scholarly journals DNA Amplification Fingerprinting Used to Distinguish Series of Cutting, Seedling, and Ivy Leaf Geranium

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 565c-565 ◽  
Author(s):  
Terri Woods Starman ◽  
Shane Abbitt
Keyword(s):  
Numerical Taxonomy ◽  
Patent Protection ◽  
Genetic Relationships ◽  
Leaf Tissue ◽  
Dna Amplification ◽  
Separate Branch ◽  
Pelargonium Peltatum ◽  
Ivy Geranium ◽  
Analysis System ◽  
Distance Estimator

The objective was to distinguish between series of cultivars of Pelargonium xhortorum (zonal geranium), Pelargonium hybrids (seed geranium), and Pelargonium peltatum (ivy leaf geranium) using DNA amplification fingerprinting (DAF) demonstrating the utility of DAF for patent protection to prevent infringement of inventor's rights. Leaf tissue of 10 plants of each cultivar of seedling geranium was bulked for DNA extraction, and cutting and ivy geranium cultivars were bulks of five plants of each cultivar. Isolated DNA from different cultivars of a series were bulked together in their respective series. Seedling geranium series included Dynamo, Glamour, Multibloom, Orbit, Pinto, and Ringo 2000. Cutting geranium series included Designer and Showcase. Ivy geraniums were from the Guillou group. Amplification was with one of two octamer primers, followed by reamplifying with one of four different mini hairpin primers. Gels were visually scored for presence or absence of bands. The four primers generated 336 bands. The average number of bands (_1000 bp) per primer was 40. Twenty percent of bands were polymorphic and distinguished between each series of cultivars. Genetic relationships were evaluated by SAHN cluster analysis based on the distance estimator of Dice using the NTSYS-pc program (Numerical taxonomy and multivariate analysis system, version 1.8). Series were grouped according to species. Seedling geraniums were in one large group, the two cutting geraniums were grouped together and the ivy leaf geraniums were a separate branch.

scholarly journals Evaluating Genetic Relationships of Geranium Using Arbitrary Signatures from Amplification Profiles

HortScience ◽  
1997 ◽  
Vol 32 (7) ◽  
pp. 1288-1291 ◽  
Author(s):  
Terri Woods Starman ◽  
Shane Abbitt
Keyword(s):  
Cluster Analysis ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Principal Coordinate Analysis ◽  
Separate Branch ◽  
Amplification Protocol ◽  
Pelargonium Peltatum ◽  
Ivy Geranium ◽  
And Cluster Analysis ◽  
Distance Estimator

Our objective was to distinguish between eight cultivars of two geranium species, Pelargonium ×hortorum L.H. Bailey (cutting and seed geranium) and Pelargonium peltatum (L.) L'Hér. ex Ait. (ivy geranium), and evaluate their genetic relationships using the nucleic acid scanning techniques of DNA amplification fingerprinting (DAF) and/or arbitrary signatures from amplification profiles (ASAP). Cultivars used in the study represented three commercial types: cutting, seed, and ivy geranium. Two seed geranium cultivars from each of the Dynamo and Orbit series were included. Cutting geranium cultivars were `Designer Lilac Chiffon' and `Starburst Red' and the ivy geraniums were `Bernardo Guiber' and `Vinco Guivin'. The ASAP amplification protocol used one of two arbitrary octamer primers, followed by reamplification with one of four different minihairpin primers. ASAP profiles were complex, with 66% of bands being polymorphic and useful in distinguishing between cultivars. Genetic relationships were evaluated by principal coordinate analysis and cluster analysis based on the Jaccard distance estimator. This analysis grouped cultivars by species according to commercial type, i.e., seed geraniums were in one large group, the cutting geraniums were grouped together, and the ivy geraniums were a separate branch.

scholarly journals Distinguishing Poinsettia Cultivars and Evaluating Their Genetic Relationships using DNA Fingerprinting

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 500A-500
Author(s):  
Terri Woods Starman ◽  
Shane Abbitt
Keyword(s):  
Dna Fingerprinting ◽  
Numerical Taxonomy ◽  
Genetic Relatedness ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Euphorbia Pulcherrima ◽  
Pedigree Data ◽  
Analysis System ◽  
Distance Estimator

The objective was to distinguish between cultivars and evaluate genetic relatedness of poinsettia (Euphorbia pulcherrima) using two methods of DNA fingerprinting—DNA Amplification Fingerprinting (DAF) and Arbitrary Signatures from Amplification Profiles (ASAP). Eleven red poinsettia cultivars were studied, including `Celebrate 2', `Darlyne', `Freedom Red', `Lilo', `Nutcracker Red', `Peterstar Red', `Petoy', `Red Sails', `Supjibi', `V-14 Glory', and `V-17 Angelika'. Amplification was with 10 octamer primers. Gels were visually scored for presence or absence of bands. The 10 primers generated 336 bands. The average number of bands (≈1000 bp) per primer was 34 ranging from 19 to 43. Thirty-one percent of bands were polymorphic and distinguished between each cultivar. The number of unique profiles varied from two to nine. Genetic relationships were evaluated by SAHN cluster analysis based on the distance estimator of Jaccard using the NTSYS-pc program (Numerical taxonomy and multivariate analysis system, version 1.8). The resulting dendrogram closely agreed with known pedigree data. ASAP analysis was used to further assess cultivar identification of two cultivars that were genetically and morphologically similar. Markers were found that separated `Nutcracker Red' and `Peterstar Red'. ASAP analysis separated cultivars within the Freedom series that DAF failed to distinguish. Two cultivars in the Freedom series, `Jingle Bells' and `Marble', were characterized from other cultivars in the series with ASAP.

scholarly journals DNA Amplification Fingerprinting Identifies Closely Related Chrysanthemum Cultivars

1996 ◽  
Vol 121 (6) ◽  
pp. 1043-1048 ◽  
Author(s):  
M.C. Scott ◽  
G. Caetano-Anollés ◽  
R.N. Trigiano
Keyword(s):  
Cluster Analysis ◽  
Patent Protection ◽  
Average Distance ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Dna Polymorphisms ◽  
Arithmetic Means ◽  
Pair Group ◽  
Bulked Dna ◽  
Phylogenetic Studies

DNA amplification fingerprinting (DAF) was used to study genetic relationships between closely related chrysanthemum cultivars (Dendranthema grandiflora Tzvelev.). Twenty-one cultivars were examined that belonged to the Anne, Blush, Boaldi, Charm, Davis, and Pomona series (families). The genetic variability of cultivars within and between series was evaluated using eleven arbitrary octamer primers. A few polymorphic characters uniquely identified closely related cultivars within each of the series. In contrast, many DNA polymorphisms were observed between members of the different series. Phenetic patterns were established by unweighted pair group cluster analysis using arithmetic means (UPGMA) and principal coordinate analysis (PCO). The average distance between series was 10-fold greater than between cultivars within a series. DNA from all cultivars belonging to a series were also bulked to generate profiles containing unique amplified products for each series. Cluster analysis and PCO of bulked DNA clearly grouped Charm and Pomona together. However, series grouping did not correspond to morphology of inflorescence types. The results demonstrate the utility of the DAF technique in distinguishing clonal materials and its potential use for patent protection, phylogenetic studies, and for identifying useful markers in breeding applications.

scholarly journals Phylogenetic Analysis of the Darkfin Hind, Cephalopholis urodeta (Serranidae) Using Partial Mitochondrial CO1 Gene Sequences (Analisis Filogenetik Cephalopholis urodeta (Serranidae) Menggunakan Runutan Gen CO1 Mitokondria Parsial)

2015 ◽  
Vol 20 (1) ◽  
pp. 38 ◽  
Author(s):  
Yanti Ariyanti ◽  
Achmad Farajallah ◽  
Irma Shita Arlyza
Keyword(s):  
Pacific Ocean ◽  
Arabian Sea ◽  
North Pacific Ocean ◽  
Genetic Relationships ◽  
Gene Segment ◽  
Sampling Point ◽  
Tissue Samples ◽  
South Sulawesi ◽  
Separate Branch ◽  
The World

Cephalopholis merupakan salah satu genera terbesar dalam subfamili Epinephelinae yang memiliki banyak species. Secara fenotip, C. urodeta dewasa mirip dengan juvenil C. sonnerati karena memiliki ciri mencolok yaitu garis yang menyudut pada sirip ekor. Untuk memahami hubungan genetik pada spesies ikan ini, maka dilakukan analisis molekuler menggunakan ruas gen CO1. Sejumlah spesies ikan (famili Serranidae) dikumpulkan dari wilayah Sulawesi Selatan seperti Sinjai dan Kepulauan Selayar. Karakter fenotip diidentifikasi menggunakan buku katalog spesies kerapu dunia FAO, kemudian sampel yang diduga C. urodeta secara morfologi dipisahkan. Jaringan yang digunakan sebagai sumber DNA adalah jaringan otot bagian dorsal. Berdasarkan sebagian runutan gen CO1, diyakini bahwa sampel tersebut adalah C. urodeta. Runutan basa nukleotida dari sampel dibandingkan dengan 22 runutan basa nukleotida C. urodeta dari GenBank. Berdasarkan rekonstruksi pohon filogeni, C. urodeta dari Sinjai dan Kepulauan Selayar mengelompok dengan C. urodeta dari berbagai tempat seperti Polynesia, Mariana Utara, Filipina, pulau-pulau di sekitar Madagascar (Ouest, St. Gilles, Canyon, Cimetiere, Jaune) dan Adaman, sedangkan sampel dari Laut Arab di lepas pantai India berada pada cabang yang terpisah. Penelitian ini menyatakan bahwa C. urodeta yang melibatkan beberapa tempat dari berbagai perairan seperti Samudera Pasifik bagian Selatan (Polynesia), Samudera Pasifik bagian Utara (Northern Mariana), Laut China Selatan (Filipina), Teluk Bengal (Andaman), Laut Laccadive (reunion of Ouest, St. Gilles and Cimetiere), Laut Arab dan Indo Pasifik Barat (Indonesia) memiliki perbedaan jarak genetik yang kecil. Hal ini berimplikasi pada pemahaman pola migrasi spesies tersebut dan sebagai bahan pertimbangan pengambilan kebijakan konservasi. Kata kunci: Cephalopholis urodeta, CO1, filogenetik, Serranidae, Sulawesi Selatan Cephalopholis is one of the largest genera belonging to Subfamilly Epinephelinae, which has various species. Phenotypically, an adult C. urodeta similar to a juvenile of C. sonnerati, since both of them have a striking trait, two white oblique stripes or bands on the caudal fins. This work was conducted to investigate the genetic relationships of this species using CO1 gene segment. Fish were collected from several sampling point in South Sulawesi areas such as Sinjai and Selayar Island. The phenotypic characterizations were identified using the FAO species catalogue of groupers of the world, and the species that seemed to have C. urodeta morphology then separated. Tissue samples from dorsal muscle tissue were used as the source of DNA. Using part of the CO1 gene sequence, it can be confirmed that our samples are exactly C. urodeta species. The 22 C. urodeta sequences from GeneBank compared with our sequences. Interestingly, because based on the phylogenetic tree, our sequences clustered with the other C. urodeta sequences from several part of the world except the Arabian Sea off the coast of India, which is a separate branch. The present study reveals less genetic distance in C. urodeta than some other parts of the ocean as follows; South Pacific Ocean (Polynesia), North Pacific Ocean (Northern Mariana), South China Sea (Philippines), Andaman, west coast of Réunion Island, Arabian Sea and Indo West Pacific (Indonesia). This has implications for understanding the migration pattern of the species and may affect conservation policy decisions. Keywords: Cephalopholis urodeta, CO1, phylogenetics, Serranidae, South Sulawesi

scholarly journals DNA AMPLIFICATION FINGERPRINTING (DAF) IDENTIFIES CLOSELY RELATED CULTIVARS IN THREE SERIES OF CHRYSANTHEMUMS

HortScience ◽  
1995 ◽  
Vol 30 (3) ◽  
pp. 427a-427
Author(s):  
M.C. Scott ◽  
G. Caetano-Anollés ◽  
R.N. Trigiano
Keyword(s):  
Patent Protection ◽  
Average Distance ◽  
Dna Amplification ◽  
Genetic Distances ◽  
Dendranthema Grandiflora ◽  
Polymorphic Loci ◽  
Phylogenetic Studies ◽  
Upgma Cluster Analysis ◽  
Dna Profiles ◽  
Marker Comparison

The genetic distance of closely related cultivars of Dendranthema grandiflora (chrysanthemum) was assessed using DAF. Thirteen cultivars of chrysanthemum included in the study were members of the following series: Charm (five), Davis (four), and Pomona (four). The genetic variability within and between series were evaluated using 11 arbitrary octamer primers. A few polymorphic loci were evident that uniquely identified closely related cultivars within a series. In contrast, there were many polymorphisms between members of different series. Genetic distances between cultivars within and between series were calculated using marker comparison and UPGMA (cluster analysis). The average distance between series was 10-fold greater than between cultivars within a series. DNA from all cultivars belonging to a series also were bulked to generate DNA profiles containing unique amplified products for each series. Polymorphic loci that were generated by the DAF technique possibly could be used for patent protection and phylogenetic studies and may be useful in breeding for chrysanthemums.

scholarly journals Molecular Phylogeny and DNA Amplification Fingerprinting of Petunia

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 777F-778
Author(s):  
Teresa A. Cerny ◽  
Terri W. Starman
Keyword(s):  
Molecular Markers ◽  
Molecular Phylogeny ◽  
Phylogenetic Tree ◽  
Leaf Tissue ◽  
Dna Amplification ◽  
Seed Source ◽  
Polymorphic Loci ◽  
Presence And Absence ◽  
Different Sources

Seed of five species of petunia and 10 cultivars of Petunia xhybrida were obtained from several sources and plants were fingerprinted using DNA amplification fingerprinting (DAF). Within some species, variable fingerprints were generated between individual plants from the same seed source and/or different sources. Consistencies were found among DAF profiles by bulking the leaf tissue from 10 different plants, but not five plants. Each of 10 octamer primers used during the study revealed polymorphic loci between the species and cultivars. Among the 201 bands produced, 146 (73%) loci were polymorphic and these could be used to distinguish between each of the species and cultivars. Scoring for presence and absence of the amplified bands was used to generate a phylogenetic tree and to calculate the pairwise distances between each of the taxa using parsimony (PAUP) analysis. The tree generated using DAF molecular markers separated P. axillaris from P. parodii (two white-flowered species), and distinguished between the violet-flowered species, P, inflata, P. integrifolia, and P. violacea.

scholarly journals Nucleic Acid Scanning Techniques Distinguish Closely Related Cultivars of Poinsettia

HortScience ◽  
1999 ◽  
Vol 34 (6) ◽  
pp. 1119-1122 ◽  
Author(s):  
Terri Woods Starman ◽  
Xiangrong Duan ◽  
Shane Abbitt
Keyword(s):  
Cluster Analysis ◽  
Nucleic Acid ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Euphorbia Pulcherrima ◽  
Molecular Fingerprinting ◽  
Oligonucleotide Primers

DNA amplification fingerprinting (DAF) was used to evaluate the genetic relationships among 11 cultivars of poinsettia (Euphorbia pulcherrima Willd.). Amplification was with 10 octamer oligonucleotide primers that generated 336 DNA bands. Thirty-one percent of the bands were polymorphic and distinguished among cultivars. Genetic relationships were evaluated by cluster analysis, and the resulting dendrogram closely agreed with published cultivar relationships. Arbitrary signatures from amplification profiles (ASAP) were further used to characterize two cultivars, `Nutcracker Red' and `Peterstar Red', that were previously found to be genetically and morphologically similar, as well as five cultivars in the “Freedom” series. The DAF products generated with arbitrary octamer primers were reamplified with mini-hairpin decamer primers in these experiments. The ASAP profiles were complex and yielded a total of 231 bands, 38% of which were polymorphic and capable of distinguishing each Freedom cultivar. Five of the eight primer combinations distinguished `Nutcracker Red' from `Peterstar Red'. Thus, closely related cultivars of poinsettia can be separated using new and improved molecular fingerprinting protocols.

scholarly journals Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rachel Rattner ◽  
Shree Prasad Thapa ◽  
Tyler Dang ◽  
Fatima Osman ◽  
Vijayanandraj Selvaraj ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Range ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Weed Species ◽  
Protein Coding ◽  
Spiroplasma Citri ◽  
Beet Leafhopper ◽  
Separate Branch

Abstract Background Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas. Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3–3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3–3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597–2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3–3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.

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