scholarly journals Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae)

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Dmitry V. Politov ◽  
Maryana M. Belokon ◽  
Yuri S. Belokon ◽  
Tatyana A. Polyakova ◽  
Anna V. Shatokhina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Identification ◽  
Microsatellite Loci ◽  
Pcr Amplification ◽  
Test System ◽  
Populus Tremula ◽  
Individual Identification ◽  
Practical Applications ◽  
Ssr Loci ◽  
Low Probability

Testing systems for molecular identification of micropropagated elite aspen (Populus tremula L.) genotypes were developed on the base on microsatellite (SSR) loci. Out of 33 tested microsatellite loci, 14 were selected due to sustainable PCR amplification and substantial variability in elite clones of aspen aimed for establishment of fast-rotated forest plantations. All eight tested clones had different multilocus genotypes. Among 114 trees from three reference native stands located near the established plantations, 80 haplotypes were identified while some repeated genotypes were attributed to natural clones which appeared as a result of sprouting. The selected set of SSR markers showed reliable individual identification with low probability of appearance of identical aspen genotypes (a minimum of 4.8·10-10 and 1 × 10−4 for unrelated and related individuals, resp.). Case studies demonstrating practical applications of the test system are described including analysis of clonal structure and levels of genetic diversity in three natural aspen stands growing in the regions where plantations made of elite clones were established.

scholarly journals The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leaved Festuca species (Poaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9227
Author(s):  
Przemysław P. Tomczyk ◽  
Marcin Kiedrzyński ◽  
Iwona Jedrzejczyk ◽  
Monika Rewers ◽  
Pawel Wasowicz
Keyword(s):  
Genetic Diversity ◽  
Flow Cytometry ◽  
Population Genetics ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Model Organisms ◽  
Ploidy Levels ◽  
Hybrid Complex ◽  
Ssr Loci

Background Microsatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina—F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae—as a mountain and narrow endemic species and F. amethystina—a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context. Methods The ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented. Results Flow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them. Conclusions The transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes.

scholarly journals Polymorphisms in SSR-loci associated with E genes in soybean mutant lines offer perspective for breeding

2019 ◽  
Vol 6 (3) ◽  
pp. 45-55
Author(s):  
D. Zharikova ◽  
G. Chebotar ◽  
E. Aksyonova ◽  
I. Temchenko ◽  
S. Chebotar
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Vegetation Period ◽  
Vegetative Period ◽  
Soybean Cultivars ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Soybean Plants ◽  
Mutant Lines ◽  
And Control

Aim. To analyse genetic diversity in 10 new soybean lines created by using the chemical mutagens D-6, DMSSO-11, DMSSO-12, DMSNPIR-11, DUDMS12, D12DMC-11B obtained from four cultivars Femida, Oksana, Podils’ka 416, Zolotysta. The microsatellite (MS) markers Satt100, Satt229, Satt319, Satt354, Satt365, Sat_038 were used. These markers are linked with genes, which determine sensitivity of soybean plants to photoperiod and time to maturation. Methods of DNA extraction, PCR, MS-analysis, fi eld trial, one-way analysis of variance (ANOVA) have been applied. Results. Parental cultivars, mutant lines and control genotypes were characterized by alleles of microsatellite loci, 25 alleles of 6 microsatellite loci were detected. Signifi cant differences between investigated lines were detected in three year fi eld trials for traits − days to maturation (DTM) and length of the vegetative period (LV). We have revealed effects of the factor «Alleles of MS-locus», so alleles of Satt100 locus affected all traits except DTF (days to fl owering); alleles of Satt319 and Satt354 affected DTM and LV; Sat_038 affected DTF and S-F (duration of the period shoots-fl owering). Lines with alleles 167 bp at Satt100 and 175 bp at Satt319 loci (that marks dominant E7) were shown to have a longer vegetation period and later maturity, than other. The lines with allele 247 bp at Sat_038 fl owered earlier, than lines with a 245 bp allele, and the lines with allele 232 bp at Satt354 reached maturity later, than lines with other alleles at this locus. Conclusions. We have found that applied mutagens induce changes in the soybean genome and by using these mutagens it is possible to effectively increase genetic diversity in loci associated with genes/loci that determine time of maturity and/or photoperiod sensitivity of soybean, enabling to obtain soybean cultivars with different terms of maturity and yield. The microsatellite markers, particularly Sat_038, Satt100, Satt319 and Satt354 that were applied in our study are considered to be useful tools for marker assisted breeding of soybean cultivars with programmed time of development. We did not observe signifi cant effects of «Alleles of MS-locus Satt229» that is known to be linked with E3 on the investigated agronomical traits. For soybean genotypes with the E7 allele the DTF was longer for 3-9 days and LV for 10-11 days. In lines with an allele of 175 bp at locus Satt319 the S-F period was 6-9 days shorter

Assessment of the genetic diversity of microsatellite loci of horses of Heavy Draft breeds

2018 ◽  
pp. 39-44
Author(s):  
N. Blohina ◽  
◽  
L. Khrabrova ◽  
A. Zaitcev ◽  
I. Gavrilicheva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci

scholarly journals Stand out from the Crowd: Small-Scale Genetic Structuring in the Endemic Sicilian Pond Turtle

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 343
Author(s):  
Luca Vecchioni ◽  
Federico Marrone ◽  
Marco Arculeo ◽  
Uwe Fritz ◽  
Melita Vamberger
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Small Scale ◽  
Moderate Degree ◽  
Geographical Pattern ◽  
Genetic Structuring ◽  
Pond Turtle ◽  
Emys Trinacris ◽  
Polymorphic Microsatellite ◽  
Entire Distribution

The geographical pattern of genetic diversity was investigated in the endemic Sicilian pond turtle Emys trinacris across its entire distribution range, using 16 microsatellite loci. Overall, 245 specimens of E. trinacris were studied, showing high polymorphic microsatellite loci, with allele numbers ranging from 7 to 30. STRUCTURE and GENELAND analyses showed a noteworthy, geographically based structuring of the studied populations in five well-characterized clusters, supported by a moderate degree of genetic diversity (FST values between 0.075 and 0.160). Possible explanations for the genetic fragmentation observed are provided, where both natural and human-mediated habitat fragmentation of the Sicilian wetlands played a major role in this process. Finally, some conservation and management suggestions aimed at preventing the loss of genetic variability of the species are briefly reported, stressing the importance of considering the five detected clusters as independent Management Units.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Molecular Pathotyping of Plasmodiophora brassicae—Genomes, Marker Genes, and Obstacles

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 259
Author(s):  
Arne Schwelm ◽  
Jutta Ludwig-Müller
Keyword(s):  
Molecular Identification ◽  
Plasmodiophora Brassicae ◽  
Marker Genes ◽  
Future Perspectives ◽  
Genomic Information ◽  
Practical Applications ◽  
Genome Information

Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.

scholarly journals Isolation and Characterization of Microsatellite Loci of Clarias macrocephalus and Their Application to Genetic Diversity Study

1999 ◽  
Vol 65 (4) ◽  
pp. 520-526 ◽  
Author(s):  
Uthairat Na-Nakorn ◽  
Nobuhiko Taniguchi ◽  
Estu Nugroho ◽  
Shingo Seki ◽  
Wongpathom Kamonrat
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Isolation And Characterization ◽  
Clarias Macrocephalus ◽  
Genetic Diversity Study ◽  
Diversity Study

The spatial genetic structure of bank vole (Myodes glareolus) and yellow-necked mouse (Apodemus flavicollis) populations: The effect of distance and habitat barriers

2009 ◽  
Vol 59 (2) ◽  
pp. 169-187 ◽  
Author(s):  
Michal Kozakiewicz ◽  
Alicja Gryczyńska–Siemiątkowska ◽  
Hanna Panagiotopoulou ◽  
Anna Kozakiewicz ◽  
Robert Rutkowski ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Bank Vole ◽  
Microsatellite Loci ◽  
Myodes Glareolus ◽  
Apodemus Flavicollis ◽  
Island Populations ◽  
Local Populations ◽  
Bank Vole Myodes Glareolus ◽  
Yellow Necked Mouse

AbstractHabitat barriers are considered to be an important factor causing the local reduction of genetic diversity by dividing a population into smaller sections and preventing gene flow between them. However, the “barrier effect” might be different in the case of different species. The effect of geographic distance and water barriers on the genetic structure of populations of two common rodent species – the yellow-necked mouse (Apodemus flavicollis) and the bank vole (Myodes glareolus) living in the area of a lake (on its islands and on two opposite shores) was investigated with the use of microsatellite fragment analysis. The two studied species are characterised by similar habitat requirements, but differ with regard to the socio-spatial structure of the population, individual mobility, capability to cross environmental barriers, and other factors. Trapping was performed for two years in spring and autumn in north-eastern Poland (21°E, 53°N). A total of 160 yellow-necked mouse individuals (7 microsatellite loci) and 346 bank vole individuals (9 microsatellite loci) were analysed. The results of the differentiation analyses (FST and RST) have shown that both the barrier which is formed by a ca. 300 m wide belt of water (between the island and the mainland) and the actual distance of approximately 10 km in continuous populations are sufficient to create genetic differentiation within both species. The differences between local populations living on opposite lake shores are the smallest; differences between any one of them and the island populations are more distinct. All of the genetic diversity indices (the mean number of alleles, mean allelic richness, as well as the observed and expected heterozygosity) of the local populations from the lakeshores were significantly higher than of the small island populations of these two species separated by the water barrier. The more profound “isolation effect” in the case of the island populations of the bank vole, in comparison to the yellow-necked mouse populations, seems to result not only from the lower mobility of the bank vole species, but may also be attributed to other differences in the animals' behaviour.

scholarly journals Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Katherine L. James ◽  
Thushan I. de Silva ◽  
Katherine Brown ◽  
Hilton Whittle ◽  
Stephen Taylor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Blood Plasma ◽  
De Novo ◽  
A Priori ◽  
Pcr Amplification ◽  
Hiv Vaccine ◽  
Whole Genome ◽  
Plasma Samples ◽  
Target Enrichment ◽  
Rna Seq

ABSTRACTAccurate determination of the genetic diversity present in the HIV quasispecies is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in coinfected subjects. The majority of traditional and next-generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Additionally, target enrichment through PCR requiresa priorisequence knowledge, which is lacking for HIV-2. Therefore, a target enrichment free method of library preparation would be valuable for the field. We applied an RNA shotgun sequencing (RNA-Seq) method without PCR amplification to cultured viral stocks and patient plasma samples from HIV-2-infected individuals. Libraries generated from total plasma RNA were analyzed with a two-step pipeline: (i)de novogenome assembly, followed by (ii) read remapping. By this approach, whole-genome sequences were generated with a 28× to 67× mean depth of coverage. Assembled reads showed a low level of GC bias, and comparison of the genome diversities at the intrahost level showed low diversity in the accessory genevpxin all patients. Our study demonstrates that RNA-Seq is a feasible full-genomede novosequencing method for blood plasma samples collected from HIV-2-infected individuals.IMPORTANCEAn accurate picture of viral genetic diversity is critical for the development of a globally effective HIV vaccine. However, sequencing strategies are often complicated by target enrichment prior to sequencing, introducing biases that can distort variant frequencies, which are not easily corrected for in downstream analyses. Additionally, detaileda priorisequence knowledge is needed to inform robust primer design when employing PCR amplification, a factor that is often lacking when working with tropical diseases localized in developing countries. Previous work has demonstrated that direct RNA shotgun sequencing (RNA-Seq) can be used to circumvent these issues for hepatitis C virus (HCV) and norovirus. We applied RNA-Seq to total RNA extracted from HIV-2 blood plasma samples, demonstrating the applicability of this technique to HIV-2 and allowing us to generate a dynamic picture of genetic diversity over the whole genome of HIV-2 in the context of low-bias sequencing.

scholarly journals Molecular Characterization and Similarity Relationships among Flue-Cured Tobacco (Nicotiana tabacum L.) Genotypes Using Simple Sequence Repeat Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 247
Author(s):  
Soheila GHOLIZADEH ◽  
Reza DARVISHZADEH ◽  
Babak ABDOLLAHI MANDOULAKANI ◽  
Iraj BERNOUSI ◽  
Seyed Reza ALAVI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Allele Number ◽  
Nicotiana Tabacum L ◽  
Ssr Loci ◽  
Actual Degree ◽  
Similarity Relationships

Characterization of genetic diversity has long been a major goal in tobacco breeding programs. Information on genetic diversity is essential for a rational use of genetic resources. In the present study, the genetic variation among 72 flue-cured tobacco genotypes was evaluated using microsatellite markers (SSRs). A set of 104 alleles was generated at 30 SSR loci. The mean number of alleles per locus (na) and the effective allele number (ne) were 3.467 and 2.358, respectively. The expected heterozygosity ranged from 0.29 to 0.75 with average of 0.54. Several methods were used to construct the similarity matrices and dendrograms. The co-phenetic correlation coefficient, which is a measure of the correlation between the similarities represented on the dendrograms and the actual degree of similarity, was calculated for each dendrogram. Among the different methods, the highest value (r=0.76368) was observed for the UPGMA created based on Jaccard’s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccard’s similarity coefficient ranged from 0.08 to 0.84, suggesting the presence of high molecular genetic variability among the studied tobacco genotypes. Based on UPGMA clustering method all studied flue-cured tobacco genotypes, except for ‘Glustinusa Rasht’, were placed in three distinct groups. We observed an obvious heterotic pattern in the studied flue-cured germplasm corresponding to genetic distances and classification dendrogram, which persuades exploitation of heterosis in flue-cured tobaccos.

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