scholarly journals Inter- and Intraspecific RAPD Variation in Four Ipomoea Species

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 773A-773
Author(s):  
Dapeng Zhang ◽  
Wanda W. Collins
Keyword(s):  
Genetic Similarity ◽  
Rapd Analysis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Similarity Coefficients ◽  
Ipomoea Trifida ◽  
Pair Group ◽  
Ipomoea Triloba ◽  
Ipomoea Species ◽  
Unweighted Pair Group Method

Randomly amplified polymorphic DNA (RAPD) analysis was performed on 18 accessions belonging to four different species of the genus Ipomoea, including sweetpotato and three related species. Twenty-two out of 30 primers tested revealed polymorphisms among these four species. Eight primers were selected on the basis of the number and repeatability of polymorphism produced. With these, a total of 98 different DNA bands were obtained and 85% of them were polymorphic. Based on the presence/absence of the bands, a genetic similarity among accessions and among species was calculated. Unweighted pair-group method with arithmetical averages (UPGMA) based on the similarity coefficients clearly discriminated these four species. Ipomoea trifida and sweetpotato share more genetic similarity. Ipomoea triloba and I. leucantha fall into another cluster. This study demonstrated that RAPD techniques can be a very useful tool for genotype/accession identification and studying the genetic relationship among genotypes/accessions of sweetpotato and among species of Ipomoea.

scholarly journals Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

2004 ◽  
Vol 129 (5) ◽  
pp. 690-697 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Genetic Similarity ◽  
Near Infrared ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Limited Information ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Ornamental Foliage Plants ◽  
Pair Group

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.

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 Molecular Analysis of Hybrids among the Ornamental Eucalypts Eucalyptus macrocarpa, E. pyriformis, and E. youngiana

2001 ◽  
Vol 126 (3) ◽  
pp. 336-339 ◽  
Author(s):  
Kirsty Neaylon ◽  
Kate L. Delaporte ◽  
Margaret Sedgley ◽  
Graham G. Collins ◽  
John G. Conran
Keyword(s):  
Genetic Similarity ◽  
Minimum Spanning Tree ◽  
Molecular Data ◽  
Pcr Analysis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Mature Trees ◽  
Pair Group ◽  
Polymerase Chain

The potential for hybridization among three species of Eucalyptus L'Hér in the Series Macrocarpae, E. macrocarpa Hook (Mottlecah), E. pyriformis Turcz. (pear-fruited mallee), and E. youngiana F. Muell. (large-fruited mallee), was investigated using molecular data generated by randomly amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) analysis. Samples of DNA from seedlings derived from controlled pollinations, and from different individuals from each species, were amplified with six different 10-mer primers. The presence or absence of RAPD fragments was used to generate a dendrogram based on genetic similarity, an ordination derived by multidimensional scaling (MDS), and a minimum spanning tree (MST) to show the relative links and dissimilarities between the individuals tested. Two clusters were identified on the unweighted pair-group method arithmetric average dendrogram. The first included all of the E. macrocarpa genotypes and all but one of the E. macrocarpa hybrids. The second included all of the E. youngiana and E. pyriformis genotypes and their hybrids. The MDS ordinations placed the hybrid seedlings between the parent species. From the 30 progeny investigated, 28 were assessed from the molecular data to be hybrids from controlled pollinations. The remaining two seedlings appeared to be derived from self-pollination. The parentage of two mature trees, thought to be natural hybrids involving the three species, was also investigated. One was confirmed as a cross between E. youngiana and E. pyriformis, but the second was less certain because of its low genetic similarity to all other individuals, and may be a hybrid involving species not included in this study.

scholarly journals 555 Estimation of Genetic Diversity among Citrullus Accessions using RAPD Markers

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 491D-491
Author(s):  
Amnon Levi ◽  
Claude E. Thomas ◽  
Anthony P. Keinath ◽  
Todd C. Wehner
Keyword(s):  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Plant Introduction ◽  
Group Method ◽  
Similarity Coefficients ◽  
High Confidence ◽  
Core Collections ◽  
The Third ◽  
Pair Group

Genetic relatedness was estimated among 42 U.S. plant introduction (PI) accessions of the genus Citrullus (37 PIs of which were reported to have disease resistance and five watermelon cultivars) using 30 RAPD primers. These primers produced 662 RAPD markers that could be scored with high confidence. Based on these markers, genetic similarity coefficients were calculated, and a dendrogram was constructed using the unweighted pair-group method with arithmatic average (UPGMA). The analysis delineated three major clusters. The first cluster consisted of a group of five watermelon cultivars, a group of C. lanatus var. lanatus accessions and a group of C. lanatus var. lanatus accessions that contained some C. lanatus var. citroides genes. The second cluster consisted of the C. lanatus var. citroides accessions, while the third cluster consisted of the C. colocynthis accessions. The two C. lanatus clusters differentiated from each other and from the C. colocynthis cluster at the level of 58.8% and 38.9% genetic similarity. Our results indicate that closely related Citrullus PIs may have resistances to the same diseases. Thus, molecular markers may be a useful tool in the development of core collections of Citrullus PIs with resistance to diseases.

Evaluation of variability in five linseed (Linum usitatissimum L.) genotypes using agro‐morphological characters and RAPD analysis

2011 ◽  
Vol 1 (1) ◽  
pp. 43-47
Author(s):  
Towseef Mohsin Bhat ◽  
Rajdeep Kudesia ◽  
Manoj Kumar Srivastava ◽  
Sazada Sidiqqui
Keyword(s):  
Linum Usitatissimum ◽  
Rapd Analysis ◽  
Morphological Characters ◽  
Germination Percentage ◽  
Arithmetic Mean ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Linum Usitatissimum L ◽  
Pair Group ◽  
Number Of Leaves

Analysis of the extent and distribution of genetic diversity in crop plants is essential for optimizing sampling and breeding strategies. Morphological characters and Randomly amplified polymorphic DNA (RAPD) was used to estimate genetic variability among 5 genotypes of linseed (Linum usitatissimum L). Selected four RAPD primers generated 140 bands, 80 of which were found to be polymorphic. All the primers produced polymorphic amplification products, however the extent of polymorphism varied with each primer .The percentage of polymorphism generated by primer was OPG‐03 (85.029%), OPH‐12(45.94%), OPC‐02(45.94%) and OPG‐18(64.28%). Great variation among morphological characters viz., root length, stem diameter, number of leaves, germination percentage and radicle length was observed. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram obtained from cluster analysis using Jaccard’s similarity coefficient resulted into three clusters. Cluster1 comprised of two genotypes (Jawhar and saharda), cluster II also comprised of two genotypes (T‐397 and KL‐1) and cluster III consisted of only one genotype Garima, which was interesting to observe that the Garima was distinct from all other four experimental varieties and sole constituent of cluster III. All the genotypes could be discriminated from one another using combined profiles of 4 primers.

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 Use of AFLP molecular markers for estimating genetic similarity of alfalfa (Medicago sativa L. Sl.)

2009 ◽  
Vol 60 (1) ◽  
pp. 61-71 ◽  
Author(s):  
Agnieszka Dobrzycka ◽  
Zbigniew Broda ◽  
Jan Bocianowski ◽  
Anna Ćwiklinska
Keyword(s):  
Molecular Markers ◽  
Medicago Sativa ◽  
Genetic Similarity ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Means ◽  
Pair Group ◽  
Hierarchical Grouping ◽  
Synthetic Populations ◽  
Medicago Sativa L

Use of AFLP molecular markers for estimating genetic similarity of alfalfa (Medicago sativaL. Sl.)The aim of study was to determine genetic similarity among sixteen alfalfa populations using the AFLP technique. Plant material was selected considering the high genotypic variability. It included populations of different origin: native forms of alfalfa (secondary ecotypes), inbred lines, single hybrids, synthetic populations, varieties and mutants. Analysis was carried out using 10 combinations of primers. It was noticed, that in case of the studied alfalfa populations, the highest polymorphism was obtained using primers with three selective nucleotides. The genetic similarity coefficients were calculated by the method of Nei and Li. Those coefficients were used for the hierarchical grouping of objects by the unweighted pair group method of arithmetic means. Results of the grouping were presented in the form of dendrogram. Values of coefficients ranged from 0.3311 (between the inbred F line and the Ulstar variety) to 0.8076 (between ecotype 27 and the synthetic population Syn 7-3). Dendrogram of genetic similarity obtained in this way did not fully correspond with the known data about the studied populations' origin. Considering the genetic similarity, inbreed line F was the most outlying from the studied populations of alfalfa.

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.

scholarly journals Genetic Variability in Bangladeshi Aromatic Rice through RAPD Analysis

2014 ◽  
Vol 3 (3) ◽  
pp. 107 ◽  
Author(s):  
Mehfuz Hasan ◽  
Mohammad Sharif Raihan
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Oryza Sativa L ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Aromatic Rice ◽  
Similarity Coefficients ◽  
Rice Varieties ◽  
Pair Group ◽  
Minimum Number

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.

AFLP fingerprinting analysis of genetic polymorphism of 12 indigenous chicken breeds

2007 ◽  
Vol 4 (1) ◽  
pp. 33-38 ◽  
Author(s):  
Gao Yu-Shi ◽  
Tu Yun-Jie ◽  
Tong Hai-Bing ◽  
Wang Ke-Hua ◽  
Chen Kuan-Wei
Keyword(s):  
Dna Fingerprinting ◽  
Genetic Similarity ◽  
Group Method ◽  
Similarity Coefficients ◽  
Indigenous Chicken ◽  
Aflp Data ◽  
Pair Group ◽  
Pooled Dna ◽  
Chicken Breeds ◽  
Polymorphic Bands

AbstractA total of six amplified fragment length polymorphism (AFLP) primer combinations were used to detect genetic variation of pooled DNA in a sample of 12 chicken breeds indigenous to China, and AFLP DNA fingerprinting of each chicken breed was constructed. Polymorphic bands, specific bands and genetic similarity coefficients of 12 chicken breeds were calculated from AFLP data. A total of 279 polymorphic bands were generated by the six primer combinations, giving, on average, 46.5 polymorphic markers detected per primer combination. Nine specific bands were produced in the pooled DNA of Jiuyuan black and Dongxiang black chickens. However, one specific band was produced in the pooled DNA of Wenchang and Xingyi bantam chickens. An unweighted-pair-group method using average linkages (UPGMA) cluster analysis revealed that the 12 chicken breeds could be divided into three groups. Genetic similarity coefficients and the UPGMA tree of the 12 chicken breeds were consistent with their breeding history as well as their geographical distribution. Based on AFLP DNA fingerprinting, genetic diversity, genetic relationship and identification of chicken breeds can be analysed.

Sign in / Sign up

Export Citation Format

Share Document