scholarly journals Randomly Amplified Polymorphic DNA Analysis in the Genus Hosta

HortScience ◽  
2005 ◽  
Vol 40 (5) ◽  
pp. 1243-1245 ◽  
Author(s):  
Roger J. Sauve ◽  
Suping Zhou ◽  
Yingchun Yu ◽  
Wolfram George Schmid
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Traits ◽  
Phylogenetic Clustering ◽  
Single Primer ◽  
Cluster 2

A randomly amplified polymorphic DNA (RAPD) technique was used to identify and determine the phylogenetic relationships of 37 hosta accessions representing the major subgenera, sections and groups in the genus Hosta. Results of this study show that RAPD markers were able to differentiate not only the main groups, whose plants shared many genetic traits, but also cultivars within a species. Some accessions were identified by a single primer while others had high intercross linkage and required many markers for their separation. The phylogenetic clustering showed that H. plantaginea, the only night-blooming species, and H. ventricosa, the only known natural tetraploid, are unique and should be classified separately. The four species in the subgenus Bryocles, section Lamellatae H. venusta, H. minor, H. capitata, and H. nakaiana have very low genetic similarity since they do not share many amplified fragments. The other accessions were classified into four main clusters; cluster 1: H. venusta, H. tardiva, H. pycnophylla, H. tsushimensis `Ogon', H. montana, H. tibae, H. montana f. macrophylla, H. kikutii `Kikutii', H. longissima `Longifolia', H. rectifolia `Rectifolia', H. takahashii and H.`Undulata'; cluster 2: H. laevigata, H. sieboldiana, H. pycnophylla × H. longipes f. latifolia, H. longipes `Urajiro' and H. ibukiensis; cluster 3: H. capitata, H. kikutii `Polyneuron', H. nigrescens, H. kikutii `Yakusimensis', H. pachyscapa, H. kikutii `Caput-Avis', H. longipes f. latifolia, H. hypoleuca, H. okamotoi, H. densa and H. takiensis; and cluster 4: H. aequinoctiiantha, H. rupifraga, H. `Amanuma', H. minor and H. kikutii `Densa'.

scholarly journals Identification of Pecan Cultivars and Their Genetic Relatedness as Determined by Randomly Amplified Polymorphic DNA Analysis

2001 ◽  
Vol 126 (4) ◽  
pp. 474-480 ◽  
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna ◽  
Average Value

Genetic variation among pecan [Carya illinoinensis (Wangenh.) C. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint is presented for each of the pecan genotypes studied. The genetic relatedness between 43 cultivars was estimated using 100 RAPD markers. Genetic distances, based on the similarity coefficient of Nei & Li, varied from 0.91 to 0.46, with an average value of 0.66 among all cultivars. The phenetic dendrogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships.

The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 874-883 ◽  
Author(s):  
Nikolas Nikolaidis ◽  
Zacharias G. Scouras
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Dna Analysis ◽  
Restriction Site ◽  
Species Group ◽  
The Other ◽  
Complex Species ◽  
Restriction Site Maps ◽  
Montium Subgroup

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related. Key words : mtDNA restriction site maps, mtDNA size variations, Drosophila, phylogeny.

scholarly journals Molecular Evolution of Large Virulence Plasmid inShigella Clones and EnteroinvasiveEscherichia coli

2001 ◽  
Vol 69 (10) ◽  
pp. 6303-6309 ◽  
Author(s):  
Ruiting Lan ◽  
Brad Lumb ◽  
David Ryan ◽  
Peter R. Reeves
Keyword(s):  
Escherichia Coli ◽  
Molecular Evolution ◽  
Phylogenetic Relationships ◽  
Shigella Flexneri ◽  
The Other ◽  
Lateral Transfer ◽  
Virulence Plasmid ◽  
Main Body ◽  
Chromosomal Genes ◽  
Cluster 2

ABSTRACT Three genes, ipgD, mxiC, and mxiA,all in the invasion region of the Shigella virulence plasmid, were sequenced from strains representing a range ofShigella serotypes and from two enteroinvasiveEscherichia coli (EIEC) isolates. The plasmids can be classified into two relatively homogeneous sequence forms which are quite distinct. pINV A plasmids are found in Shigella flexneri strains F6 and F6A, S. boydii strains B1, B4, B9, B10, B14, and B15, S. dysenteriae strains D3, D4, D6, D8, D9, D10, and D13, and the two EIEC strains (M519 and M520). pINV B plasmids are present in S. flexneristrains F1A, F2A, F3A, F3C, F4A, and FY, two S. boydiistrains (B11 and B12), and S. sonnei. The D1 pINV plasmid is a recombinant with ipgD gene more closely related to those of pINV A but with mxiA andmxiC genes more closely related to those of pINV B. The phylogenetic relationships of the plasmid and those of the chromosomal genes of Shigella strains are largely consistent. The cluster 1 and cluster 3 strains tested (G.M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567–10572, 2000) have pINV A and pINV B plasmids, respectively. However, of the three cluster 2 strains (B9, B11, and B15), B9 and B15 have pINV A while B11 has a pINV B plasmid. Those Shigella (D8 and D10 and S. sonnei) and EIEC strains which do not group with the main body of Shigella strains based on chromosomal genes were found to have plasmids belonging to one or the other of the two types and must have acquired these by lateral transfer.

scholarly journals Analysis of Genetic Diversity among Selected Grasspea (Lathyrus sativus L.) Genotypes Using RAPD Markers

2007 ◽  
Vol 62 (11-12) ◽  
pp. 869-874 ◽  
Author(s):  
Durga P. Barik ◽  
Laxmikanta Acharya ◽  
Arup K. Mukherjee ◽  
Pradeep K. Chand
Keyword(s):  
Rapd Markers ◽  
Molecular Level ◽  
Crop Improvement ◽  
Dna Amplification ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Similar Morphology ◽  
Molecular Weights ◽  
Breeding Programmes ◽  
Lathyrus Sativus L

Randomly amplified polymorphic DNA (RAPD) technique was applied to assess the genetic variability among five selected genotypes of grasspea. Out of 30 random decamer primers tested for the present investigation 20 showed reproducible DNA amplification. A total of 257 loci were amplified of which 159 were polymorphic including 57 genotype-specific unique bands. Amplicons had molecular weights ranging from 3.0 kb to 0.1 kb. Majority amplicons were shared by most of the genotypes which indicated a very narrow genetic gap between them. The dendrogram constructed on the basis of RAPD data showed two clusters. The local genotype collected from Nayagarh was grouped along with IC-120451 and IC-120453, sharing a common node at an 82% similarity level. The other genotypes, IC-120478 and IC-120487, were located in the second clade having a common node at 84% similarity level. The investigation showed that though all the genotypes of grasspea were of apparently similar morphology there exists polymorphism at the molecular level, which can be exploited in breeding programmes aimed at crop improvement.

scholarly journals Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 42-50
Author(s):  
Muhammad Khoerol Anam ◽  
Adi Amurwanto ◽  
Kusbiyanto Kusbiyanto ◽  
Hendro Pramono ◽  
M Husein Sastranegara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Differences ◽  
Population Genetic Study ◽  
Randomly Amplified Polymorphic Dna ◽  
High Genetic Diversity ◽  
Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software.  The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations.  Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

scholarly journals Genetic Diversity in Muscadine and American Bunch Grapes Based on Randomly Amplified Polymorphic DNA (RAPD) Analysis

1996 ◽  
Vol 121 (6) ◽  
pp. 1020-1023 ◽  
Author(s):  
Xianping Qu ◽  
Jiang Lu ◽  
Olusola Lamikanra
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Average Genetic Distance ◽  
Separate Study ◽  
Randomly Amplified Polymorphic Dna ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically distinct types of grapes belonging to the subgenera Euvitis and Muscadinia in the genus Vitis are cultivated in the United States. The former is commonly called bunch grapes while the latter is usually called muscadine. Genetic diversity among these grapes was investigated using RAPD markers. Sixteen grape cultivars, with parentage including V. rotundifolia Michx., V. vinifera L., and several American Vitis species, were used for the RAPD analysis. A total of 156 RAPD markers was produced from 19 random primers, over 90% of which was polymorphic among the muscadine and the bunch grapes. Polymorphisms were lower within each subgenus. Relationships between these two subgenera were estimated based on band-sharing and cluster analysis. The average genetic distance between the bunch and the muscadine grape cultivars was 0.45. The results based on DNA analysis agree with isozyme data obtained from a separate study, which demonstrated that muscadine grapes share very few common alleles with American bunch grapes and European grapes.

scholarly journals Genetic Diversity among Witchhazel Cultivars Based on Randomly Amplified Polymorphic DNA Markers

1997 ◽  
Vol 122 (4) ◽  
pp. 529-535 ◽  
Author(s):  
Robert D. Marquard ◽  
Eric P. Davis ◽  
Emily L. Stowe
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
North American ◽  
Dna Markers ◽  
Rapd Markers ◽  
North American Species ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
The North ◽  
Sib Families

Forty selections, including 37 cultivars of Hamamelis spp., were evaluated for genetic similarities using randomly amplified polymorphic DNA (RAPD) markers. Cluster analysis identified seven groups, which included three groups of H. ×intermedia cultivars, two groups of H. vernalis, and one group each of H. mollis and H. japonica. Three H. ×intermedia cultivars, `Arnold Promise', `Westerstede', and `Carmine Red', did not group closely with the other 20 cultivars of H. ×intermedia. Selections of the North American species H. vernalis were quite distinct from the Asiatic selections. However, data are presented that suggest hybridization exist between Asiatic Hamamelis spp. and H. vernalis. Genetic similarities between known half-sib families provides evidence that the cultivar pairs `Arnold Promise'—`Winter Beauty' and `Carmine Red'—`Hiltingbury' are, themselves, not likely half-sibs.

scholarly journals Identification of Poinsettia Cultivars Using RAPD Markers

HortScience ◽  
1997 ◽  
Vol 32 (1) ◽  
pp. 122-124 ◽  
Author(s):  
Jing-Tian Ling ◽  
Roger Sauve ◽  
Nick Gawel
Keyword(s):  
Cluster Analysis ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
The Other ◽  
Euphorbia Pulcherrima ◽  
Randomly Amplified Polymorphic Dna ◽  
Upgma Cluster Analysis ◽  
Leaf Tissues ◽  
Components Analysis

Randomly amplified polymorphic DNA (RAPD) techniques were used to compare the DNA from leaf tissues of nine commercial poinsettia (Euphorbia pulcherrima Wild ex Klotzsch) cultivars. Amplification occurred in 57 out of 60 (95%) tested primers. Nine primers that revealed polymorphisms among cultivars were selected for further evaluation. Forty-eight RAPD bands were scored from these primers, and 33 (69%) were polymorphic. All tested cultivars could be discriminated with seven bands generated from primers OPB7 and OPC13. Results of a UPGMA cluster analysis and principal components analysis placed the nine cultivars into two groups: one group consisted of `Jingle Bells', `Supjibi', and `V-17 Angelika', the other of `V-14 Glory', `Red Sails', `Jolly Red', and `Freedom'. `Lilo Red' and `Pink Peppermint' belonged to the latter group, but were relatively distant from other cultivars in that group. These results indicate that RAPDs are efficient for identification of poinsettia cultivars and for determination of the genetic relationships among cultivars.

Genetic characterization of dahlem red layers by PCR-RAPD

2016 ◽  
Author(s):  
Ch. Shivaprasad ◽  
B. Rarmesh Gupta ◽  
R. N. Chatterjee
Keyword(s):  
Genetic Distance ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Characterization ◽  
Dna Polymorphisms ◽  
Randomly Amplified Polymorphic Dna ◽  
Band Frequency

A total of one hundred Randomly Amplified Polymorphic DNA (RAPD) markers were utilized to detect the DNA polymorphisms in a total of 48 full sib mated, half sib mated and non-in bred groups of Dahlem Red birds. Twenty one per cent of the primers tested yielded distinct polymorphic RAPD profiles. Out of 341 amplified bands 204 bands (59.82 %) were found to be polymorphic. The genetic similarity ranged from 83.94 to 87.90 % and, 81.14 to 85.25 % with in group based on band sharing and frequency respectively. Full sib group showed higher genetic similarity then non-in bred group. The genetic similarity based on band frequency ranged from 88.07 to 90.18 %, based on band frequency varied from 72.78 to 79.53 percent. The full sib and half sib groups showed maximum genetic similarity. The genetic distance between full sib and non-inbred groups was found to be the maximum (0.3176), while it was minimum between full sib and half sib groups.

Study of Genetic Diversity among the Seeded Banana Found in the Northeast Region of India by RAPD (Randomly Amplified Polymorphic DNA) Analysis

2017 ◽  
Vol 5 (2) ◽  
pp. 85-92 ◽  
Author(s):  
Premabati Thangjam ◽  
◽  
Robert Thangjam
Keyword(s):  
Dna Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
The Other ◽  
Resolving Power ◽  
Sustainable Utilization ◽  
Randomly Amplified Polymorphic Dna ◽  
Dissimilarity Index ◽  
Marker Index ◽  
Northeast Region

The RAPD (Random Amplified Polymorphic DNA) technique was used to evaluate the genetic variation among twenty one wild bananas found in the northeastern region. Out of the ten primers used eight give 100% polymorphism. Among the ten primers used UBC-425 gives the highest polymorphic information content, resolving power as well as highest marker index. The highest dissimilarity index was obtained between the sample MZ1 (Changkha from Mizoram) and AR12 (kutikol from Arunachal) scoring the dissimilarity index of 0.85 whilst the lowest/highest dissimilarity/similarity was found between AS13 and AS14 (Athiakol and Bhimkol from Assam) scoring the dissimilarity index of 0.17. This result indicates that AS13 and AS14 were more closely related as compared with all the other accessions studied while MZ1 and AR12 were highly dissimilar. Dendrogram based on Nei’s coefficient reveals two major groups which were again sub-grouped into six minor clusters. The dendrogram was not able to clearly distinguish the different genome groups in the study. The study reveals significant level of diversity among the wild bananas studied and it could be utilized for future conservation and sustainable utilization of the genetic resources.

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