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.

scholarly journals Investigating the Spatiotemporal Genetic Structure of Phytophthora capsici in Michigan

2001 ◽  
Vol 91 (10) ◽  
pp. 973-980 ◽  
Author(s):  
K. H. Lamour ◽  
M. K. Hausbeck
Keyword(s):  
Fragment Length Polymorphism ◽  
Aflp Marker ◽  
Phytophthora Capsici ◽  
Group Method ◽  
Analysis Of Molecular Variance ◽  
Arithmetic Average ◽  
Pair Group ◽  
Average Cluster ◽  
Over Time ◽  
F Statistics

Phytophthora capsici isolates were recovered from pepper and cucurbit hosts at seven locations in Michigan from 1998 to 2000. Isolates were characterized for compatibility type (CT), mefenoxam sensitivity (MS), and amplified fragment length polymorphism (AFLP) marker profiles. In total, 94 AFLP bands were resolved. Individual populations were highly variable. Within populations, 39 to 49% of the AFLP bands were polymorphic and estimated heterozygosities ranged from 0.16 to 0.19. Of the 646 isolates fingerprinted, 70% (454) had unique AFLP profiles. No clones were recovered between years or locations. Pairwise F statistics (ΦST) between populations from different locations ranged from 0.18 to 0.40. A tree based on unweighted pair-group method with arithmetic average cluster analysis indicates discrete clusters based on location. Isolates from the same location showed no clustering based on the year of sampling. Analysis of molecular variance partitioned variability among (40%) and within populations (60%). The overall estimated ΦST was 0.34 (SD = 0.03). A1/A2 CT ratios were ≈1:1, and MS frequencies were similar between years for the two locations sampled over time. These data suggest that P. capsici persists in discrete outcrossing populations and that gene flow among locations in Michigan is infrequent.

Amplified fragment length polymorphism and mitochondrial sequence data detect genetic differentiation and relationships in endangered southwestern U.S.A. ambersnails (Oxyloma spp.)

2000 ◽  
Vol 78 (10) ◽  
pp. 1845-1854 ◽  
Author(s):  
Mark P Miller ◽  
Larry E Stevens ◽  
Joseph D Busch ◽  
Jeff A Sorensen ◽  
Paul Keim
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Population Genetic ◽  
Fragment Length Polymorphism ◽  
Sequence Data ◽  
Amplified Fragment Length Polymorphism ◽  
Group Method ◽  
Exact Test ◽  
Additional Information ◽  
Pair Group

The Kanab ambersnail (Oxyloma haydeni kanabensis) is a federally endangered mollusc currently known to reside in two locations in the southwestern U.S.A. To determine the extent of within- and between-population genetic variation of this taxon, the amplified fragment length polymorphism (AFLP) technique was used to generate 110 genetic markers among individuals sampled from the two Kanab ambersnail populations and from the only two known southwestern populations of the Niobrara ambersnail (Oxyloma haydeni haydeni) in Utah and northern Arizona. Additional information was obtained from sequence data of cytochrome b and cytochrome oxidase I gene fragments. Results suggest high levels of differentiation among populations, as evidenced through the application of UPGMA (unweighted pair-group method with arthimetic averaging) clustering, F statistics, and Fisher's exact test. Various levels of within-population genetic diversity were observed among populations. Expected heterozygosities ranged from 0.239 to 0.086 under a model assuming Hardy-Weinberg genotypic proportions and ranged from 0.205 to 0.061 under an obligate-selfing completely homozygous model. Results from cluster analyses showed that one Kanab ambersnail population and one Niobrara ambersnail population were more similar than the two Kanab ambersnail populations studied (supported by >80% of bootstrap replicates). These findings were further supported through the phylogenetic analysis of both mito chondrial gene fragments. The data suggest that taxonomic designations need revision, an act that will likely affect the protected status of some of the populations.

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

2009 ◽  
Vol 134 (4) ◽  
pp. 428-434 ◽  
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.

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

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
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

Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 295-302 ◽  
Author(s):  
Kaan Yilancioglu ◽  
Selim Cetiner
Keyword(s):  
Vitis Vinifera ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Genetic Erosion ◽  
Principal Component ◽  
Distinct Group ◽  
Group Method ◽  
Local Cultivars ◽  
Pair Group ◽  
Selected Subset

Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

scholarly journals Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽  
2007 ◽  
Vol 91 (12) ◽  
pp. 1556-1563 ◽  
Author(s):  
R. G. Bhat ◽  
G. T. Browne
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Data ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Horticultural Crops ◽  
Pair Group ◽  
Phytophthora Citricola ◽  
High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

scholarly journals Genetic Diversity and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

2006 ◽  
Vol 131 (2) ◽  
pp. 242-249 ◽  
Author(s):  
Jelka Šustar-Vozlič ◽  
Marko Maras ◽  
Branka Javornik ◽  
Vladimir Meglič
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Seed Protein ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Group Method ◽  
Phaseolus Vulgaris L ◽  
Pair Group ◽  
High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

scholarly journals Investigation of the Origin of Aronia mitschurinii using Amplified Fragment Length Polymorphism Analysis

HortScience ◽  
2013 ◽  
Vol 48 (5) ◽  
pp. 520-524 ◽  
Author(s):  
Peter J. Leonard ◽  
Mark H. Brand ◽  
Bryan A. Connolly ◽  
Samuel G. Obae
Keyword(s):  
North America ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Wild Populations ◽  
Pair Group ◽  
Black Chokeberry ◽  
Fourth Species ◽  
Distinct Morphology

Aronia Medik., commonly known as chokeberry, is a genus of deciduous, multistemmed, rosaceous shrubs native to eastern North America. Three species of chokeberry are commonly accepted, A. arbutifolia (L.) Pers., red chokeberry, A. melanocarpa (Michx.) Elliott, black chokeberry, and A. prunifolia (Marshall) Rehder, or purple chokeberry. In Europe, a fourth species of human origin is recognized as Aronia mitschurinii A.K.Skvortsov & Maitul. In North America this type of Aronia is described as cultivars of A. melanocarpa, including ‘Viking’, ‘Nero’, and ‘Aron’. This species is characterized by near homogeneity of the population, tetraploidy, and a distinct morphology with more robust stems, wider leaf blades, and larger fruits than wild populations of A. melanocarpa. It has been proposed that this genotype originated from Russian pomologist Ivan Michurin’s early 20th century experiments involving Aronia × Sorbus hybridization. In this study we used amplified fragment length polymorphic (AFLP) markers to elucidate the relationships of A. mitschurinii to wild North American Aronia, ×Sorbaronia C.K. Schneid, Sorbus L., and six additional genera from subtribe Pyrinae (Rosaceae). Data from seven primer combinations were interpreted by the NTSYSpc software package into a similarity matrix using Jaccard’s coefficient. Clustering of AFLP similarity data using the unweighted pair group method with arithmetic mean (UPGMA) identified A. mitschurinii as distinct from wild Aronia, grouping it close to ×Sorbaronia fallax C. K. Schneid. and ×Sorbaronia ‘Ivan’s Beauty’. Non-metric multidimensional scaling (nMDS) also demonstrated a relationship between A. mitschurinii, ×Sorbaronia fallax, a ×Sorbaronia × Aronia backcross and compound-leaved Sorbus.

scholarly journals Genetic Variation among Isolates of Sarcocystis neurona, the Agent of Protozoal Myeloencephalitis, as Revealed by Amplified Fragment Length Polymorphism Markers

2006 ◽  
Vol 74 (6) ◽  
pp. 3448-3454 ◽  
Author(s):  
H. M. Elsheikha ◽  
H. C. Schott ◽  
L. S. Mansfield
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Epidemiological Data ◽  
Didelphis Virginiana ◽  
Group Method ◽  
Molecular Technique ◽  
Sarcocystis Neurona ◽  
Pair Group

ABSTRACT Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

scholarly journals Diversidad genética de aislados de Phytophthora infestans colectados en zonas productoras de papa y tomate de Guatemala

2018 ◽  
Vol 5 (2) ◽  
pp. 151-161
Author(s):  
Jose Alejandro Ruiz-Chutan ◽  
Julio E. Berdúo-Sandoval ◽  
Amilcar Sánchez-Pérez
Keyword(s):  
Phytophthora Infestans ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Arithmetic Mean ◽  
Group Method ◽  
Pair Group ◽  
Unweighted Pair Group Method

Phytophthora infestans (Mont) DeBary es el agente causal de la enfermedad conocida como tizón tardío, la cual ha sido catalogada como la enfermedad de plantas más devastadora reportada en la historia de la humanidad. Este patógeno afecta plantas de importancia económica de la familia Solanaceae, como el tomate y la papa. P. infestans es un oomicete heterotálico y necesita de dos tipos de apareamiento, A1 y A2, para presentar una reproducción sexual, la cual es la principal vía por la que este patógeno incrementa su grado de diversidad, a través de una recombinación de su material genético, que representa el mayor desafío para el manejo de la enfermedad. Este estudio determinó el nivel de variabilidad genética, a través del marcador molecular amplified fragment length polymorphism (AFLP), de 22 aislados de P. infestans colectados en diferentes zonas productoras de papa y tomate. Con el perfil de bandas generado por el marcador molecular, se realizó un análisis cluster creando un dendograma de tipo unweighted pair group method with arithmetic mean (UPGMA), con el índice de Dice, mediante una matriz de distancias genéticas. Los aislados fueron situados en tres grupos principales, los cuales responden al lugar de procedencia y al tipo de planta hospedera. 

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