scholarly journals Genetic Diversity of Orobanche crenata Populations in Ethiopia Using Microsatellite Markers

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Gashaw Belay ◽  
Kassahun Tesfaye ◽  
Aladdin Hamwieh ◽  
Seid Ahmed ◽  
Tiegist Dejene ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Distance ◽  
Faba Bean ◽  
Polymorphic Information Content ◽  
Hot Spot ◽  
Molecular Techniques ◽  
Orobanche Crenata ◽  
Parasitic Weed ◽  
South Gondar

Orobanche crenata is a parasitic weed that causes considerable yield losses on food legumes in Ethiopia and the Mediterranean region. Understanding the genetic diversity of Orobanche crenata using molecular techniques generate useful information in managing the weed through resistance breeding. This study aimed at assessing the genetic diversity of O. crenata populations collected from major faba bean growing areas of Ethiopia. A total of 96 samples were collected from the Orobanche-infested faba bean farmer field. The genetic diversity of the population was studied using 30 O. cumana SSR markers. The results showed that 11 SSRs were functional and transferable markers to study the diversity of O. crenata populations. The average number of alleles, gene diversity, heterozygosity, and polymorphic information content values for the SSR loci were 9.6, 0.82, 0.38, and 0.80, respectively. The pairwise genetic similarity analysis showed the lowest genetic distance between samples collected from South Gondar and South Wollo (0.12) while the highest genetic distance (0.48) was found between South Gondar and North Wollo. The analysis of molecular variance result indicated that the variation among individuals was a major source of genetic variation (55%) followed by within individuals (43%) and among populations (2%) variation. The output of population genetic structure analysis indicated the presence of two major groups irrespective of the area of collection or region of origin. Besides, the outcome of the spatial autocorrelation computation indicated a significant and positive genetic correlation between samples collected under a 28 km radius. In general, the absence of geographic region based genetic structure presumably demonstrates the expansion of the parasitic weed between farming sites upon its recent introduction to the country. Thus, the clear absence of population differentiation warrants screening faba bean population in hot spot area.

scholarly journals GBS analysis of Orobanche crenata populations in Algeria supports local adaptation and host-specialization

2021 ◽  
Author(s):  
Farah Bendaoud ◽  
Gunjune Kim ◽  
Hailey Larose ◽  
James Westwood ◽  
Nadjia Zermane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Principal Components ◽  
Faba Bean ◽  
Isolation By Distance ◽  
Host Specialization ◽  
Nucleotide Polymorphisms ◽  
Vegetable Crops ◽  
Orobanche Crenata ◽  
Parasitic Weed

Crenate broomrape (Orobanche crenata Forsk.) is a serious long-standing parasitic weed problem in Algeria, mainly affecting legumes but also vegetable crops. Unresolved questions for parasitic weeds revolve around the extent to which these plants undergo local adaptation, especially with respect to host specialization, which would be expected to be a strong selective factor for obligate parasitic plants. In the present study, the Genotyping-By-Sequencing (GBS) approach was used to analyze genetic diversity and population structure of 10 Algerian O. crenata populations with different geographical origins and host species (faba bean, pea, chickpea, carrot and tomato). In total, 8,004 high-quality single-nucleotide polymorphisms were obtained and used across the study. Genetic diversity and relationships of 95 individuals from 10 populations were studied using model-based ancestry analysis, principal components analysis, discriminant analysis of principal components, and phylogeny approaches. The genetic differentiation (FST) between pairs of populations was lower between adjacent populations and higher between geographically separated ones, but no support was found for isolation by distance. Further analyses identified four genetic clusters and revealed evidence of structuring among populations and hosts with more evident structuring among hosts than strictly along a geographic gradient. In the most striking example, O. crenata growing on pea had a distinct SNP profile from those growing on faba bean or other crops. These results illustrate the potential of GBS to reveal the dynamics of parasitic weed dispersal and adaptation.

Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers

2018 ◽  
Vol 66 (6) ◽  
pp. 335
Author(s):  
T. Pan ◽  
P. Yan ◽  
M. Yang ◽  
H. Wang ◽  
I. Ali ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Yangtze River ◽  
The Yangtze River ◽  
Geographic Scale ◽  
Widespread Species ◽  
Bufo Gargarizans ◽  
Toad Bufo

Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

scholarly journals Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

2021 ◽  
Vol 10 (16) ◽  
pp. e187101623025
Author(s):  
Daniele Paula Maltezo ◽  
Julliane Dutra Medeiros ◽  
Ana Aparecida Bandini Rossi
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Group Method ◽  
Mato Grosso ◽  
Copaifera Langsdorffii ◽  
Genetic Structure And Diversity ◽  
Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81.  The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

scholarly journals Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot

2019 ◽  
Author(s):  
Sangeeta Angom ◽  
Chongpi Tuboi ◽  
Mirza Ghazanfar Ullah ◽  
Syed Ainul Hussain
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Polymorphic Information Content ◽  
Distance Sampling ◽  
Northeast India ◽  
Biodiversity Hotspot ◽  
Evolutionary Potential ◽  
Female Ratio ◽  
Management Regime ◽  
Rare Alleles

AbstractThe population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. Northeast India is a stronghold of the species; however, in recent years the population has been getting fragmented, and it is vulnerable to extinction. We examined the demographic and genetic structure of a small hog deer population in the floating meadows of Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. We used a double-observer distance sampling method to derive the hog deer abundance and population structure. We also derived the genetic diversity of the population through microsatellite screening and bottleneck detection. Our study revealed that the abundance of the deer in the park was 1.82–4.32 individuals/km2. The adult male to female ratio and fawn to doe ratio were 36.2 ± 1.9 males/100 females and 16.5 ± 0.4 fawns/100 females, respectively. The mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (HO) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (HE) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03). The observed allelic distribution reveals that the population has not encountered any genetic bottleneck in the recent past. Although the population is declining, it still retains some rare alleles, and the genetic diversity is 50%. This diversity will probably not affect the short-term population growth but may affect the evolutionary potential by limiting the selection flexibility. Conservation measures coupled with a scientifically sound management regime may help the persistence of the population in the region at a time when the population still retains rare alleles and maintains reproductive fitness.

scholarly journals ASSESSMENT OF GENETIC DIVERSITY AND RELATIONSHIPS AMONG GRAPEVINE CULTIVARS ORIGINATING IN CENTRAL AND EASTERN EUROPE AND NORTH AMERICA USING ISSR MARKERS

2019 ◽  
Vol 18 (5) ◽  
pp. 141-152
Author(s):  
Anna Lisek ◽  
Jerzy Lisek
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Molecular Techniques ◽  
Resolving Power ◽  
Vitis Vinifera L ◽  
Phenotypic Differences ◽  
High Degree ◽  
Issr Primers

The study shows genetic diversity of 38 Vitis vinifera L. cultivars and hybrids originating in North America and Europe, including cultivars selected in Poland, which have not been characterized with the use of DNA markers yet. The agrobiological features of the genotypes selected for testing, indicate that they may be useful for the breeding of new cultivars and grape production. The use of 12 ISSR primers allowed to obtain 94.4% of polymorphism. The polymorphic information content (PIC) value was high and varied between 0.829 and 0.953 with an average of 0.897. The resolving power (Rp) ranged between 3.678 and 8.892 with an average of 6.347. Primers UBC 809, UBC 810, UBC 812, UBC 855, UBC 891 and UBC 810 were found to be highly effective (informative). Similarity coefficient ranged between 0.167 and 1.0, which indicates high degree of diversity of tested  grape cultivars. Tested cultivars were grouped in 3 main clusters; one of them was further divided into 6 subclusters. ‘Pannonia Kincse’ and ‘Danmarpa Polonia’ were not differentiated. Phenotypic differences among those two cultivars suggest that ‘Danmarpa Polonia’ might be a clone of ‘Pannonia Kincse’ and other molecular techniques must be used to differentiate them. Morphological and agrobiological characters of cultivars support the results obtained by ISSR markers.

scholarly journals Small-scale spatial genetic structure of Asarum sieboldii metapopulation in a valley

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Hyeon Jin Jeong ◽  
Jae Geun Kim
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Forest Understory ◽  
Small Scale ◽  
Low Density ◽  
Stochastic Events

Abstract Background Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short seed dispersal distance by ants as their seed distributor. It is known that many flowers of A. sieboldii depend on self-fertilization. Because these characteristics can affect negatively in genetic structure, investigating habitat structure and assessment of genetic structure is needed. A total of 27 individuals in a valley were sampled for measuring genetic diversity, genetic distance, and genetic differentiation by RAPD-PCR. Results The habitat areas of A. sieboldii metapopulation were relatively small (3.78~33.60 m2) and population density was very low (five to seven individuals in 20×20 m quadrat). The habitat of A. sieboldii was a very shady (relative light intensity = 0.9%) and mature forest with a high evenness value (J = 0.81~0.99) and a low dominance value (D = 0.19~0.28). The total genetic diversity of A. sieboldii was quite high (h = 0.338, I = 0.506). A total of 33 band loci were observed in five selected primers, and 31 band loci (94%) were polymorphic. However, genetic differentiation along the valley was highly progressed (Gst = 0.548, Nm = 0.412). The average genetic distance between subpopulations was 0.387. The results of AMOVA showed 52.77% of variance occurs among populations, which is evidence of population structuring. Conclusions It is expected that a small-scale founder effect had occurred, an individual spread far from the original subpopulation formed a new subpopulation. However, geographical distance between individuals would have been far and genetic flow occurred only within each subpopulation because of the low density of population. This made significant genetic distance between the original and new population by distance. Although genetic diversity of A. sieboldii metapopulation is not as low as concerned, the subpopulation of A. sieboldii can disappear by stochastic events due to small subpopulation size and low density of population. To prevent genetic isolation and to enhance the stable population size, conservative efforts such as increasing the size of each subpopulation or the connection between subpopulations are needed.

scholarly journals Evaluation of genetic variations and phylogeny of the most popular pear (Pyrus communis L.) cultivars in Duhok city using AFLP markers

2018 ◽  
Vol 6 (1) ◽  
pp. 1-10
Author(s):  
Shaymaa H. Ali ◽  
Hemin E. Othman ◽  
Payman A. Abdullah-Zibari ◽  
Jaladet M.S. Jubrael
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Pyrus Communis ◽  
Aflp Markers ◽  
Aflp Data ◽  
Powerful Technique ◽  
Pyrus Communis L

Introduction: Genotyping and evaluation of genetic variation and polymorphic information content of the locally cultivated pear (Pyrus communis L.) might play an important role in building the genetic bank. These are also immensely important for present and future pear breeding program in the region. Methods: In the current study, AFLP markers have been employed to estimate the level of genetic diversity and to assess the phylogeny among the seven most popular pear cultivars in Duhok city. Results: Eight selective primer combinations generated a total of 653 AFLP fragments from which 445 (68.2%) fragments were polymorphic. The number of visible amplified products per primer combination were varied and ranged from 66 to 96 bands. The highest percentage of polymorphism (78.4%) was observed by the primer pair P174/M182, while the lowest percentage of polymorphism (58.6%) was observed by the primer pair P174/M100. The highest PIC (0.85) was obtained with the primer combination P174/M182, while, the lowest PIC (0.49) was obtained by the primer combination P174/M307. The genetic distance was ranged from 0.1348 (between Danimarki and Amreki cultivars) to 0.3131 (between Italy and Zaafaran2 cultivars). Based on the AFLP data, all the seven pear genotypes were successfully clustered into two separate clusters (C1 and C2) with an out-group of Itali cultivar. Conclusions: Overall, it can be concluded that there was high polymorphism among the studied genotypes. Also, it can be stated that the AFLP was a reliable and a powerful technique in genotyping and discriminating of respective pear cultivars.

scholarly journals The Number of Target Molecules of the Amplification Step Limits Accuracy and Sensitivity in Ultradeep-Sequencing Viral Population Studies

2017 ◽  
Vol 91 (16) ◽  
Author(s):  
Romain Gallet ◽  
Frédéric Fabre ◽  
Yannis Michalakis ◽  
Stéphane Blanc
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Faba Bean ◽  
Viral Population ◽  
Ssdna Virus ◽  
Target Molecules ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Sequencing Procedure

ABSTRACT The invention of next-generation sequencing (NGS) techniques marked the coming of a new era in the detection of the genetic diversity of intrahost viral populations. A good understanding of the genetic structure of these populations requires, first, the ability to identify the different isolates or variants and, second, the ability to accurately quantify them. However, the initial amplification step of NGS studies can impose potential quantitative biases, modifying the variant relative frequencies. In particular, the number of target molecules (NTM) used during the amplification step is vastly overlooked although of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In the present article, we investigated quantitative biases in an NGS study of populations of a multipartite single-stranded DNA (ssDNA) virus at different steps of the procedure. We studied 20 independent populations of the ssDNA virus faba bean necrotic stunt virus (FBNSV) in two host plants, Vicia faba and Medicago truncatula. FBNSV is a multipartite virus composed of eight genomic segments, whose specific and host-dependent relative frequencies are defined as the “genome formula.” Our results show a significant distortion of the FBNSV genome formula after the amplification and sequencing steps. We also quantified the genetic bottleneck occurring at the amplification step by documenting the NTM of two genomic segments of FBNSV. We argue that the NTM must be documented and carefully considered when determining the sensitivity and accuracy of data from NGS studies. IMPORTANCE The advent of next-generation sequencing (NGS) techniques now enables study of the genetic diversity of viral populations. A good understanding of the genetic structure of these populations first requires the ability to identify the different isolates or variants and second requires the ability to accurately quantify them. Prior to sequencing, viral genomes need to be amplified, a step that potentially imposes quantitative biases and modifies the viral population structure. In particular, the number of target molecules (NTM) used during the amplification step is of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In this work, we used 20 replicated populations of the multipartite faba bean necrotic stunt virus (FBNSV) to estimate the various limitations of ultradeep-sequencing studies performed on intrahost viral populations. We report quantitative biases during rolling-circle amplification and the NTM of two genomic segments of FBNSV.

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