scholarly journals GENETIC FINGERPRINTING OF SNAP BEAN CULTIVARS WITH RAPD MARKERS

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 573g-574
Author(s):  
Paul Skroch ◽  
Jim Nienhuis
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Pedigree Information ◽  
Banding Patterns ◽  
Snap Bean ◽  
Marker Data ◽  
Varietal Identification ◽  
The One ◽  
And Control

The genetic variation in a population of one hundred Snap Bean varieties, including processing and garden types, was studied using RAPD markers. All one hundred genotypes were distinguished by unique combinations of banding patterns. These unique “fingerprints” were tested for repeatability. Certain bands were very reliable and can be used for varietal identification. The RAPD marker data was also used to estimate genetic relationships among a subset of the one hundred lines. The results of the analysis agreed with known pedigree information. These markers will allow more precise monitering and control of germplasm by those who are involved with the breeding and production of superior seed.

scholarly journals Genetic and Pathogenic Analyses of Colletotrichum gloeosporioides Isolates from Strawberry and Noncultivated Hosts

2004 ◽  
Vol 94 (5) ◽  
pp. 446-453 ◽  
Author(s):  
C. L. Xiao ◽  
S. J. MacKenzie ◽  
D. E. Legard
Keyword(s):  
Rapd Markers ◽  
Colletotrichum Gloeosporioides ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Crown Rot ◽  
Inoculum Sources ◽  
Marker Data ◽  
Colletotrichum Spp ◽  
Species Specific

Colletotrichum crown rot of strawberry in Florida is caused primarily by Colletotrichum gloeosporioides. To determine potential inoculum sources, isolates of Colletotrichum spp. from strawberry and various noncultivated plants growing in the areas adjacent to strawberry fields were collected from different sites. Species-specific internal transcribed spacer primers for C. gloeosporioides and C. acutatum were used to identify isolates to species. Random amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among isolates recovered from noncultivated hosts and diseased strawberry plants. Selected isolates also were tested for pathogenicity on strawberry plants in the greenhouse. In all, 39 C. gloeosporioides and 3 C. acutatum isolates were recovered from diseased strawberry crowns, and 52 C. gloeosporioides and 1 C. acutatum isolate were recovered from noncultivated hosts. In crown inoculation tests, 18 of the 52 C. gloeosporioides isolates recovered from noncultivated hosts were pathogenic to strawberry. Phylogenetic analysis using RAPD marker data divided isolates of C. gloeosporioides from noncultivated hosts into two separate clusters. One cluster contained 50 of the 52 isolates and a second cluster contained 2 isolates that were homothallic in culture. Isolates from strawberry were interspersed within the cluster containing the 50 isolates that were recovered from noncultivated hosts. The results are not inconsistent with the hypothesis that C. gloeosporioides isolates obtained from strawberry and noncultivated hosts adjacent to strawberry fields are from the same population and that noncultivated hosts can serve as potential inoculum sources for Colletotrichum crown rot of strawberry.

Identification and assessment of genetic relationships in three Chlorophytum species and two high yielding genotypes of C. borivilianum through RAPD markers

Biologia ◽  
2011 ◽  
Vol 66 (2) ◽  
Author(s):  
Sanghamitra Samantaray ◽  
Tarun Patel ◽  
K. Geetha ◽  
Satyabrata Maiti
Keyword(s):  
Rapd Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Banding Patterns ◽  
Major Cluster ◽  
Breeding Programmes ◽  
Important Input ◽  
Identification And Characterization

AbstractConservation of identified germplasm is an important component for efficient and effective management of plant genetic resources. Since Chlorophytum species are important medicinal plants, studies were carried out for identification and establish genetic relationships in three species of Chlorophytum and two high yielding genotypes of Chlorophtum borivilianum using RAPD markers. Out of one hundred primers tested, 47 decamers amplified a total of 454 distinct bands ranging from 0.25–3.0 kbp to identify and to evaluate genetic relationships between and among three species of Chlorophytum and two genotypes of Chlorophtum borivilianum. The cluster analysis indicated that three species of Chlorophytum and two genotypes (NRCCB-1 and NRCCB-2) of C. borivilianum formed two major clusters. The first major cluster constituted C. arundinaceum and C. tuberosum, and the second major cluster composed of two subclusters; the first subcluster represented NRCB-1 and NRCB-2 where as the second subcluster represented C. borivilianum. Thus, the RAPD markers have the potential for identification and characterization of genetic relatedness among the species and genotypes. C. borivilianum along with two genotypes also showed similar banding patterns which could be chosen as candidate markers for differentiating the other two species such as C. arundinaceum and C. tuberosum. This would helpful for breeding programmes and provides an important input in conservation biology.

scholarly journals Development of EST-PCR Markers for DNA Fingerprinting and Genetic Relationship Studies in Blueberry (Vaccinium, section Cyanococcus)

2003 ◽  
Vol 128 (5) ◽  
pp. 682-690 ◽  
Author(s):  
Lisa J. Rowland ◽  
Smriti Mehra ◽  
Anik L. Dhanaraj ◽  
Elizabeth L. Ogden ◽  
Janet P. Slovin ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Cdna Library ◽  
Dna Fingerprinting ◽  
Genetic Relationships ◽  
Pedigree Information ◽  
Similarity Coefficients ◽  
Pcr Markers ◽  
Marker Data ◽  
General Utility ◽  
Caps Markers

Because randomly amplified polymorphic DNA (RAPD) is the only type of molecular marker that has been used extensively in blueberry (Vaccinium spp.) for mapping and DNA fingerprinting of cultivars, there is a need to develop a new, robust marker system. Expressed sequence tags (ESTs) produced from a cDNA library, derived from RNA from floral buds of cold acclimated plants, were used to develop EST-PCR markers for blueberry. Thirty clones, picked at random from the cDNA library, were single-pass sequenced from the 5' and 3' ends. Thirty PCR primer pairs were designed from the ends of the best quality sequences that were generated and were tested in amplification reactions with genomic DNA from 19 blueberry genotypes, including two wild selections (the original parents of a mapping population), and 17 cultivars. Fifteen of the 30 primer pairs resulted in amplification of polymorphic fragments that were detectable directly after ethidium bromide staining of agarose gels. Several of the monomorphic amplification products were digested with the restriction enzyme AluI and approximately half resulted in polymorphic-sized fragments (cleaved amplified polymorphic sequences or CAPS markers). The polymorphic EST-PCR and CAPS markers developed in this study distinguished all the genotypes indicating that these markers should have general utility for DNA fingerprinting and examination of genetic relationships in blueberry. Similarity values were calculated based on the molecular marker data, and a dendrogram was constructed based on the similarity matrix. Coefficients of coancestry were calculated for each pair of genotypes from complete pedigree information. A fair correlation between similarity coefficients calculated from marker data and coefficients of coancestry was found.

Genetic Similarity Among Broccoli Inbreds “Essentially Derived” from Commercial Cultivars

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 546e-546 ◽  
Author(s):  
Mark W. Farnham ◽  
Jiang Lu ◽  
Julie M. Villand
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Doubled Haploids ◽  
Threshold Level ◽  
Pedigree Information ◽  
Dimensional Scaling ◽  
Similarity Indices ◽  
Related Group

DNA markers can assess close genetic relationships between individuals of a crop as when one variety is developed (i.e., “essentially derived”) from another. An acceptable threshold, based on empirical results, should be established for a crop to indicate what constitutes an “essentially derived” variety in the absence of clear pedigree information. Empirical data could help settle infringements of intellectual property rights, but appropriate data are not being generated for most crops. Thus, our objectives were to characterize genetic relationships among broccoli varieties “essentially derived” from known parents using random amplified polymorphic DNA (RAPD) markers as a measure of genotype and to provide an empirical basis for threshold levels in this crop. Six F1 broccoli hybrids and three inbred lines (doubled-haploids) developed from each of the hybrids (24 entries) were evaluated by RAPD analysis. RAPD assays were conducted using 23 different oligonucleotide 10-mers. Of 179 RAPD bands scored, 94 were polymorphic among the entries. Similarity indices were computed from RAPD data, and a multi-dimensional scaling (MDS) plot was constructed. Similarity indices for all pairwise comparisons ranged from 0.40 to 0.90. `High Sierra' and it's derived lines were the most closely related group with indices from 0.81 to 0.90. With `High Sierra', `Sultan', and `Marathon', the three derived lines were more closely related to their respective parental hybrids than were any other entries. The hybrids `Futura', `Everest', and `Viking' were more genetically similar to other entries than to their derived lines. A threshold level based on data from `High Sierra', `Marathon', `Sultan', and their derived lines would not identify “essentially derived” lines developed from other hybrids.

scholarly journals Testing for Genetic Purity in Petunia and Cyclamen Seed Using Random Amplified Polymorphic DNA Markers

HortScience ◽  
1997 ◽  
Vol 32 (2) ◽  
pp. 246-247 ◽  
Author(s):  
Zhang Jianhua ◽  
Miller B. McDonald ◽  
Patricia M. Sweeney
Keyword(s):  
Dna Markers ◽  
Petunia Hybrida ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Cyclamen Persicum ◽  
Genetic Purity ◽  
Banding Patterns ◽  
Rapd Makers ◽  
Seed Crops

This study examined the use of random amplified polymorphic DNA (RAPD) markers as a means to identify cultivars of petunia (Petunia hybrida Vilm) seedlings and cyclamen (Cyclamen persicum Mill.) seeds and to determine the genetic purity within cyclamen seeds. Bulked samples of six petunia and five cyclamen hybrid cultivars, respectively, produced consistent RAPD marker profiles. Evaluation of individual seeds from a single cyclamen hybrid produced polymorphic banding patterns that were attributed to genetic variability present in the female and male inbred parents. These results show that RAPD makers can be used to quickly assess the genetic purity of selected cultivars of these two flower seed crops.

461 PB 292 MAPPING RAPD MARKER DIVERSITY IN PHASEOLUS VULGARIS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 497c-497
Author(s):  
Paul Skroth ◽  
Jim Nienhuis ◽  
Geunhwa Jung ◽  
Dermont Coyne
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Good Tool ◽  
Germplasm Collections ◽  
Efficient Construction ◽  
Two Populations

Knowledge of genetic relationships and genetic diversity among accessions is essential for the efficient construction, maintainance and utilization of large ex-situ germplasm collections. Furthermore, streamlining of large collections into care collections necessitates validation of germplasm sampling techniques. DNA molecular markers provide potentially unbiased estimators of genome diversity end may facilitate organization, maintainance, and sampling of plant genetic resources. Our data suggests that RAPD markers will be o good tool for testing tore collection concepts and organizing genetic diversity in common bean. However, the genomic distribution of markers is unknown. Currently we are using recombinant inbred (RI) populations to place RAPD markers in the context of the bean genetic map. We hove evaluated the the distribution of RAPD markers in three RI populations: Bat93 × Jalo EEP558, PC50 × Xan159, and BAC6 × HT7719. Cultivated P.vulgaris has two primary renters of diversity Mesoamerican and Andean, the RI populations used for mapping RAPD markers ore Meso × Andean, Andean × Andean, and Meso × Meso crosses respectively. In the Bat93 × Jalo EEP558 population 383 markers have been mapped for a map length of 735 cM. However, approximately 150 of these markers ore members of 9 dusters which span only 90 cM. This inter gone pool mop is being integrated with linkage mops constructed in the other two populations to compare within and between gene pool marker distributions and to evaluate clustering of markers on the different mops. Implications for the application of RAPD markers will be discussed.

scholarly journals Genetic Diversity Based on Randomly Amplified Polymorphic DNA (RAPD) and Its Relationship with the Performance of Diploid Potato Hybrids

1997 ◽  
Vol 122 (6) ◽  
pp. 740-747 ◽  
Author(s):  
M.M. Paz ◽  
R.E. Veilleux
Keyword(s):  
Genetic Distance ◽  
Combining Ability ◽  
Rapd Markers ◽  
Tuber Yield ◽  
Genetic Relationships ◽  
Field Evaluation ◽  
Banding Patterns ◽  
In Vitro Plantlets ◽  
Better Than

RAPD analysis was conducted on in vitro plantlets of Solanum phureja Juz. & Buk. monoploids and diploid heterozygous pollinators. Among 60 decamer primers screened, 11 did not show polymorphism while some primers produced complex banding patterns or faint bands that were difficult to score. Genetic distance estimates were based on 151 polymorphic RAPD markers of 208 bands scored using 33 primers. Simple matching and Jaccard coefficients were calculated to estimate genetic similarity (GS). Genetic distance (GD=1-GS) among genotypes ranged from 0.0 to 0.664. Cluster analysis yielded groups of genotypes that were consistent with known genomic compositions or genetic relationships inferred from their pedigree. Field evaluation of 14 F1 families resulting from five S. phureja doubled monoploids (DMs) crossed to three heterozygous pollinators (IDs) revealed significant differences in total tuber number, total tuber yield, average tuber mass, and vigor. Total tuber yield per family ranged from 174 to 404 g per plant and was significantly lower than the control `Kennebec'. The general combining ability of DM BARD 13-14/202 was superior to other DM parents. Specific combining ability was observed in progeny of AD2-4/3s.8 H ID 4. Among male parents, ID 8 performed better than ID 4 or ID 5. Using simple matching, the largest parental genetic distance was always associated with the highest total tuber yield among progenies of DM parents. A similar trend was obtained using Jaccard coefficients. Based on our results, RAPD markers may facilitate the identification of diverse parents to maximize the expression of heterosis in S. phureja hybrids.

scholarly journals Development of SCAR Markers for DNA Fingerprinting and Germplasm Analysis of American Cranberry

2002 ◽  
Vol 127 (4) ◽  
pp. 677-684 ◽  
Author(s):  
James J. Polashock ◽  
Nicholi Vorsa
Keyword(s):  
Dna Fingerprinting ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Germplasm Collection ◽  
Polymorphic Markers ◽  
American Cranberry ◽  
Primer Sets ◽  
Germplasm Analysis

DNA fingerprinting has been useful for genotypic classification of American cranberry (Vaccinium macrocarpon Ait.). Polymerase chain reaction (PCR) based methodologies including randomly amplified polymorphic DNA (RAPD) markers are relatively easy to use, and inexpensive as compared to other methods. However, RAPD markers have some limitations including seamless interlaboratory transferability and susceptibility to certain types of error. An alternative method, sequence characterized amplified regions (SCARs), was developed for cranberry germplasm analysis. Nine primer sets were designed from RAPD-identified polymorphic markers for use in two multiplex PCR reactions. These primer sets generated 38 markers across a cranberry germplasm collection. Estimates of genetic relatedness deduced from employment of the RAPD and SCAR methods were compared among 27 randomly chosen cranberry germplasm accessions. Although both methods produced comparable results above 0.90 coefficient of similarity, branches below this level exhibited variation in clustering. SCAR and RAPD markers can be employed for identifying closely related genotypes. However, the inferences of more distant genetic relationships are less certain. SCAR marker reactions provided more polymorphic markers on a per reaction basis than RAPD marker reactions and as such more readily separated closely related progeny. When SCAR primers were fluorescent dye-labeled for computerized detection and data collection, reduced marker intensity relative to unlabeled reactions was one problem encountered.

scholarly journals 335 ORGANIZATION OF ARTICHOKE, CYNARA SCOLYMUS L., BASED ON RAPD MOLECULAR MARKER BANDING PATTERNS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 478e-478
Author(s):  
Jan G. Tivang ◽  
Neal DeVos ◽  
James Nienhuis ◽  
Paul Skroch
Keyword(s):  
Rapd Markers ◽  
Diversity Index ◽  
Genetic Relationships ◽  
Banding Patterns ◽  
Band Frequency ◽  
Tukey Test ◽  
Breeding Populations ◽  
Homogeneity Of Variance ◽  
The Mean ◽  
Highly Correlated

Individual heads (capitula) from five discrete artichoke, Cyara scolymus L., populations were evaluated using RAPD markers. One vegetatively-propagated cultivar; Green Globe; two seed-propagated cultivars, Imperial Star and Big Heart XR-1; and two breeding populations were examined. Twenty-seven RAPD primers were scored yielding 2 to 16 polymorphic bands resulting in a total of 178 bands. Our objective was to determine if RAPD markers could be used to distinguish between and within populations. The genetic relationships among populations as well as among individuals within each population were estimated using the ratio of discordant to total bands scored. Data reduction (MDS) provided a plot indicating five clusters corresponding to the five populations. Confirmation of the presence of five discrete clusters was obtained by analysis of variance of the marker frequencies. The genetic diversity index (GDI) was calculated for each populations as the pooled variance of band frequency for each population. The GDI values were highly correlated to the mean genetic distance within each population. The homogeneity of variance for the GDI values associated with each population were compared using the Siegel-Tukey test for homogeneity of spread.

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