scholarly journals Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism

2008 ◽  
Vol 54 (No. 10) ◽  
pp. 447-452 ◽  
Author(s):  
R. Talebi ◽  
A.M. Naji ◽  
F. Fayaz
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Aflp Analysis ◽  
Geographical Patterns ◽  
Upgma Dendrogram ◽  
Secondary Center ◽  
Center Of Diversity ◽  
Diverse Origin

The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions from diverse origin using AFLP markers. On average, 13 polymorphic bands per primer were observed in AFLP analysis. The average polymorphic information content (PIC) was 0.71, ranging from 0.48 to 0.92. The lowest and the highest PIC value were recorded for primer P-GAG/M-GC and P-AT/M-GC, respectively. The average GD, based on Fst values among the 21 accessions was 0.42, ranging from 0.61 to 0.16. From the UPGMA dendrogram, it is discernible that material taken for the analysis can be divided in four clusters. The results indicate that the greatest genetic diversity occurs in Afghanistan, Iran and Lebanon. In many cases, the diversity between individuals of an accession is as great as between individuals of different accessions. Based on DNA markers it is concluded that there are three centers of diversity for chickpea: Pakistan-Afghanistan, Iran-Turkey and Syria-Lebanon. India and Ethiopia, which were previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

Genetic analysis of mango landraces from Mexico based on molecular markers

2009 ◽  
Vol 7 (03) ◽  
pp. 244-251 ◽  
Author(s):  
Didiana Gálvez-López ◽  
Sanjuana Hernández-Delgado ◽  
Maurilio González-Paz ◽  
Enrique Noe Becerra-Leor ◽  
Miguel Salvador-Figueroa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Geographical Origin ◽  
Genetic Recombination ◽  
Genetic Relationships ◽  
Mangifera Indica ◽  
Aflp Analysis ◽  
Significant Genetic Differentiation ◽  
Simple Sequence

Genetic diversity and relationships among 112 mango (Mangifera indica) plants native to 16 states of Mexico and four controls [three mango cultivars (Ataulfo, Manila and Tommy Atkins) and one accession ofMangifera odorata] were evaluated based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Mango germplasm shows broad dispersion through Mexico and genetically similar germplasm from different agroecological regions has previously been found by our group. Both AFLP and SSR analyses indicated high genetic similarity among mango populations that were clustered in two major groups: mangos from Gulf of Mexico coastline and mangos from Pacific Ocean coastline and locations far away from the sea. The highest genetic diversity was found within plants from each state, and significant genetic differentiation (FST = 0.1921, AFLPs and 0.1911, SSRs) was also observed among mango populations based on geographical origin and genetic status (cultivars versus landraces). Heterozygosity values ranged from low (0.38) to moderate (0.68), and no heterozygote deficits were found. The highest genetic variability was found in mango populations from Tabasco, Michoacán and Oaxaca. Data suggested that mangoes are subjected to natural or induced pollination, so segregation as well as genetic recombination plays major roles on genetic diversification of Mexican mangos. AFLP analysis was more robust than SSR for determining the genetic relationships among mango landraces from Mexico.

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 diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers

2002 ◽  
Vol 37 (8) ◽  
pp. 1105-1114 ◽  
Author(s):  
Edson Barcelos ◽  
Philippe Amblard ◽  
Julien Berthaud ◽  
Marc Seguin
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Oil Palm ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Aflp Analysis ◽  
Elaeis Oleifera ◽  
French Guyana ◽  
And Cluster Analysis

The objective of this work was to evaluate the genetic diversity, its organization and the genetic relationships within oil palm (Elaeis oleifera (Kunth) Cortés, from America, and E. guineensis (Jacq.), from Africa) germplasm using Restriction Fragment Length Polymorphism (RFLP) and Amplified Fragment Length Polymorphism (AFLP). In complement to a previous RFLP study on 241 E. oleifera accessions, 38 E. guineensis accessions were analyzed using the same 37 cDNA probes. These accessions covered a large part of the geographical distribution areas of these species in America and Africa. In addition, AFLP analysis was performed on a sub-set of 40 accessions of E. oleifera and 22 of E. guineensis using three pairs of enzyme/primer combinations. Data were subjected to Factorial Analysis of Correspondence (FAC) and cluster analysis, with parameters of genetic diversity being also studied. Results appeared congruent between RFLP and AFLP. In the E. oleifera, AFLP confirmed the strong structure of genetic diversity revealed by RFLP, according to geographical origin of the studied material, with the identification of the same four distinct genetic groups: Brazil, French Guyana/Surinam, Peru, north of Colombia/Central America. Both markers revealed that genetic divergence between the two species is of the same magnitude as that among provenances of E. oleifera. This finding is in discrepancy with the supposed early tertiary separation of the two species.

scholarly journals Molecular variation among isolates of Fusarium species

2015 ◽  
Vol 43 (2) ◽  
pp. 207-212
Author(s):  
A Al-Daoude ◽  
A Shoaib ◽  
Mie Arabi ◽  
M Jawhar
Keyword(s):  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Fusarium Species ◽  
Genetic Distances ◽  
Aflp Analysis ◽  
Fusarium Spp ◽  
Phylogenetic Groups ◽  
Banding Patterns ◽  
North West ◽  
Upgma Dendrogram

Twelve different isolates of Fusarium spp. collected from wheat grown in Syria were analyzed using amplified fragment length polymorphism (AFLP) markers. AFLP analysis allowed differentiation between species on the basis of banding patterns. A total of 654 scorable DNA bands were scored, of which 296 (44.54 %) were polymorphic. UPGMA dendrogram, based on Nei's genetic distances, showed that isolates formed three phylogenetic groups; one of them did not fall into clades correlated to the origin or colour of the isolate, which suggests a regional dispersal of these species. However, isolates belonging to F. culmorum and F. equiseti collected from north-west of Syria and ICARDA, respectively fell into two separate sub-clusters. The level of genetic variability detected within Fusarium isolates by AFLP analysis confirmed that it is a reliable, efficient, and effective marker technology for determining genetic relationships in Fusarium spp. DOI: http://dx.doi.org/10.3329/bjb.v43i2.21674 Bangladesh J. Bot. 43(2): 207-212, 2014 (September)

scholarly journals Genetic Diversity of Rhubarb Cultivars

2008 ◽  
Vol 133 (4) ◽  
pp. 587-592 ◽  
Author(s):  
Joseph C. Kuhl ◽  
Veronica L. DeBoer
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Length Polymorphism ◽  
Genetic Relationship ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
18Th Century ◽  
Pedigree Information ◽  
Aflp Analysis ◽  
Fingerprint Analysis

The genus Rheum L., commonly known as rhubarb, is composed of ≈60 species, primarily distributed throughout northern and central Asia. Rhubarb species have been used for medicinal purposes for thousands of years; however, it was not until the 18th century that the culinary use of petioles was first reported. Although the origin(s) of culinary rhubarb is not clear, it is thought that they originated from hybridization of rhubarb species originally brought to Europe for medicinal purposes. Most rhubarb cultivars lack pedigree information, and the genetic relationship among cultivars is largely unknown. Amplified fragment length polymorphism (AFLP) markers were generated for fingerprint analysis of 37 cultivars and four putative Rheum species accessions. Ten EcoRI and MseI primer combinations were analyzed for a total of 1400 scored polymorphisms, with an average of 140 polymorphisms per primer combination. Results show at least two clusters of related cultivars, as well as distantly related accessions. This study provides an estimate of rhubarb cultivar genetic diversity using AFLP analysis.

scholarly journals AFLP Analysis for Genetic Diversity in Capsicum Annuum and Related Species

2006 ◽  
Vol 1 (3) ◽  
pp. 1934578X0600100
Author(s):  
Sanjog T. Thul ◽  
Ajit K. Shasany ◽  
Mahendra P. Darokar ◽  
Suman P. S. Khanuja
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Great Degree ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Variation Analysis ◽  
Average Similarity ◽  
Geographical Locations

Intra- and inter-specific genetic variation analysis was conducted using amplified fragment length polymorphism (AFLP) profiling in Capsicum accessions in the germplasms collected from different geographical locations in India. A total of 24 accessions were investigated belonging to six species, namely C. annuum, C. baccatum, C. chinence, C. eximium, C. frutescens and C. luteum. Average similarity within the 15 accessions of C. annuum was highest (100%) between accessions CIMAP/CA45 and CIMAP/CA49 obtained from IISR, Kerala and 43% among the species CIMAP/CC1 and CIMAP/CB2. In this analysis, accessions were clustered more pronouncedly according to their geographical locations than to their taxonomic labels. A great degree of intermixing of present day domesticated chillies is evident from the present study.

Genetic diversity analysis of kenaf ( Hibiscus cannabinus L.) using AFLP (amplified fragment length polymorphism) markers

2008 ◽  
Vol 7 (02) ◽  
pp. 122-126 ◽  
Author(s):  
Rouxlene Coetzee ◽  
Liezel Herselman ◽  
Maryke T. Labuschagne
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
North America ◽  
El Salvador ◽  
Fragment Length Polymorphism ◽  
Hibiscus Cannabinus ◽  
Aflp Analysis ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
The Usa

Nineteen kenaf genotypes from Cuba, Taiwan, the USA, El Salvador, Guatemala, Russia, Spain and Indonesia, and three wild types collected in South Africa were analysed for genetic diversity using AFLP analysis. All could be uniquely distinguished from one another, but only a low level of genetic diversity was present. The most distinct accession, Guatemala 4, was 85% similar to all other accessions. The accessions clustered more or less according to known pedigree and/or origin. Two of the three wild types (Hibiscus cannabinusc andH. cannabinusa) clustered separately from the commercial and Russian accessions. One of the wild types,H. cannabinusb clustered with some of the commercial accessions. Commercial accessions in the first subgroup all originated from central and North America, and surrounding islands (Cuba and El Salvador). The Russian accessions are all grouped together. The second subgroup was the only group that contained accessions from different geographical origins.

scholarly journals Assessment of Diversity in Claviceps africana and Other Claviceps Species by RAM and AFLP Analyses

2000 ◽  
Vol 90 (10) ◽  
pp. 1126-1130 ◽  
Author(s):  
Paul W. Tooley ◽  
Nichole R. O'Neill ◽  
Erin D. Goley ◽  
Marie M. Carras
Keyword(s):  
United States ◽  
South Africa ◽  
Genetic Diversity ◽  
Puerto Rico ◽  
Fragment Length Polymorphism ◽  
The United States ◽  
Aflp Analysis ◽  
Indian Isolates ◽  
Claviceps Africana ◽  
Primer Sets

Genetic diversity among isolates of Claviceps africana, the sorghum ergot pathogen, and isolates of other Claviceps spp. causing ergot on sorghum or other hosts, was analyzed by random amplified microsatellite (RAM) and amplified fragment length polymorphism (AFLP) analyses. Of the RAM primer sets tested, one revealed polymorphism in C. africana isolates, with Australian and Indian isolates possessing a unique fragment. AFLP analysis, in addition to clearly distinguishing Claviceps spp., revealed polymorphisms in C. africana. A group of isolates from the United States, Puerto Rico, and South Africa exhibited 95 to 100% similarity with one another. Several isolates from Isabela, Puerto Rico were 100% similar to an isolate from Texas, and another isolate from Puerto Rico was identical with one from Nebraska. Australian and Indian isolates showed greater than 90% similarity with isolates from the United States., Puerto Rico, and South Africa. A number of polymorphisms existed in the United States group, indicating that the recently introduced population contains multiple genotypes. Isolates of C. sorghicola, a newly described sorghum pathogen from Japan, were very distinct from other species via RAM and AFLP analyses, as were isolates from outgroups C. purpurea and C. fusiformis. Both RAM and AFLP analysis will be useful in determining future patterns of intercontinental migration of the sorghum ergot pathogen, with the AFLP method showing greater ability to characterize levels of intraspecific variation.

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

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1175-1180 ◽  
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.

scholarly journals Genetic Diversity among Botulinum Neurotoxin-Producing Clostridial Strains

2006 ◽  
Vol 189 (3) ◽  
pp. 818-832 ◽  
Author(s):  
K. K. Hill ◽  
T. J. Smith ◽  
C. H. Helma ◽  
L. O. Ticknor ◽  
B. T. Foley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Property ◽  
Animal Species ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Rrna Gene ◽  
Botulinum Neurotoxins ◽  
The Common ◽  
Multiple Strains ◽  
The 16S Rrna Gene

ABSTRACT Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism.

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