The application of RAPD markers for potato cultivar identification

1997 ◽  
Vol 48 (8) ◽  
pp. 1213 ◽  
Author(s):  
Rebecca Ford ◽  
Paul W. J. Taylor
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Rapd Marker ◽  
Potato Cultivar ◽  
Specific Marker ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Polymorphic Bands

Where morphological techniques had failed, closely related potato cultivars were differentiated using random amplified polymophic DNA (RAPD) analysis based on the polymerase chain reaction. Total gemomic DNA was extracted from young sprout tissue from harvested tubers. Of 63 10-mer oligonucleotide primers screened, 51 primers produced a total of 256 amplification products of which 33 were polymorphic between the cultivars assessed. Polymorphic bands were selected to produce cultivar-specific markers to identify correctly suspect material in commercial plantings. Furthermore, a cultivar-specific RAPD marker was shown to be sufficiently robust and stringent for the identification of potential cultivar contamination in the field. DNA titration experiments revealed that a specific marker for cv. Sebago could be detected in a DNA admixture at a ratio of 1× cv. Sebago to 5 × cv. Exton. A commercial block of cv. Exton was thus randomly sampled and the level of cultivar purity assessed.

scholarly journals Development of a Specific Polymerase Chain Reaction-Based Assay for the Identification of Fusarium oxysporum f. sp. ciceris and Its Pathogenic Races 0, 1A, 5, and 6

2003 ◽  
Vol 93 (2) ◽  
pp. 200-209 ◽  
Author(s):  
María del Mar Jiménez-Gasco ◽  
Rafael M. Jiménez-Díaz
Keyword(s):  
Polymerase Chain Reaction ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Specific Primer ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Pcr Assays ◽  
Pathogenic Races ◽  
Scar Primers

Specific primers and polymerase chain reaction (PCR) assays that identify Fusarium oxysporum f. sp. ciceris and each of the F. oxysporum f. sp. ciceris pathogenic races 0, 1A, 5, and 6 were developed. F. oxysporum f. sp. ciceris- and race-specific random amplified polymorphic DNA (RAPD) markers identified in a previous study were cloned and sequenced, and sequence characterized amplified region (SCAR) primers for specific PCR were developed. Each cloned RAPD marker was characterized by Southern hybridization analysis of Eco RI-digested genomic DNA of a subset of F. oxysporum f. sp. ciceris and nonpathogenic F. oxysporum isolates. All except two cloned RAPD markers consisted of DNA sequences that were found highly repetitive in the genome of all F. oxysporum f. sp. ciceris races. F. oxysporum f. sp. ciceris isolates representing eight reported races from a wide geographic range, nonpathogenic F. oxysporum isolates, isolates of F. oxysporum f. spp. lycopersici, melonis, niveum, phaseoli, and pisi, and isolates of 47 different Fusarium spp. were tested using the SCAR markers developed. The specific primer pairs amplified a single 1,503-bp product from all F. oxysporum f. sp. ciceris isolates; and single 900- and 1,000-bp products were selectively amplified from race 0 and race 6 isolates, respectively. The specificity of these amplifications was confirmed by hybridization analysis of the PCR products. A race 5-specific identification assay was developed using a touchdown-PCR procedure. A joint use of race 0- and race 6-specific SCAR primers in a single-PCR reaction together with a PCR assay using the race 6-specific primer pair correctly identified race 1A isolates for which no RAPD marker had been found previously. All the PCR assays described herein detected up to 0.1 ng of fungal genomic DNA. The specific SCAR primers and PCR assays developed in this study clearly identify and differentiate isolates of F. oxysporum f. sp. ciceris and of each of its pathogenic races 0, 1A, 5, and 6.

scholarly journals 663 PB 101 IDENTIFICATION OF POINSETTIA CULTIVARS USING RAPD MARKERS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 527g-528
Author(s):  
Jing-Tian Ling ◽  
Roger Sauve ◽  
Nick Gawel
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Patent Protection ◽  
Cultivar Identification ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Base Pairs ◽  
Ctab Method ◽  
Leaf Tissues ◽  
Polymerase Chain

The development of scoreable genetic markers in poinsettia will be valuable for cultivar identification and for use in patent protection. In this study, polymerase chain reaction (PCR) and randomly amplified polymorphic DNA (RAPD) techniques were investigated for their feasibility in the identification of poinsettia cultivars. DNA was extracted from leaf tissues using the CTAB method. Thirty-six out of 39 (92.4%) primers amplified poinsettia DNA. The size of the amplified DNA fragments ranged from 140 to 2,000 base pairs. On average, 5.4 bands (range 1 - 13) were obtained per primer. A total of 195 bands were obtained; 49 (25.1%) bands were polymorphic in the 9 tested poinsettia cultivars. All tested cultivars could be discriminated with the banding profiles generated from 2 primers. RADP markers provide a consistently reliable and efficient technique for the identification of poinsettia cultivar.

Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Parental Origin ◽  
Chain Reaction ◽  
Stylosanthes Hamata ◽  
Polymerase Chain

The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping.Key words: genetic mapping, molecular markers, polymerase chain reaction, Stylosanthes hamata, Stylosanthes scabra.

Genetic differentiation of Indian camel (Camelus dromedarius) breeds using random oligonucleotide primers

2006 ◽  
Vol 39 ◽  
pp. 77-88 ◽  
Author(s):  
S.C. Mehta ◽  
B.P. Mishra ◽  
M.S. Sahani
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Variability ◽  
Genetic Differentiation ◽  
Population Subdivision ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Dna Profile ◽  
Oligonucleotide Primers ◽  
Polymerase Chain ◽  
Polymorphic Bands

SummaryThe camel population in India is facing a severe decline which demands that immediate steps are taken to ensure its conservation. Characterisation is an integral part of the conservation program. The Polymerase Chain Reaction-Randomly Amplified Polymorphic DNA profile of unrelated camels of the Bikaneri (29), Jaisalmeri (30) and Kachchhi (18) breeds were analyzed. Reproducible polymorphic bands with varying frequencies among the three breeds of camel were obtained with five oligonucleotide primers. A total of 75 bands were amplified, of which 27 (36%) were polymorphic. The probability of obtaining identical fingerprints was observed to be the lowest in primer GC-10 (5.7%) followed by OP-08 (8.7%), GT-10 (11.3%), G-2 (15.5%) and G-1 (80%). Breed informative bands were amplified. The maximum genetic variability was observed in the Bikaneri (0.80±0.05) followed by the Kachchhi (0.84±0.06) and the Jaisalmeri (0.87±0.05) breeds. The inter-breed genetic distance estimates indicated a closer relationship in the Bikaneri-Kachchhi camels, (0.075), followed by the Jaisalmeri-Kachchhi (0.106) and Bikaneri-Jaisalmeri (0.132) breeds. A similar genetic relationship was observed when the degree of population subdivision was measured between the Bikaneri-Kachchhi (0.529), Jaisalmeri-Kachchhi (0.558) and Bikaneri-Jaisalmeri (0.566) breeds.

Detection of rye chromosome 2R using the polymerase chain reaction and sequence-specific DNA primers

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 19-22 ◽  
Author(s):  
J.-H. Lee ◽  
R. A. Graybosch ◽  
D. J. Lee
Keyword(s):  
Polymerase Chain Reaction ◽  
Wheat Chromosome ◽  
Specific Marker ◽  
Chain Reaction ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Wheat Lines ◽  
Dna Primers

Sequences derived from a rye gamma secalin gene were used as primers in polymerase chain reactions using DNA obtained from a series of wheat and triticale genetic stocks. A 473-bp fragment, the predicted size based on the distance between the selected primers, was found only in rye, triticales, and wheat lines carrying rye chromosome 2RS. Use of triticale lines with various wheat chromosome substitutions confirmed the chromosomal origin of the rye-specific marker. The presence of the 473-bp PCR product was always associated with the production of 75K secalins in grain samples. Thus, the primer sequences, and the clone of origin (pSC503), were both derived from the SEC-2 locus of rye chromosome 2RS.Key words: wheat (Triticum aestivum), rye (Secale cereale), chromosomal translocations, chromosomal substitutions, DNA polymerase chain reaction, sequence-specific primers.

scholarly journals Genetic diversity assessment using RAPD primers in insecticide resistant populations of diamondback moth Plutella xylostella (Linn.)

2015 ◽  
Vol 7 (1) ◽  
pp. 219-225 ◽  
Author(s):  
V. Sunitha ◽  
T.V. K. Singh ◽  
V. Ramesh Babu ◽  
J. Satyanarayana
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Genetic Variability ◽  
Plutella Xylostella ◽  
Rapd Markers ◽  
Diamondback Moth ◽  
Chain Reaction ◽  
Diversity Assessment ◽  
Polymerase Chain ◽  
Cluster A

Genetic diversity in acephate, spinosad and Cry2Ab resistant Plutella xylostella collected from three states of India was assessed by RAPD markers. The DNA extracted from larvae was subjected to polymerase chain reaction using 10 RAPD primers. The highest number alleles (7) were produced by primer ABA-13, followed by six alleles each by primers ABA-2, 7, 8, 11, 14; five alleles each were produced by ABA-4, 9, 10, 12. UPGMA analysis clustered the acephate, spinosad and Cry2Ab treated P.xylostella populations into two groups with overall similarity level of 33%, 27% and 34% respectively. Cluster A consisted 11 samples while Cluster B consisted only F1 of acephate and spinosad treated Karnataka population. In Cry2Ab treated population Cluster B comprised 11 samples and Cluster A had out grouped singly i.e. F0 generation from Karnataka. The genetic variability between the acephate, spinosad and Cry2Ab treated populations ranged from 33 to 69%, 27 to 56% and 34 to 69% respectively. Acephate and spinosad treated F1 population and Cry2Ab treated F0 population from Karnataka were out grouped from rest of the populations.

scholarly journals Simultaneous Detection of the Defoliating and Nondefoliating Verticillium dahliae Pathotypes in Infected Olive Plants by Duplex, Nested Polymerase Chain Reaction

Plant Disease ◽  
2003 ◽  
Vol 87 (12) ◽  
pp. 1487-1494 ◽  
Author(s):  
J. Mercado-Blanco ◽  
D. Rodríguez-Jurado ◽  
S. Parrilla-Araujo ◽  
R. M. Jiménez-Díaz
Keyword(s):  
Polymerase Chain Reaction ◽  
Verticillium Dahliae ◽  
Nested Pcr ◽  
Simultaneous Detection ◽  
Specific Marker ◽  
In Planta ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Olive Trees

Pathogen-free certified planting material and accurate detection of Verticillium dahliae pathotypes infecting the plant are key components of successful management of Verticillium wilt of olive. Use of a nested-polymerase chain reaction (PCR) procedure developed in earlier studies for in planta detection of the defoliating (D) and nondefoliating (ND) V. dahliae pathotypes resulted in ambiguous detection of the pathogen in some cases, due to heterologous amplification of the D-associated marker in ND-infected olive plants. In the present study, an improved procedure was developed that eliminates ambiguity and reduces time and cost for detection of D and ND V. dahliae in olive. The improved procedure is based on the simultaneous amplification of both an ND- and a new D-specific marker by means of duplex, nested PCR. The procedure was effective in the rapid and unequivocal detection of the D and ND V. dahliae in both artificially inoculated, own-rooted olive plants and naturally infected adult olive trees of different cultivar, age, and growing conditions. Furthermore, the duplex, nested-PCR procedure detected simultaneously the D and ND pathotypes in adult olive trees naturally infected by both pathotypes and in young olive plants that were double-inoculated with D and ND isolates under controlled conditions.

scholarly journals Polymerase Chain Reaction Fingerprinting of Erwinia amylovora has a Limited Phylogenetic Value but Allows the Design of Highly Specific Molecular Markers

2008 ◽  
Vol 98 (3) ◽  
pp. 260-269 ◽  
Author(s):  
Arantza Rico ◽  
M. Elena Führer ◽  
Amaya Ortiz-Barredo ◽  
Jesús Murillo
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Epidemiological Studies ◽  
Northern Spain ◽  
Chain Reaction ◽  
Arbitrary Primers ◽  
Polymerase Chain ◽  
Polymorphic Bands

Erwinia amylovora, the causal agent of fire blight, is genetically very homogeneous, and current methodologies provide insufficient or contradictory information about the probable dispersal routes of the pathogen. With the final aim to obtain specific and reliable molecular markers for different lineages of the pathogen, we studied the molecular basis of rep-polymerase chain reaction (PCR) polymorphism using seven different arbitrary primers to fingerprint 93 E. amylovora strains from different countries, including Spain. Polymorphism was very low, and was displayed by only 11 E. amylovora strains, which produced 22 polymorphic bands. Five of 11 polymorphic bands cloned contained DNA that was present in more than 85% of the strains, whereas six bands were due to DNA present exclusively in the strains producing the rep-PCR polymorphism. Also, five of the polymorphic bands were due to the possession of either the ubiquitous plasmid pEA29, of plasmid pEU30, which was exclusively found in strains from North America, or of a 35-kb cryptic plasmid, present only in 28 strains from Northern Spain. We designed primer pairs from several cloned polymorphic bands that allowed the specific identification of the strains producing the polymorphism. Our results indicate that rep-PCR is not adequate for constructing genealogies of E. amylovora, although the strategy illustrated here, as well as the designed primers, can be used effectively in epidemiological studies with this pathogen.

Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa

Genome ◽  
1992 ◽  
Vol 35 (1) ◽  
pp. 84-87 ◽  
Author(s):  
C. S. Echt ◽  
L. A. Erdahl ◽  
T. J. McCoy
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapd Markers ◽  
Genome Mapping ◽  
Polymerase Chain Reaction Amplification ◽  
Random Amplified Polymorphic Dna ◽  
Rapid Development ◽  
Arbitrary Sequence ◽  
Chain Reaction ◽  
Backcross Population ◽  
Polymerase Chain

Polymerase chain reaction was used, with single 10-mer primers of arbitrary sequence, to amplify random regions of genomic DNA from a diploid cultivated alfalfa backcross population. Segregation of the random amplified polymorphic DNA (RAPD) fragments was analysed to determine if RAPD markers are suitable for use as genetic markers. Of the 19 primers tested, 13 amplified a total of 37 polymorphic fragments, of which 28 (76%) segregated as dominant Mendelian traits. RAPD markers appear useful for the rapid development of genetic information in species like alfalfa where little information currently exists or is difficult to obtain.Key words: random amplified polymorphic DNA, polymerase chain reaction amplification, genome mapping, restriction fragment length polymorphism, Medicago sativa.

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