AFLP Analysis of Genetic Relationships among Container-grown Anthurium Cultivars

Anthurium is the largest genus in the family Araceae, consisting of about 1000 species. Anthuriums are valued for their colorful spathes and traditionally used as cut flowers. With the introduction of compact cultivars through breeding, a series of container-grown cultivars have been released and widely produced as flowering foliage plants. However, limited information is available about genetic relatedness among these container-grown cultivars. This study analyzed genetic relationships of 58 cultivars 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 94 to 115 scorable fragments. A total of 647 AFLP fragments were detected of which 401 were polymorphic (67%). All cultivars were clearly differentiated by their AFLP finger-prints. A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UPGMA) technique and a principal coordinated analysis (PCA) was used to analyze the relationships. The 58 cultivars were divided into three clusters; clusters I, II, and III had 40, 10, and 8 cultivars, respectively. Most commonly grown cultivars were positioned in cluster I, where had Jaccard similarity coefficients among them ranged from 0.7 to 0.98. Eighteen of the 40 shared Jaccard similarity coefficient of 0.8 or higher, indicating that genetic diversity for cultivated container-grown Anthurium is needed.

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Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.5.0690 ◽

2004 ◽

Vol 129 (5) ◽

pp. 690-697 ◽

Cited By ~ 4

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.

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Genetic Relationships of Spathiphyllum Cultivars Analyzed by AFLP Markers

HortScience ◽

10.21273/hortsci.41.4.968a ◽

2006 ◽

Vol 41 (4) ◽

pp. 968A-968 ◽

Cited By ~ 1

Author(s):

Jianjun Chen ◽

Richard J. Henny ◽

Pachanoor S. Devanand ◽

Chih-Cheng T. Chao

Keyword(s):

Near Infrared ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Aflp Markers ◽

Group Method ◽

Similarity Coefficients ◽

Breeding Lines ◽

Arithmetic Average ◽

Commercial Cultivars ◽

Peace Lily

Peace lily (Spathiphyllum Schott) is one of the most popular tropical ornamental foliage plants and is used worldwide for interiorscaping. However, little information is available on the genetic relationships of cultivars. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed genetic relatedness of 63 commercial cultivars and breeding lines. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. 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). The 63 cultivars were divided into four clusters. All commercial cultivars or breeding lines resulted from crosses of some of the cultivars, a total of 45, were positioned in cluster I with Jaccard's similarity coefficients between 0.61 and 0.88. There was only one cultivar in cluster II. Cluster III contained 16 cultivars; they are either species or breeding lines generated from interspecific hybridization. Cluster IV had one unknown species. This study provides genetic evidence as to why cultivars from cluster I and III are not readily crossable because the Jaccard's similarity coefficient between the two clusters was only 0.35. Results also indicate that commercial cultivars are genetically close. Strategies for increasing genetic diversity of cultivated peace lily should be sought for future breeding efforts.

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Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers

Genome ◽

10.1139/g02-093 ◽

2002 ◽

Vol 45 (6) ◽

pp. 1175-1180 ◽

Cited By ~ 29

Author(s):

F J Massawe ◽

M Dickinson ◽

J A Roberts ◽

S N Azam-Ali

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Geographic Origin ◽

Bambara Groundnut ◽

Aflp Markers ◽

Group Method ◽

Aflp Analysis ◽

Vigna Subterranea ◽

Marker Assisted Breeding ◽

Pair Group

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.Key words: under-utilized, African legume, molecular markers.

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Polymorphism and Genetic Relationships among Tea Genotypes from Turkey Revealed by Amplified Fragment Length Polymorphism Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.134.4.428 ◽

2009 ◽

Vol 134 (4) ◽

pp. 428-434 ◽

Cited By ~ 9

Author(s):

Salih Kafkas ◽

Sezai Ercişli ◽

Yıldız Doğan ◽

Yaşar Ertürk ◽

Ayhan Haznedar ◽

...

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Amplified Fragment Length Polymorphism ◽

Group Method ◽

Aflp Analysis ◽

Black Sea Region ◽

Pair Group

Individuals in most countries around the world drink tea (Camellia sinensis). Tea drinking has attained ceremonial status in many places as a social and medicinal beverage. Although tea is of great importance in Turkey's economy, little is known about the pattern of genetic variation among the various tea genotypes grown in Turkey. A total of 32 tea genotypes found at the Ataturk Tea and Horticulture Research Institute in the eastern Black Sea region of Turkey were sampled. Fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis were applied for molecular characterization. The AFLP analysis with six primer combinations generated 835 fragments of which 567 were polymorphic, corresponding to 69.8% polymorphism. Resolving powers of the AFLP primers ranged from 62.6 to 81.9, yielding a total of 437.8; the polymorphic information content (PIC) ranged from 0.76 to 0.83, with an average of 0.79. Genetic similarity values ranged from 0.68 to 0.92, with an average of 0.76. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) and principal coordinate analysis (PCoA) revealed that all tea genotypes could be clearly divided into four distinct clusters. The results of this study will provide valuable information to the tea cultivar breeding program for the purpose of parental selection.

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Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

Canadian Journal of Plant Science ◽

10.4141/p04-110 ◽

2006 ◽

Vol 86 (1) ◽

pp. 251-257 ◽

Cited By ~ 16

Author(s):

Zhao Weiguo ◽

Zhou Zhihua ◽

Miao Xuexia ◽

Wang Sibao ◽

Zhang Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Pair Group ◽

Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

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555 Estimation of Genetic Diversity among Citrullus Accessions using RAPD Markers

HortScience ◽

10.21273/hortsci.35.3.491d ◽

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.

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Genetic Diversity and Relationships among Local Olive (Olea europeaea L.) Genotypes from Gaziantep Province and Notable Cultivars in Turkey, Based on SSR Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44210439 ◽

2016 ◽

Vol 44 (2) ◽

pp. 557-562

Author(s):

Ebru SAKAR ◽

Hulya UNVER ◽

Mehmet ULAS ◽

Biljana LAZOVIC ◽

Sezai ERCISLI

Keyword(s):

Ssr Markers ◽

Genetic Relationships ◽

Group Method ◽

Similarity Coefficients ◽

Olive Cultivar ◽

Banding Patterns ◽

Pair Group ◽

Ssr Analysis ◽

Ssr Primers ◽

Similarity Ratio

Olive and olive oil have a prominent place in the cultures of the countries within the Mediterranean basin including Turkey. The genetic relationships among 30 olive (Olea europaea L.) genotypes sampled from Gaziantep province in Turkey were examined using 10 simple sequence repeat (SSR) markers (DCA9, DCA11, DCA15, DCA18UDO4, UDO9, UDO11, UDO12, UDO22, UDO24). Also, three well known Turkish and one foreign olive cultivar were also included within the SSR analysis. The number of alleles per locus of the SSR markers ranged from 5 (DCA15, UDO9) to 14 (DCA9) (average 7.9), for a total of 79 alleles. Similarity coefficients were calculated on the basis of 79 amplified bands. A dendrogram was created according to the 10 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed all of the genotypes/cultivars to be distinguished. According to the dendrogram, the 33 olive genotypes and cultivars were clustered into five main clusters. The most closely related genotypes were 'Oguzeli 3' and 'Yavuzeli 1' with 0.80 similarity ratio. The most genetically divergent cultivars were 'Yavuzeli 6' and 'Kilis Yaglik' (0.30), 'Yavuzeli 6' and 'Saurani' (0.20), 'Nizip 7' and 'Yavuzeli 4' (0.15), 'Islahiye 5' and 'Nizip Yaglik' (0.10). In conclusion, SSR analysis can be an efficient method for olive genotypes and cultivar identification and can offer valuable informative data to identify olive genotypes and cultivars grown in Turkey.

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AFLP Analysis of Intraspecific Variation Between Monilinia laxa Isolates from Different Hosts

Plant Disease ◽

10.1094/pdis-92-12-1616 ◽

2008 ◽

Vol 92 (12) ◽

pp. 1616-1624 ◽

Cited By ~ 17

Author(s):

Tjasa Gril ◽

Franci Celar ◽

Alenka Munda ◽

Branka Javornik ◽

Jernej Jakse

Keyword(s):

Genetic Diversity ◽

Host Plants ◽

Genetic Relationships ◽

Host Specialization ◽

Group Method ◽

Aflp Analysis ◽

Monilinia Laxa ◽

Model Based Clustering ◽

Pair Group ◽

Taxonomic Grouping

We analyzed with an amplified fragment length polymorphism (AFLP) marker system the genetic diversity and relationships among 67 Monilinia laxa isolates obtained from different host plants. From a total of 1,089 amplified bands scored using 20 primer combinations with two selective nucleotides, 354 were polymorphic and further used in genetic diversity analysis. Genetic relationships among isolates were assessed with different phenetic approaches, including unweighted pair group method with arithmetic mean clustering and principal coordinate analysis; the population's differentiation estimate was analyzed by molecular variance; and model-based clustering was employed to infer population structure. All four analyses clearly showed significant differences between isolates from apple trees and isolates from other host plants. No further grouping according to any other host plant was observed. The results indicate host specialization of apple isolates and support the taxonomic grouping of apple isolates.

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Analysis of Genetic Relationships of Calathea Species and Cultivars by AFLP Markers

HortScience ◽

10.21273/hortsci.39.4.888a ◽

2004 ◽

Vol 39 (4) ◽

pp. 888A-888

Author(s):

Jianjun Chen* ◽

Richard Henny ◽

C. Thomas Chao ◽

Pachanoor Devanand

Keyword(s):

Genetic Relationships ◽

Aflp Markers ◽

Group Method ◽

Similarity Coefficients ◽

Low Light ◽

Ornamental Foliage Plants ◽

Pair Group ◽

Light Levels ◽

The Family ◽

Tropical America

Calathea, the largest genus in the family Marantaceae, is composed of 100 species native to tropical America in moist or swampy forest habitats. Because of their brilliant patterns of leaf color and different textures plus ability to tolerate low light levels, calatheas have been widely produced as ornamental foliage plants for interiorscaping. Thus far, genetic relationships among its species and cultivars have not been documented. This study analyzed the relationships of 34 cultivars across 14 species using amplified fragment length polymorphism (AFLP) markers. Six EcoR I + 2/Mse I + 3 primer set combinations were used in this investigation. Each selected primer set generated 105 to 136 scorable fragments. A total of 733 AFLP fragments were detected of which 497 were polymorphic (68%). A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UP-GMA) technique and a principal coordinated analysis (PCOA) was used to analyze the relationships. The 34 cultivars were divided into four clusters. Cluster I had 19 cultivars derived from C. roseo-picta and C. loesnerii with Jaccard's similarity coefficients from 0.74 to 0.97, of which six are somaclonal variants or sports and two cultivars are genetic identical. Only C. kennedeae `Helen' is positioned in cluster II. Cluster III had 10 cultivars across seven species; Jaccard's similarity coefficients among them varied from 0.41 to 0.63. Four species were situated in cluster IV with Jaccard's similarity between 0.27 to 0.41. Results from this study indicate that broadening of genetic diversity is needed for cultivars in cluster I as they are the most commonly grown calatheas but genetically are very close.

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Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection Between Pathogenicity and Molecular Diversity

Journal of Fungi ◽

10.3390/jof7090713 ◽

2021 ◽

Vol 7 (9) ◽

pp. 713

Author(s):

Abdelhameed Elameen ◽

Svein Stueland ◽

Ralf Kristensen ◽

Rosa F. Fristad ◽

Trude Vrålstad ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Genetic Relationships ◽

Geographic Origin ◽

Mantel Test ◽

Group Method ◽

Aflp Analysis ◽

Its Sequencing ◽

Sequencing Data ◽

Pair Group

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of Saprolegnia spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 Saprolegnia spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 Saprolegnia sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the Saprolegnia isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of Saprolegnia spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (r2 = 0.8317).

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