scholarly journals Identification of Grape (Vitis) Rootstocks Using Sequence Characterized Amplified Region DNA Markers

HortScience ◽  
1996 ◽  
Vol 31 (2) ◽  
pp. 267-268 ◽  
Author(s):  
Hong Xu ◽  
Alan T. Bakalinsky
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Scar Markers ◽  
Polymorphic Markers ◽  
Sequence Characterized Amplified Region ◽  
Annealing Temperatures

Five sequence characterized amplified region (SCAR) DNA markers were reevaluated at substantially higher annealing temperatures than originally reported; four were polymorphic among nine rootstocks tested. Four new informative SCAR markers also are reported, based on redesigning primers from previously cloned random amplified polymorphic DNA (RAPD) markers. Based on the eight polymorphic markers, rootstocks MG 420A, MG101-14, Richter 99, Couderc 3309, and Kober 5BB were distinguishable. Riparia Gloire and Couderc 1616 could be distinguished from the others, but not from one another, and SO4 and 5C also could be distinguished from the others, but not from one another.

scholarly journals 666 PB 110 RANDOM AMPLIFIED POLYMORPHIC DNA MARKERS ARE INADEQUATE FOR FINGERPRINTING GRAPE ROOTSTOCKS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 528c-528
Author(s):  
Alan T. Bakalinsky ◽  
Hong Xu ◽  
Diane J. Wilson ◽  
S. Arulsekar
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Restriction Site ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Base Length ◽  
Specific Primer ◽  
Annealing Temperatures ◽  
Individual Reaction ◽  
Length Variant

A total of eight random amplified polymorphic DNA (RAPD) markers were generated in a screen of 77 primers of 10-base length and were detected reproducibly among nine different grape (Vitis) rootstocks. Occasional failed amplifications could not be explained rationally nor easily corrected by systematic replacement of individual reaction components. In an effort to improve their reliability, the RAPD markers were cloned, their termini sequenced, and new sequence-specific primer pairs were synthesized based on addition of 10 to 14 bases to the 3' termini of the original 10-mers. Six pairs of the new primers were evaluated at their optimal and higher-than optimal annealing temperatures. One primer pair amplified a product the same size as the original RAPD marker in all rootstocks, resulting in loss of polymorphism. Post-amplification digestion with 7 different restriction endonucleases failed to reveal restriction site differences. Three primer pairs amplified an unexpected length variant in some accessions. Two other pairs of primers amplified a number of unexpected bands. Better approaches for exploiting the sequence differences that account for the RAPD phenomenon will be discussed.

scholarly journals Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis

HortScience ◽  
1998 ◽  
Vol 33 (1) ◽  
pp. 140-142 ◽  
Author(s):  
Jean-Guy Parent ◽  
Danièle Pagé
Keyword(s):  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Rubus Idaeus ◽  
Scar Markers ◽  
Certification Program ◽  
Red Raspberry ◽  
Sequence Characterized Amplified Region

Five polymorphic random amplified polymorphic DNA (RAPD) markers for 13 red raspberry (Rubus idaeus L.) and two purple raspberry (R. idaeus L. × R. occidentalis L.) cultivars were cloned and their termini sequenced. Sequence-specific 24-mer primer pairs were synthesized as extended RAPD primers and used in sequence characterized amplified region (SCAR) DNA analysis. All primer pairs generated polymorphic SCAR markers of the original RAPD marker sizes and length variants. Markers from four of the primer pairs could be easily scored and were adequate to identify the raspberry cultivars of the certification program of the province of Quebec.

scholarly journals Evaluation of SCAR Markers to Identify Raspberry Cultivars

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 856B-856 ◽  
Author(s):  
Jean-Guy Parent ◽  
Daniele Page
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Sequence Information ◽  
Scar Markers ◽  
Certification Program ◽  
Reaction Conditions ◽  
Sequence Characterized Amplified Region ◽  
Sequence Method ◽  
Scar Primers

Random amplified polymorphic DNA (RAPD) markers are used in Quebec's certification program to verify the identity of raspberry cultivars. However, sequence characterized amplified region (SCAR) markers, less sensitive to modifications in reaction conditions, could be derived from RAPD markers. Our objective was to evaluate the potential of SCAR markers to replace the RAPD ones. Five RAPD markers obtained with primer OPG06 (length of 520, 700, 825, 1450, and 2000 bp) were cloned in pTZ/PC or pCRII vectors. Extremities of the cloned markers were sequenced by the nonradioactive silver sequence method using pUC/M13 forward and reverse primers. Sequence information was used to make SCAR primers, similar in length to standard PCR primers. Some SCAR primers were elongated RAPD primers, whereas others were from internal regions. Ability of primer pairs and combination of primer pairs to discriminate cultivars of our certification program was compared with their RAPD counterparts as well as with the technical feasibility of both methods.

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 844-851 ◽  
Author(s):  
K. F. Yu ◽  
K. P. Pauls
Keyword(s):  
Chromosome Segregation ◽  
Dna Markers ◽  
Rapd Markers ◽  
Molecular Mapping ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Female Parent ◽  
Linkage Groups ◽  
Double Reduction ◽  
Chromatid Segregation

An F1 population was used to analyze the inheritance of random amplified polymorphic DNA (RAPD) markers in tetraploid alfalfa. Of the 32 RAPD markers that were used for a segregation analysis in this study, 27 gave ratios that are consistent with random chromosome and random chromatid segregation at meiosis. However, among all of the RAPD markers (121) that were screened in this study, only one example of a double reduction, that is typical of chromatid segregation, was observed. These results indicate that random chromosome segregation is likely the predominant but not the exclusive mode of inheritance for tetraploid alfalfa. χ2 analyses of cosegregation for RAPD marker pairs derived from the female parent revealed nine linkages that fell into four linkage groups. The recombination fractions among linked marker pairs ranged from 1 to 37%. These are the first molecular linkage groups reported in tetraploid alfalfa. In addition, various strategies for molecular mapping in the tetraploid alfalfa genome are proposed that should be of interest to plant breeders who are planning to use molecular markers for alfalfa or other tetraploid species.Key words: RAPD markers, tetraploid alfalfa, segregation, linkage groups.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

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

HortScience ◽  
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.

scholarly journals 332 GENETIC SIMILARITIES AMONG CHINESE VEGETABLE BRASSICAS USING RANDOM AMPLIFIED POLYMORPHIC DNA MARKERS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 478b-478
Author(s):  
Jianping Ren ◽  
Warren F. Lamboy ◽  
lames R. McFerson ◽  
Stephen Kresovich ◽  
Jianping Ren
Keyword(s):  
Chinese Cabbage ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Chinese Kale ◽  
Diversity Assessment ◽  
Wide Range ◽  
Germplasm Accessions ◽  
Chinese Vegetable ◽  
Vegetable Brassicas

Fifty-two germplasm accessions of Chinese vegetable Brassicas were analyzed using 112 random amplified polymorphic DNA (RAPD) markers. The array of material examined spanned a wide range of morphological, geographic, and genetic diversity, and included 30 accessions of Brassica rapa (Chinese cabbage, pakchoi, turnip, broccoletto), 18 accessions of B. juncea (leaf, stem, and root mustards), and 4 accessions of B. oleracea ssp.alboglabra (Chinese kale). The RAPD markers unambiguously identified all 52 accessions. Net and Li genetic similarities were computed and used in UPGMA cluster analyses. Accessions and subspecies clustered into groups corresponding to the three species, but some accessions of some subspecies were most closely related to accessions belonging to another subspecies. Using genetic similarities, it was found that Chinese cabbage is more. likely to have been produced by hybridization of turnip and pakchoi, than as a selection from either turnip or pakchoi alone. RAPD markers provide a fast, efficient technique for diversity assessment that complements methods currently in use in genetic resources collections.

scholarly journals POLYMORPHISMS OF RAPD MARKERS IN CELERY CULTIVARS

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 660e-660
Author(s):  
Xiaofeng Yang ◽  
Carlos F. Quiros
Keyword(s):  
North America ◽  
Dna Markers ◽  
Rapd Markers ◽  
Cultivar Identification ◽  
Random Amplified Polymorphic Dna ◽  
The Other ◽  
Apium Graveolens ◽  
Isozyme Markers ◽  
Genetic Base ◽  
The Relationship

Celery cultivars (Apium graveolens var. dulce) in North America have a narrow genetic base. Twenty-two celery, one celeriac and one annual cultivar were screened for polymorphic RAPD (Random Amplified Polymorphic DNA) markers with 28 arbitrary 10-mer primers. Among the total 231 bands obtained, 28 (12%) of the bands were polymorphic among the 24 accessions screened, but only 18 (7.8%) were polymorphic within the 22 celery cultivars. These markers are sufficient to distinguish each of the cultivars used. The average number of marker differences is 6.2 between two celery cultivars, 13.5 between the celeriac and the remaining cultivars, and 16.5 between the annual and the other cultivars. The relationship among the celery cultivars disclosed from this study is basically consistent with that observed using total protein and isozyme markers. RAPD technology provides a new alternative for cultivar identification in celery.

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.

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