Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn

Random amplified polymorphic DNA (RAPD) markers were used to characterize a part of a sea buckthorn gene bank collected for plant breeding purposes. Molecular markers were generated in 55 cultivars and accessions, representing five subspecies of Hippophae rhamnoides L. and intraspecific hybrids between different subspecies. Sixty-three markers were used to generate a Dice's similarity coefficient matrix of pairwise comparisons between individual RAPD profiles. Cluster (UPGMA) and principal co-ordinate analyses, based on this matrix, revealed clustering of plants into groups which generally correspond to their taxonomic classification or geographic origin. The analysis of molecular variance (AMOVA) was found useful for estimating components of genetic variation between and within taxonomic and geographic groups of accessions and cultivars. Whereas both alternatives for grouping the material (taxonomic or geographic origin) resulted in significant between-group variation, the major part of molecular variance (approximately 75%) was still attributed to variation within groups. We conclude that the RAPD analysis is useful for clarification of taxonomic and geographic origin of accessions and cultivars of sea buckthorn.

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Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.1.64 ◽

2001 ◽

Vol 126 (1) ◽

pp. 64-71 ◽

Cited By ~ 87

Author(s):

A. Belaj ◽

I. Trujillo ◽

R. de la Rosa ◽

L. Rallo ◽

M.J. Giménez

Keyword(s):

Gel Electrophoresis ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Group Method ◽

Polymorphic Markers ◽

Germplasm Bank ◽

Banding Patterns ◽

Olive Cultivars

Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigación y Formación Agraria “Alameda del Obispo” in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar-specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.

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Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽

10.1139/g01-096 ◽

2001 ◽

Vol 44 (6) ◽

pp. 995-999 ◽

Cited By ~ 25

Author(s):

H I Amadou ◽

P J Bebeli ◽

P J Kaltsikes

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Bambara Groundnut ◽

International Institute ◽

Tropical Agriculture ◽

Vigna Subterranea ◽

Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

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Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽

10.1139/g95-025 ◽

1995 ◽

Vol 38 (2) ◽

pp. 201-210 ◽

Cited By ~ 89

Author(s):

F. N. Wachira ◽

R. Waugh ◽

W. Powell ◽

C. A. Hackett

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Southeast Asia ◽

Camellia Sinensis ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Systematic Assessment ◽

Tree Crop ◽

Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

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Morphological, Chemical, and Genetic Characteristics of Korean Native Thyme Bak-Ri-Hyang (Thymus quinquecostatus Celak.)

Antibiotics ◽

10.3390/antibiotics9060289 ◽

2020 ◽

Vol 9 (6) ◽

pp. 289

Author(s):

Minju Kim ◽

Jun-Cheol Moon ◽

Songmun Kim ◽

Kandhasamy Sowndhararajan

Keyword(s):

Essential Oil ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Essential Oil Composition ◽

Similarity Coefficient ◽

Gas Chromatography Mass Spectrometry ◽

Aromatic Plant ◽

Oil Composition ◽

Genetic Characteristics

Bak-ri-hyang (Thymus quinquecostatus Celak.) is an important medicinal and aromatic plant in Korea. T. quinquecostatus population and is always mixed with other thyme cultivars during cultivation and marketing. Hence, this study aimed to determine the genetic variability and the essential oil composition of three Korean native thyme, T. quinquecostatus cultivars collected from the Wolchul, Jiri, and Odae mountains, in comparison with six commercial thyme cultivars (T. vulgaris), to distinguish Bak-ri-hyang from other thyme cultivars. The composition of essential oils obtained from nine individuals was analyzed by gas chromatography–mass spectrometry (GC–MS). The random amplified polymorphic DNA (RAPD) analysis was accomplished using 16 different primers. The GC–MS analysis revealed that Wolchul, creeping, golden, and orange cultivars belong to the geraniol chemotype. Whereas the Odae, lemon, and silver cultivars belong to the thymol chemotype. Further, linalool was the most abundant component in carpet and Jiri cultivars. The RAPD analysis demonstrated that all thyme cultivars showed characteristic RAPD patterns that allowed their identification. In total, 133 bands were obtained using 16 primers, and 124 bands were polymorphic, corresponding to 93.2% polymorphism. Cluster analysis of RAPD markers established the presence of clear separation from nine thyme cultivars. The highest dissimilarity and similarity coefficient of the RAPD markers were 0.58 and 0.98, respectively. According to the RAPD patterns, the nine thyme cultivars could be divided into two major clusters. Among three Korean cultivars, the Wolchul and Odae cultivars were placed into the same cluster, but they did not show identical clustering with their essential oil compositions. The findings of the present study suggest that RAPD analysis can be a useful tool for marker-assisted identification of T. quinquecostatus from other Thymus species.

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Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

Legume Research - An International Journal ◽

10.18805/lr-3907 ◽

2018 ◽

Author(s):

Indu Rialch ◽

Rama Kalia ◽

H. K. Chaudhary ◽

B. Kumar ◽

J. C. Bhandari ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Rapd Markers ◽

Agronomic Traits ◽

Rapd Analysis ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Similarity Coefficient ◽

Breeding Programme ◽

Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

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

Australian Journal of Botany ◽

10.1071/bt96131 ◽

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.

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676 PB 160 IDENTIFICATION AND CLASSIFICATION OF PISTACHIO (Pistacia vera L.) CULTIVARS WITH RAPD MARKERS

HortScience ◽

10.21273/hortsci.29.5.529f ◽

1994 ◽

Vol 29 (5) ◽

pp. 529f-529

Author(s):

J.I. Hormaza ◽

L. Dollo ◽

V.S. Polito

Keyword(s):

Rapd Markers ◽

Geographical Origin ◽

Cultivar Identification ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Pistacia Vera ◽

Polymorphic Markers ◽

Molecular Phenotype ◽

And Cluster Analysis

The Random Amplified Polymorphic DNA (RAPD) technique was used to characterize 15 cultivars of pistachio (Pistacia vera L.). A total of 37 polymorphic markers were considered in this study. Each cultivar exhibited a unique molecular phenotype and, as a consequence, can be uniquely fingerprinted. A similarity and cluster analysis based on the amplified fragments produced two distinct groups which are consistent with the known geographical origin of the cultivars. Our results suggest that RAPD analysis can provide a new alternative for cultivar identification and classification of pistachio.

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Use RAPD Technique for Characterization of Genotypical Variability of Maize Germplasm from SCDA Turda

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Agriculture ◽

10.15835/buasvmcn-agr:5078 ◽

2010 ◽

Vol 67 (1) ◽

Author(s):

Rodica POP ◽

Doru PAMFIL ◽

Monica HÂRŢA ◽

Ioan HAŞ ◽

Iulia POP

Keyword(s):

Rapd Markers ◽

Rapd Analysis ◽

Genetic Relationships ◽

Germplasm Collection ◽

Genetic Distances ◽

Maize Germplasm ◽

Upgma Dendrogram ◽

Maize Genotypes ◽

Polymorphic Bands

Genetic analysis with RAPD markers has been extensively used to determine diversity among maize genotypes. The aim of the present study was to estimate genetic relationships among 70 genotypes, provided from SCDA Turda Cluj germplasm collection. RAPD analysis was performed with 14 decamer primers. These primers generated, among the studied genotypes, a number of polymorphic bands comprised between 13 bands (OPA 04) and 7 bands (OPAL 20). The highest numbers of polymorphic bands were obtained with primer OPA 04, respectively 13 bands, following by OPO 12 (12 polymorphic bands), OPAB 11 and OPA 17 (11 polymorphic bands). Lowest number was obtained with primer OPAL 20, respectively 7 polymorphic bands. Genetic distances were established using Nei-Li coefficient and UPGMA dendrogram was constructed with RAPDistance 1.04 software. The built dendrogram shows phylogenetic relationships between genotypes analyzed.

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

HortScience ◽

10.21273/hortsci.32.3.452f ◽

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.

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Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210643 ◽

2020 ◽

Vol 21 (6) ◽

Author(s):

RATIBA BΟUSBA ◽

SARA GUERAICHE ◽

MALIKA RACHED KANOUNI ◽

RABAH BΟUNAR ◽

ABDELHAMID DJEKΟUNE ◽

...

Keyword(s):

Durum Wheat ◽

Triticum Durum ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Genotypic Diversity ◽

Allelic Frequency ◽

Breeding Programs ◽

Diversity Assessment ◽

Local Genotypes

Abstract. Bousba R, Gueraiche S, Kanouni MR, Bounar R, Djekoune A, Khammar H, Nadia Y. 2020. Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis. Biodiversitas 21: 2696-2701. Knowledge of genetic variability in durum wheat (Triticum durum Desf.) is of major importance in the development of breeding programs and the preservation of local landrace resources. The objective of this study is to highlight the molecular polymorphism among six durum wheat genotypes from different origins and characterized by different sensitivity to drought tolerance (tolerant, semi-tolerant, and non-tolerant). 15 Random Amplified Polymorphic DNA (RAPD) markers were used to assess the molecular diversity of these genotypes. Our results show a total of one hundred and sixty-nine amplicons, where one hundred and twenty-four are polymorphic bands. The number of bands per primer ranged from two (OPJ-06) to fifteen bands (primers OPE-13 and OPB-01). The values of the Allelic frequency varied from 1 (OPJ-06) to 0.20 (OPA-17) and 0.19 (OPE-13, OPO-06, B-19 and OPA-20). Also, the values of the coefficient of genetic similarity range from 0.69 to 0.80, these results indicate a large variation between tested genotypes. According to the dendrogram generated by the RAPD approach, we obtained four distinct groups: the first one (G1) contains GTADUR and KORIFFLA x SHAM, the second group (G2) contains the local genotype BIDI-17. However, the genotype WAHA was in the third group (G3), the fourth and fifth groups contained the genotypes CIRTA and TELL, respectively. A complementary analysis was done to estimate genetic differentiation, using CPA Analysis that indicated four groups among the six genotypes, where, the local genotypes BIDI-17 and CIRTA were classified together. For allele’s richness, the local genotypes show in this investigation, the highest values in comparison to the introduced genotypes, which suggested the performance of the RAPD markers (high polymorphism and fast genetic analysis). The molecular markers RAPD-PCR type, despite their non-specific characteristics, has shown a strong aptitude for genetic characterization in durum wheat and a high level of polymorphism, which makes it possible in a preliminary study to make exploitable discrimination. These results may be helpful in the improvement and varietal selection, and useful in accelerating breeding programs of durum wheat.

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