scholarly journals Rose Germplasm Analysis with RAPD Markers

HortScience ◽  
1999 ◽  
Vol 34 (2) ◽  
pp. 341-345 ◽  
Author(s):  
C.H. Jan ◽  
D.H. Byrne ◽  
J. Manhart ◽  
H. Wilson
Keyword(s):  
Rapd Markers ◽  
Group Method ◽  
Similarity Matrix ◽  
Arithmetic Means ◽  
Pair Group ◽  
Traditional Classification ◽  
Germplasm Analysis ◽  
The Rose ◽  
Unweighted Pair Group Method

The genus Rosa consists of more than 100 species classified into four subgenera, Eurosa, Platyrhodon, Hesperhodos, and Hulthemia, and distributed widely throughout the northern hemisphere. The subgenus Eurosa includes 11 sections. The other subgenera are monotypic. One hundred and nineteen accessions and 213 markers of 36 rose species that include eight sections of the subgenus Eurosa and one species each from the subgenera Hesperhodos and Platyrhodon were used to calculate a similarity matrix, which was clustered with the unweighted pair group method using arithmetic means (UPGMA). The RAPD markers distinguished between all the rose accessions, and species grouped into their respective sections. Therefore, classification of Rosa using RAPD data generally supports traditional classification. The Asian rose sections (Laevigatae, Banksianae, Bracteatae, Pimpinellifoliae, Chinenses, and Synstylae) were consistently separated from the primarily North American sections (Cassiorhodon and Carolinae). The Cassiorhodon and Carolinae sections were grouped together with the subgenera Hesperhodos and Platyrhodon. Both subgenera separated out at the same level as sections within the subgenus Eurosa, suggesting that they are more appropriately classified as sections within the subgenus Eurosa. Sections Cassiorhodon and Carolinae overlapped, and are probably best grouped as one section as previously suggested.

scholarly journals Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

2016 ◽  
Vol 25 (2) ◽  
pp. 223-229 ◽  
Author(s):  
Kuasha Mahmud ◽  
KM Nasiruddin ◽  
MA Hossain ◽  
L Hassan
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Sugarcane Varieties ◽  
Main Cluster ◽  
Pair Group ◽  
The Relationship ◽  
Linkage Distance

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Paloma Abad ◽  
Bernardo Pascual ◽  
José V. Maroto ◽  
Salvador López-Galarza ◽  
María J. Vicente ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Wild Populations ◽  
Arithmetic Average ◽  
Yellow Nutsedge ◽  
Pair Group ◽  
High Level ◽  
Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

scholarly journals Identities and Relationships among Chinese Vegetable Brassicas as Determined by Random Amplified Polymorphic DNA Markers

1995 ◽  
Vol 120 (3) ◽  
pp. 548-555 ◽  
Author(s):  
Jianping Ren ◽  
James R. McFerson ◽  
Rugang Li ◽  
Stephen Kresovich ◽  
Warren F. Lamboy
Keyword(s):  
Chinese Cabbage ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Diversity Assessment ◽  
Wide Range ◽  
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 L. (Chinese cabbage, pakchoi, turnip, and broccoletto), 18 accessions of B. juncea (L.) Czern. (leaf, stem, and root mustards), and four accessions of B. oleracea L. ssp. alboglabra (Chinese kale). The RAPD markers unambiguously identified all 52 accessions. Nei-Li similarities were computed and used in unweighed pair group method using arithmetic means (UPGMA) cluster analyses. Accessions and subspecies were clustered into groups corresponding to the three species, but some accessions of some subspecies were most closely related to accessions belonging to other subspecies. Values for Nei-Li similarities suggest 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 are a fast, efficient method for diversity assessment in Chinese vegetable brassicas that complements techniques currently in use in genetic resources collections.

Application of DNA fingerprinting for the classification of selected almond [Prunus dulcis (Miller) D. A. Webb] cultivars

2000 ◽  
Vol 40 (7) ◽  
pp. 995 ◽  
Author(s):  
F. M. Woolley ◽  
G. G. Collins ◽  
M. Sedgley
Keyword(s):  
Middle East ◽  
Prunus Dulcis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Breeding Lines ◽  
Pair Group ◽  
Commercial Cultivars ◽  
Unweighted Pair Group Method ◽  
Prunus Webbii

Almond cultivars developed in Australia are thought to have descended from 2 breeding lines, 1 from hard-shelled Spanish/Jordan types, and the other from paper-shell Californian types. However, the precise derivation of many individual Australian cultivars is uncertain. Randomly amplified polymorphic DNA (RAPD) was used to estimate the genetic similarities between 50 accessions of almond cultivars derived from Australia, California, Europe and the Middle East, and individual accessions of Prunus orientalis (Miller) D. A. Webb and Prunus webbii (Spach) Vieh. Amplification products were analysed using the simple matching coefficient and the unweighted pair group method with arithmetic averages to cluster individuals into a dendrogram. Cultivars known to have originated in Europe or the Middle East clustered in a different group from those known to have originated in California confirming the 2 suspected breeding lines. The origin of some common Australian commercial cultivars was inferred by their placement on the dendrogram, and the possible parentage of some Australian selections is discussed.

scholarly journals Molecular analysis of strawberry cultivars using RAPD, AP-PCR and STS markers

2002 ◽  
Vol 8 (2) ◽  
Author(s):  
A. Balogh ◽  
E. Kiss ◽  
A. Szőke ◽  
F. Dénes ◽  
L. Heszky
Keyword(s):  
Rapd Markers ◽  
Fragaria X Ananassa ◽  
Jaccard Index ◽  
Group Method ◽  
Pedigree Data ◽  
Similarity Coefficients ◽  
Pair Group ◽  
Data Similarity ◽  
Strawberry Cultivars ◽  
Unweighted Pair Group Method

Seventeen strawberry (Fragaria x ananassa Duch.) cultivars representing the national list of Hungary, were subjected to RAPD, AP—PCR and STS analysis. Of the 31 decamer and oligomer primers tested 26 primers produced polymorphic patterns. 45 polymorphic fragments were analysed, ranging between 200-2800 by in size. Based on the data, similarity coefficients (Jaccard index and Simple matching coefficient) were calculated, and dendrograms were constructed using the unweighted pair group method of arithmetic averages (UPGMA). The dendrograms only partly reflect the known pedigree data. Specific RAPD markers were identified for cultivars F5, Pocahontas and Rabunda.

Characterization of genotypes and genetic relationships of cili (Rosa roxburghii) and its relatives using RAPD markers

2004 ◽  
Vol 1 (2) ◽  
pp. 79-84
Author(s):  
Wen Xiao-Peng ◽  
Deng Xiu-Xin
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Arithmetic Mean ◽  
Group Method ◽  
Arbitrary Primers ◽  
Pair Group ◽  
Rosa Roxburghii ◽  
Widespread Interest ◽  
Unweighted Pair Group Method

AbstractCili (Rosa roxburghii Tratt), characterized by containing the highest vitamin C content among fruits and showing attractive senescence-retarding and cancer-preventing effects, has gained widespread interest. RAPD markers were applied to identify the seven genotypes of cili and to evaluate the genetic relationships within cili, as well as among its relatives. Sixteen arbitrary primers screened from 154 were adopted to analyse polymorphism in RAPD profiles for the 15 samples. A total of 137 RAPD bands ranging in size from 480 bp to 3.3 kb were obtained, among which 95 were polymorphic, covering 69.3% of the total bands obtained; and an average of 8.6 bands/primer was scored. The genotypes of cili and seedless cili could be identified efficiently by 14 genotype-specific bands, which were obtained from the polymorphic primers OPB-11, OPAF-16 and OPW-02. Additionally, using the unweighted pair group method with arithmetic mean, a dendrogram showing genetic relationships among the 15 samples was constructed based on cluster analysis of genetic distance. The possible origin of seedless cili and multiple-corolla cili is also discussed.

Cultivar identification in upland cotton using RAPD markers

2002 ◽  
Vol 53 (6) ◽  
pp. 637 ◽  
Author(s):  
A. A. Linos ◽  
P. J. Bebeli ◽  
P. J. Kaltsikes
Keyword(s):  
Upland Cotton ◽  
Rapd Markers ◽  
Cultivar Identification ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Gossypium Hirsutum L ◽  
Arithmetic Means ◽  
Arbitrary Primers ◽  
Pair Group ◽  
Base Cluster

Using the random amplified polymorphic DNA (RAPD) method, the identification and the genetic description of 28 upland cotton (Gossypium hirsutum L.) cultivars currently cultivated in Greece was attempted. Based on the results of a preliminary experiment using 50 ten-base arbitrary primers, 24 were selected for the main experiment. DNA bands totaling 181 were observed, 118 (65.2%) of which were polymorphic. On the average, 7.5 DNA bands were amplified per primer, 4.9 of which were polymorphic. The unique identification of all cultivars studied was made possible using 27 specific polymorphic bands (markers) corresponding to 16 primers and a specially constructed key. The genetic similarity of the cultivars was estimated using Jaccard's similarity coefficient, which ranged from 0.614 to 0.922, indicating a relatively narrow genetic base. Cluster analysis by the Unweighted Pair Group Method of Arithmetic means (UPGMA) showed that 21 of the cultivars could be placed into 3 major groups. A similar clustering of the cultivars was obtained using principal coordinate analysis.

scholarly journals Genetic Diversity of Species of Chrysanthemum and Related Genera and Groundcover Cultivars Assessed by Amplified Fragment Length Polymorphic Markers

HortScience ◽  
2013 ◽  
Vol 48 (5) ◽  
pp. 539-546 ◽  
Author(s):  
Xuejuan Chen ◽  
Ming Sun ◽  
Jianguo Liang ◽  
Hui Xue ◽  
Qixiang Zhang
Keyword(s):  
Genetic Diversity ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Aflp Marker ◽  
Group Method ◽  
Pair Group ◽  
Traditional Classification ◽  
Wild Accessions

Chrysanthemums have beautiful flowers with high ornamental value and rich genetic diversity. Amplified fragment length polymorphism (AFLP) markers were used to detect the relationships among 12 wild accessions and 62 groundcover chrysanthemum cultivars. Nineteen EcoRI/MseI primer combinations revealed 452 informative polymorphic bands with a mean of 23.8 bands and 71.5% polymorphic rate per primer pair. Jaccard’s coefficient of similarity varied from 0.64 to 0.89, indicating much genetic variation in chrysanthemums. The 74 accessions were classified into two major groups by unweighted pair group method with the arithmetic averages (UPGMA). The dendrogram showed that AFLP variability was closely correlated with both geographic distribution and traditional classification of the wild accessions. Among all accessions, genetic relationship was the most relevant factor in AFLP-marker clustering, whereas petal type was also informative. AFLP technology could be very efficient for discriminating species of chrysanthemum and its related genera and reconstruct their genetic relatedness.

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