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.

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. 

scholarly journals Genetic Relationships among Native Species and Hybrid Cultivars of Asian Dendrobium (Orchidaceae) Using Amplified Fragment Length Polymorphism Markers

HortScience ◽  
2011 ◽  
Vol 46 (2) ◽  
pp. 192-196 ◽  
Author(s):  
Gen-Fa Zhu ◽  
Dong-Mei Li
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Native Species ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Similarity Coefficient ◽  
Group Method ◽  
Plant Materials ◽  
Arithmetic Average

This study addresses the phylogenetic relationships among native species and hybrid cultivars of Asian Dendrobium by amplified fragment length polymorphism (AFLP). The plant materials of this study are composed of 37 accessions belonging to native species in China and 63 accessions proposed to be hybrid cultivars originating from Japan and Korea. Eight AFLP primer combinations produced a total of 1658 fragments with an average of 207 fragments per primer pair, of which 1655 bands were polymorphic. Specific AFLP markers were identified in 29 of 100 tested Dendrobium accessions. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Dice's similarity coefficient matrix and also average similarity of each species and cultivar. The tested 100 Asian Dendrobium accessions were grouped into seven clusters with the similarity coefficient of 0.49. A first cluster consisted of 63 hybrid cultivars, 17 species of section Dendrobium, one species of section Formosae, and one species of section Callista. A second, fourth, and seventh cluster included five, three, and two species of section Dendrobium, respectively. A third group comprised five species of section Formosae. A fifth and sixth cluster contained three and two species of section Callista, respectively. These results indicated that the genetic relationships among tested Asian Dendrobium accessions were related to their origins, morphological classification, flower color, and pedigree, to some extent.

Genetic population structure of Liza haematocheilus in north-western Pacific detected by amplified fragment length polymorphism markers

2012 ◽  
Vol 93 (2) ◽  
pp. 373-379 ◽  
Author(s):  
Zhi-Qiang Han ◽  
Gang Han ◽  
Tian-Xiang Gao ◽  
Zhi-Yong Wang ◽  
Bo-Nian Shui
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Western Pacific ◽  
Group Method ◽  
The North ◽  
Mtdna Lineages ◽  
North Western ◽  
North Western Pacific

Several divergent sympatry mtDNA lineages have been described in redlip mullet Liza haematocheilus, and this high inter-lineage divergence raises questions about the taxonomic status of L. haematocheilus lineages in the north-western Pacific. In this study, the amplified fragment length polymorphism technique was employed to examine genetic structure of L. haematocheilus and estimate the level of independence of the different mtDNA lineages in the north-western Pacific. A total of 186 bands were amplified from 91 individuals among 8 populations by 4 primer combinations and the percentage of polymorphic bands was 91.74%. The Unweighted Pair Group Method with Arithmetic Mean tree based on Nei genetic distance revealed two clusters (North Clade and South Clade). Molecular variance analysis and pairwise FST supported the separation of north and south populations of L. haematocheilus in the north-western Pacific. The incongruence between nuclear groups and mitochondrial lineages suggests the three distinct lineages do not represent cryptic species and the presence of divergent mitochondrial lineages in the same sample is a result of secondary contact after an extended period of isolation. The Pleistocene isolation and biological characteristics of species may be responsible for the genetic differentiation of L. haematocheilus.

scholarly journals Analysis of Genetic Variability among Phalaenopsis Species and Hybrids Using Amplified Fragment Length Polymorphism

2009 ◽  
Vol 134 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Yeun-Kyung Chang ◽  
Richard E. Veilleux ◽  
Muhammad Javed Iqbal
Keyword(s):  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Species Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Group Method ◽  
Aflp Analysis

Phalaenopsis is the second most valuable potted plant in the United States. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. In this study, genetic variability of 16 Phalaenopsis species and hybrids was analyzed using amplified fragment length polymorphism (AFLP) markers. Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from 100 to 350 bp and 1285 (95%) of them were polymorphic. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by the unweighted pair group method with arithmetic mean analysis clustered the germplasm into two main groups. Bootstrap values for the groups supported 70% of the clustering. A significant linear relationship (r = 0.724, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results of this study demonstrate the usefulness of AFLP analysis in Phalaenopsis and its potential application in breeding and species conservation.

Amplified fragment length polymorphism analysis reveals three distinct taxa in Carex digitalis sect. Careyanae (Cyperaceae)

2006 ◽  
Vol 84 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Bruce A. Ford ◽  
Robert F.C. Naczi ◽  
Habibollah Ghazvini ◽  
Mahmood Iranpour
Keyword(s):  
North Carolina ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Additional Species ◽  
Pair Group

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis , var. floridana , var. macropoda ). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora.

Sign in / Sign up

Export Citation Format

Share Document