA of the race 3 isolate. Both RAPD bands hybridised to a dispensable 1.2 Mb chromosome of the race 3 isolate. No other genotype-specific chromosomes or DNA sequences were identified in either the race 2 or race 3 isolates. The RAPD markers hybridised to a 2 Mb chromosome in all races of the genetically distinct biotype A pathogen which infects other species of Stylosanthes as well as S. guianensis. The experiments indicate that RAPD analysis is a potentially useful tool for obtaining genotype- and chromosome-specific DNA probes in closely related isolates of one biotype of this fungal pathogen.

scholarly journals Genetic Analysis of Histoplasma capsulatum Strains Isolated from Clinical Specimens in Thailand by a PCR-Based Random Amplified Polymorphic DNA Method

1998 ◽  
Vol 36 (10) ◽  
pp. 3073-3076 ◽  
Author(s):  
Natteewan Poonwan ◽  
Tamae Imai ◽  
Nanthawan Mekha ◽  
Katsukiyo Yazawa ◽  
Yuzuru Mikami ◽  
...  
Keyword(s):  
Reference Strain ◽  
Histoplasma Capsulatum ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Sequence Information ◽  
Clinical Specimens ◽  
American Strain ◽  
The Difference

Thirteen strains of Histoplasma capsulatum were isolated from clinical specimens, including those from AIDS patients, in Thailand. Random amplified polymorphic DNA (RAPD) analysis with three different PCR primers showed that the DNA fingerprint patterns of the Thai isolates were very similar to each other and homogeneous, with only one exceptional strain, although the patterns were clearly different from those of a reference North American strain with all primers tested. Although the difference in the DNA fingerprinting patterns was minor, Thai isolates could be classified into two to four groups. A common PCR band (about 700 bp) in the patterns of allH. capsulatum strains was extracted, and its DNA sequence was determined. A new PCR primer set for the identification of H. capsulatum species was developed based on this sequence information. This primer set was 100% successful in the identification of the reference strain as well as all Thai isolates. The results of specificity tests of the primer set for the identification of the fungus are also discussed.

scholarly journals Detection of Genetic Variation among Camellia Parents and Hybrids Using Random Amplified Polymorphic DNA (RAPD) Markers

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1121C-1121
Author(s):  
Lianghong Chen ◽  
Shizhou Wang ◽  
Mack Nelson
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Approach ◽  
Random Primers ◽  
Genomic Regions ◽  
Genotype A

The reliability of the random amplified polymorphic DNA (RAPD) technique in amplifying polymorphisim among the hybrids and their parents' genomes of the genus Camellia was evaluated. Three hybrids (`Londontowne Blush', `Ashton's Snow', and `Ashton's Cameo') and one of the parents, C. oleifrea`Plain Jane', provided by the America Camellia Society, Fort Valley, Ga., were investigated. Twenty 10-based random primers were tested in this study. Five out of 20 primers were selected for RAPD analysis based on the ability to produce unambiguously scoreable RAPD bands for evaluation and comparison of the genotypes under investigation. The five primers were selected because they produced distinct patterns of amplified bands for each tested genotype. A total of 162 RAPD bands were produced. Among the 162 bands, 86 bands showed polymorphisms. The amplified band sizes ranged from 236 to 1656 bp. These data indicate that in the three hybrids and one of the parents exist unique genomic regions. Our investigation results showed that the RAPD molecular approach can be used to discriminate genetic variation among hybrids and their parents.

scholarly journals Identification of the Edible Fig `Bianco del Cilento' by Random Amplified Polymorphic DNA Analysis

HortScience ◽  
1999 ◽  
Vol 34 (7) ◽  
pp. 1263-1265 ◽  
Author(s):  
U. Galderisi ◽  
M. Cipollaro ◽  
G. Di Bernardo ◽  
L. De Masi ◽  
G. Galano ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Southern Italy ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Accurate Identification ◽  
Banding Patterns ◽  
Campania Region ◽  
Quality Of Products

Random amplified polymorphic DNA (RAPD) analysis is currently used to estimate genetic relationships in plants. We have used RAPD analysis to distinguish six different cultivars of Ficus carica, and several of their clones, that are widespread in the Campania Region of Southern Italy. Among these cultivars, `Bianco del Cilento' has unique characteristics, and is particularly useful for drying and for the manufacture of syrups. The protection of this cultivar is important to the Campania Region. We have utilized molecular markers to allow accurate identification of this cultivar, making it possible to control the quality of products and prevent fraudulent commerce. DNA was extracted from leaves and amplified by PCR using random oligonucleotide primers. The amplification patterns obtained with five decamer primers were useful for distinguishing all six cultivars analyzed. `Bianco del Cilento' was identified by two primers. The banding patterns were scored and used in similarity value calculations to estimate genetic relationships.

scholarly journals Analisis abnormalitas tanaman kelapa sawit (Elaeis guineensis Jacq) hasil kultur jaringan dengan teknik Random Amplified Polymorphic DNA (RAPD) Analysis abnormalities of oil palm (Elaeis guineensis Jacq) from tissue culture by Random Amplified Polymorphic DNA (RAPD

2016 ◽  
Vol 69 (2) ◽  
Author(s):  
Nurita TORUAN-MATHIUS ◽  
Saro Ina Ita BANGUN ◽  
. MARIA-BINTANG
Keyword(s):  
Oil Palm ◽  
Dna Markers ◽  
Dna Analysis ◽  
Elaeis Guineensis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Elaeis Guineensis Jacq ◽  
Fruit Formation ◽  
Female Flowers ◽  
Normal Genotype

SummaryProblem in oil palm propagation throughtissue culture is the abnormality of reproductiveorgans i.e. female flowers and mantle fruits are inthe same plants or clones. Various abnormalitiesobtained between clones, and could only beidentified after fruit formation. The experimentwas conducted to analyze genetic similarities ofnormal and abnormal genotypes in the same andamong clones, and also to get a specific RAPDband as a marker for abnormalities. Six clones ofoil palm (16 genotypes) of 5-year old MK152,MK203, MK209 and MK212 with normal fruits,female flowers, and abnormal fruits (heavymantled), grown in the field, while two otherclones were MK 104 and MK 176 with normalfruits and heavy mantled. PCR reaction toamplify DNA of 16 genotypes using 15 randomprimers. Genetic similarities and dendogramwere done by NTSYS-pc, while honestly value ofUPGMA analyzed by boostrap with WinBootprogram. The results showed that OPC-07,OPC-09, OPW-19 and SC10-19 were able todetermine the differences of normal andabnormal genotypes in the same clone of sixclones tested. While other primers were onlyable to differentiate between normal andabnormal genotypes only in several clones.Genetic similarities among 16 genotypes testedwere around 0.47-0.96. Genetic similaritiesbetween normal genotype were higher than thatof among abnormal genotypes. MK176 clonewas more stable in culture as compare to otherclones. UPGMA showed that in generaly normalgenotypes and abnormal one, in the sameclones belongs to the same group. The results ofprincipalcomponent analysis showed that from 15primers tested no specific DNA band could beused as a marker for abnormalities. To obtainehave DNA markers, a more sensitive techniquefor DNA analysis is needed.RingkasanMasalah yang dihadapi dalam perbanyakantanaman kelapa sawit dengan teknik kulturjaringan adalah abnormalitas organ reproduktifyaitu terbentuknya bunga jantan dan buah manteldalam klon yang sama. Terjadinya abnormalitassangat beragam, dan teridentifikasi setelahtanaman berbuah. Penelitian ini bertujuan untukmengetahui kesamaan genetik serta penge-lompokan antar genotipe normal dan abnormaldalam klon yang sama maupun antar klon, sertamenetapkan pita DNA penciri untuk abnormalitasdengan RAPD. Enam klon kelapa sawit(16 genotipe) berumur 5 tahun yaitu MK152,MK203, MK209, dan MK212 masing-masingdengan genotipe berbuah normal, berbungajantan, dan berbuah abnormal (mantel berat). Duaklon lainnya yaitu MK104 dan MK176 masing-masing terdiri dari genotipe berbuah normal danmantel berat. Reaksi PCR untuk mengamplifikasiDNA contoh dilakukan menggunakan 15 primeracak. Kesamaan genetik dan pembuatanfenogram dilakukan dengan programNTSYS-pc. Sedang tingkat kepercayaanUPGMA ditetapkan dengan analisisbootstrap menggunakan program WinBoot.Hasil yang diperoleh menunjukkan bahwaprimer OPC-09, SC10-19, OPC-07 danOPW-19 mampu membedakan genotipenormal dan abnormal dalam klon yang samauntuk keenam kon yang diuji. Sedang primerlainnya hanya mampu menunjukkanperbedaan antar genotipe normal danabnormal dalam beberapa klon saja.Kesamaan genetik antar 16 genotipe yangdiuji berkisar antara 0,47-0,96. Kesamaangenetik antar genotipe normal lebih tinggidibandingkan dengan kesamaan genetikantar genotipe abnormal. Klon MK176lebih stabil dalam kultur dibandingkandengan klon lainnya. UPGMA menunjukkanbahwa umumnya genotipe normal danabnormal dalam klon yang sama beradadalam satu grup. Hasil analisis komponenutama menunjukkan bahwa dari 15 primeryang diuji belum mampu menghasilkan pitaDNA penciri untuk abnormalitas. Untukmendapatkan pita DNA penciri, perludilakukan analisis DNA dengan teknik yanglebih sensitif untuk mendeteksi perubahansatu basa oligonukleotida 

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