Identification of RAPD markers linked to a gene governing cadmium uptake in durum wheat

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 543-547 ◽  
Author(s):  
Greg A. Penner ◽  
Leslie J. Bezte ◽  
Dave Leisle ◽  
John Clarke
Keyword(s):  
Durum Wheat ◽  
Gel Electrophoresis ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Cadmium Uptake ◽  
Cadmium Content ◽  
Diverse Range ◽  
Selection For

Temperature sweep gel electrophoresis in combination with random amplified polymorphic DNA analysis was employed to detect two markers for a single gene governing low cadmium uptake in western Canadian durum wheat (Triticum turgidum L. var. durum). Analysis of progeny derived from a cross of the high cadmium accumulating cultivar Kyle by the low cadmium accumulating cultivar Nile resulted in linkage estimates of 4.6 (OPC-20) and 21.2 (UBC-180) cM. The closest marker (OPC-20) was shown to be useful for making low cadmium uptake selections from two other sources of low cadmium, 'Biodur' and 'Hercules'. The marker was further used to determine the genetic basis of resistance in 20 introduced durum wheat lines. Within this diverse range of germplasm the marker was correlated with cadmium contents as expected in all but two cases. Plant breeding selection for low cadmium genotypes is hindered by the high cost of chemical determination of cadmium content. Marker assisted selection for a low cadmium uptake gene offers an effective alternative.Key words: cadmium, durum wheat, RAPD markers, marker assisted selection, temperature sweep gel electrophoresis.

scholarly journals Optimizing RAPD Markers for Ginseng Genomic DNA Analysis

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 616b-616
Author(s):  
C.L. Boehm ◽  
I.K. Lee ◽  
G. Jung ◽  
H.C. Harrison ◽  
J. Nienhuis ◽  
...  
Keyword(s):  
Cetyltrimethylammonium Bromide ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Crop Improvement ◽  
Tissue Type ◽  
Tissue Samples ◽  
Sodium Ethyl ◽  
Significant Difference ◽  
Selection For

Random amplified polymorphic DNA (RAPD) may have utility as genetic markers facilitating selection in ginseng crop improvement. This experiment determined chemical buffer and root tissue-type combinations that yield repeatable bands. The results allow further experiments using RAPD markers for estimating the genetic distance between ginseng landraces, selection for crop improvement, and extensive fingerprinting for use in determining the origin of tissue samples. This experiment determined mean band yields for all combinations of dry, fresh, and powdered root with cetyltrimethylammonium bromide, potassium/sodium ethyl xanthogenate, and urea buffers. The buffers were applied in replication to the tissue-types with other extraction protocol factors constant. Replications were amplified four times with four different primers using constant PCR and agarose gel electrophoretic protocols. Distinct bands were counted in each replication, and the summation of the replication repeats considered an observation. Least squares means for several response variables were analyzed. The most significant difference found was between buffers. The buffers ctab and urea were productive, and the pex was not. Significant difference was found when buffers were crossed with tissue. The applications of urea to fresh root, ctab to dry root, urea to dry root, and ctab to powdered root were productive. Based on these results we conclude 1) urea and ctab are productive when applied to all tissue-types, 2) dry root, which is easily collected and stored, yields sufficient DNA for analysis, and 3) powdered root, often the form of commercial products that might be tested for genetic origin, will yield sufficient DNA for analysis.

scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

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.

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

2001 ◽  
Vol 126 (1) ◽  
pp. 64-71 ◽  
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.

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 DNA Markers Linked to Eastern Filbert Blight Resistance from a Hazelnut Selection from the Republic of Georgia

2011 ◽  
Vol 136 (5) ◽  
pp. 350-357 ◽  
Author(s):  
Vidyasagar R. Sathuvalli ◽  
Shawn A. Mehlenbacher ◽  
David C. Smith
Keyword(s):  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Republic Of Georgia ◽  
Sources Of Resistance ◽  
Disease Response ◽  
Distal Side ◽  
Eastern Filbert Blight ◽  
The Republic ◽  
Group 2

The hundred-year history of the european hazelnut (Corylus avellana L.) industry in the Pacific northwestern United States is threatened by eastern filbert blight (EFB) caused by the fungus Anisogramma anomala (Peck) E. Müller. Marker-assisted selection has been extensively used for ‘Gasaway’ resistance in the hazelnut breeding program at Oregon State University. Concern over possible breakdown of this single resistance gene provides an incentive to look for new sources of resistance. OSU 759.010, a selection from the Republic of Georgia, has remained free of EFB after inoculations over several years. Random amplified polymorphic DNA (RAPD) markers linked to resistance were identified by screening primers against three resistant seedlings, three susceptible seedlings, and the parents of a segregating seedling population. For the progeny OSU 759.010 × OSU 653.068, 13 linked markers were identified. The markers most closely linked to resistance were 695-1800 on the proximal side and H12-640, 373-700, 349-450, and F08-700 on the distal side. Four of the five markers also segregated in the progeny OSU 759.010 × OSU 665.076, whereas H12-640 was monomorphic. Segregation for disease response in the first population showed a surplus of resistant seedlings, approaching a 3:1 ratio, with closely linked RAPD markers showing similar ratios. In the second population, the observed segregation for disease response and associated markers did not deviate from the expected 1:1 ratio. Based on cosegregation with simple sequence repeat (SSR) markers, resistance from OSU 759.010 was assigned to linkage group 2. Resistance to EFB from ‘Gasaway’ and ‘Ratoli’ was previously mapped to linkage groups 6 and 7, respectively. Therefore, OSU 759.010 provides a novel source of EFB resistance and markers 695-1800, 373-700, 349-450, and F08-700 have potential for use in marker-assisted selection to pyramid EFB resistance alleles.

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

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.

Estimating genetic diversity in Greek durum wheat landraces with RAPD markers

2005 ◽  
Vol 56 (12) ◽  
pp. 1355 ◽  
Author(s):  
Anna Mantzavinou ◽  
Penelope J. Bebeli ◽  
Pantouses J. Kaltsikes
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Rapd Markers ◽  
Triticum Turgidum ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
The Other ◽  
Wheat Cultivars ◽  
Arbitrary Primers

Using the random amplified polymorphic DNA (RAPD) method, the genetic diversity of 19 Greek landraces and 9 cultivars of durum wheat [Triticum turgidum L. var. durum (Desf.)] was studied. Two commercial bread wheat (Triticum aestivum L.) cultivars and one genotype of Triticum monococcum L. were also included in the study. Eighty-seven arbitrary primers (10-mer) were evaluated in a preliminary experiment and 15 of them were selected for the main experiments based on the quality and reliability of their amplification and the polymorphism they revealed. A total of 150 DNA bands were obtained, 125 (83.3%) of which were polymorphic. On average, 10 DNA bands were amplified per primer, 8.3 of which were polymorphic. The genetic similarity between all pairs of genotypes was evaluated using the Jaccard’s or Nei and Li’s coefficients; the values of the former ranged from 0.153 to 0.973 while those of the latter were slightly higher (0.265–0.986). Cluster analysis was conducted by the UPGMA and the Njoin methods. Both methods broadly placed 26 durum genotypes into 1 branch while the other branch consisted of 2 subgroups: 1 included the 2 bread wheat cultivars; the other 1 consisted of 2 durum landraces, ‘Kontopouli’ and ‘Mavrotheri-Chios’, which showed an intruiging behaviour sharing bands with the bread wheat cultivars. The T. monococcum cultivar stood apart from all other genotypes.

scholarly journals Marker-Assisted Selection for Resistance to Black Shank Disease in Tobacco

Plant Disease ◽  
2002 ◽  
Vol 86 (12) ◽  
pp. 1303-1309 ◽  
Author(s):  
E. S. Johnson ◽  
M. F. Wolff ◽  
E. A. Wernsman ◽  
R. C. Rufty
Keyword(s):  
Resistance Gene ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Black Shank ◽  
Ploidy Levels ◽  
Complete Linkage ◽  
Repulsion Phase ◽  
Selection For ◽  
Haploid Plants

Bulked segregant (BSA) and random amplified polymorphic DNA (RAPD) analyses were used to identify markers linked to the dominant black shank resistance gene, Ph, from flue-cured tobacco (Nicotiana tabacum) cv. Coker 371-Gold. Sixty RAPD markers, 54 in coupling and 6 in repulsion phase linkage to Ph, were identified in a K 326-derived BC1F1 (K 326-BC1F1) doubled haploid (DH) population. Thirty RAPD markers, 26 in coupling and 4 in repulsion phase linkage to Ph, were used to screen 149 K 326-BC2F1 haploid plants. Complete linkage between the 26 coupling phase markers and Ph was confirmed by screening 149 K 326-BC2F1 DH lines produced from the haploid plants in black shank nurseries. RAPD markers OPZ-5770 in coupling and OPZ-7370 in repulsion phase linkage were used to select plants homozygous for the Ph gene for further backcrossing to the widely grown flue-cured cultivar K 326. Black shank disease nursery evaluation of 11 K 326-BC4S1 lines and their testcross hybrids to a susceptible tester confirmed linkage between Ph and OPZ-5770. The results demonstrated the efficiency of marker-assisted selection for Ph using a RAPD marker linked in coupling and repulsion. Complete linkage between 26 RAPD markers and the Ph gene was confirmed in the K 326-BC5 generation, and RAPD phenotypes were stable across generations and ploidy levels. These RAPD markers are useful in marker-assisted selection for Ph, an important black shank resistance gene in tobacco.

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