scholarly journals Microsatellites for the Neotropical Ant, Odontomachus chelifer (Hymenoptera: Formicidae)

2020 ◽  
Vol 20 (5) ◽  
Author(s):  
Alessandra S M Lemos ◽  
Marianne Azevedo-Silva ◽  
Salatiel Gonçalves-Neto ◽  
Anete P Souza ◽  
Paulo S Oliveira
Keyword(s):  
Genetic Diversity ◽  
Egg Laying ◽  
Enriched Library ◽  
Cerrado Savanna ◽  
History Of ◽  
The Mean ◽  
Polymorphism Level ◽  
Diversity Estimates ◽  
Odontomachus Chelifer

Abstract Odontomachus chelifer (Latreille) (Ponerinae) is a ground-dwelling, predominantly carnivorous ant whose colonies may contain multiple egg-laying queens and are potentially susceptible to border effects in the Brazilian savanna known as Cerrado. The ecology and natural history of O. chelifer is well studied, but very little is known about the genetic diversity of O. chelifer colonies. In this study, we developed microsatellite markers for the study of genetic variation in O. chelifer. We created a microsatellite-enriched library that resulted in the development and characterization of 22 markers, of which 18 were found to be polymorphic in the population studied. The mean expected heterozygosity was 0.59, whereas the mean rarified allelic richness was determined as 4.27 alleles per locus. The polymorphism level detected was similar to genetic diversity estimates found in other poneromorph ant species. The microsatellites developed here are likely to be useful for the investigation of colony structure, functional polygyny, breeding system, and population genetics in O. chelifer. Moreover, the description of O. chelifer’s genetic diversity is crucial for its conservation and maintenance of its ecological role in the Cerrado savanna.

scholarly journals Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

2021 ◽  
Vol 118 (34) ◽  
pp. e2104315118
Author(s):  
Pasquale Tripodi ◽  
Mark Timothy Rabanus-Wallace ◽  
Lorenzo Barchi ◽  
Sandip Kale ◽  
Salvatore Esposito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Focal Region ◽  
Nucleotide Polymorphisms ◽  
Trade Routes ◽  
Genebank Management ◽  
Capsicum Spp ◽  
History Of ◽  
Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

scholarly journals Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of Schinus molle L.

Biology ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 43 ◽  
Author(s):  
Rafael Lemos ◽  
Cristiane Matielo ◽  
Dalvan Beise ◽  
Vanessa da Rosa ◽  
Deise Sarzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Invasive Plant ◽  
Whole Genome Sequencing Data ◽  
Natural Occurrence ◽  
Sequencing Data ◽  
Dispersal Capacity ◽  
Schinus Molle ◽  
High Dispersal ◽  
History Of

Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree (Schinus molle L.) is a pioneer tree species native from South America which was introduced in North America, Europe and Africa, becoming a threat to these non-native habitats. In this study, we report the discovery and characterization of 17 plastidial (ptSSR) and seven nuclear (nSSR) markers for S. molle based on low-coverage whole-genome sequencing data acquired through next-generation sequencing. The markers were tested in 56 individuals from two natural populations sampled in the Brazilian Caatinga and Pampa biomes. All loci are moderately to highly polymorphic and revealed to be suitable for genetic monitoring of new invasions, for understanding the history of old invasions, as well as for genetic studies of native populations in their natural occurrence range and of orchards established with commercial purposes.

scholarly journals TU-DAMD employment for molecular characterization of Salvia judaica and Salvia palaestina species

2021 ◽  
Vol 65 (1) ◽  
pp. 11-16
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Annealing Temperature ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Marker Index ◽  
C Cycle ◽  
Separated Sets ◽  
Polymorphism Level

Genetic diversity in perennial Salvia judaica Boiss (Judean sage) and Salvia palaestina Benth (Palestinian sage) species using touch-up directed amplification of minisatellite region DNA (TU-DAMD) has been performed in two separated sets; in the first set (set A) the initial annealing temperature was increased from 50 °C to 55 °C, whereas, in the second one (set B), it increased from 55 °C to 60 °C by 0.5 °C/cycle during the first 10 PCR amplification cycles. Fifteen DAMD primers have been tested for each set. Set (A) produced 89.39% polymorphism level (P%) with polymorphic information content (PIC) average of 0.33 and marker index (MI) average of 3.96. Whereas, in set (B) these values were recorded to be 94.02%, 0.34 and 3.98 for P%, PIC and MI, respectively. Data showed that the two mentioned sets successfully highlighted high polymorphism level between the two studied Salvia sp. This work studies genetic diversity of S. judaica and S. palaestina species using TU-DAMD test as a novel molecular marker.

scholarly journals Short Note: Isolation and Characterization of 12 Polymorphic Microsatellite Markers in Engelhardia roxburghiana (Juglandaceae)

2014 ◽  
Vol 63 (1-6) ◽  
pp. 109-112 ◽  
Author(s):  
Dan-Dan Zhang ◽  
Pi Luo ◽  
Ying Chen ◽  
Zheng-Feng Wang ◽  
Wan-Hui Ye ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Short Note ◽  
Screening Method ◽  
Wide Distribution ◽  
Enriched Library ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
Polymorphic Microsatellite

Abstract Engelhardia roxburghiana is a common half evergreen tree with a wide distribution in southeast Asia. Despite its ecological and pharmaceutical values, its genetic diversity is poorly studied. Our objective was to develop nuclear microsatellite markers to investigate the level of genetic diversity within and among populations in the future. Using the microsatellite-enriched library and PCR-based screening method, 12 microsatellite markers were developed and showed polymorphism in a population. The number of alleles per locus for these 12 microsatellites ranged from four to 15. The observed and expected heterozygosities ranged from 0.358 to 0.897 and from 0.369 to 0.886, respectively. The developed microsatellites will be useful for studying genetic diversity and population structure in E. roxburghiana.

New pieces on genetic diversity and evolutionary history of hepatitis B virus: Characterization of the novel subgenotype F6

2017 ◽  
Vol 47 ◽  
pp. 140-142 ◽  
Author(s):  
Laura Noelia Mojsiejczuk ◽  
Carolina Torres ◽  
María Belén Pisano ◽  
Viviana Re ◽  
Rodolfo Héctor Campos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Evolutionary History ◽  
The Novel ◽  
B Virus ◽  
History Of

scholarly journals Isolation and Characterization of Microsatellites For The Endangered Endemic Tree Nothofagus Alessandrii (Nothofagaceae)

2021 ◽  
Author(s):  
Cristian Torres-Díaz ◽  
Moisés A. Valladares ◽  
Marco A. Molina-Montenegro ◽  
Freddy Mora-Poblete
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Genetic Connectivity ◽  
Mean Values ◽  
Isolation And Characterization ◽  
Genetic Diversity And Structure ◽  
Hardy Weinberg Equilibrium ◽  
The Mean ◽  
Pooled Sample

Abstract Nothofagus alessandrii (Nothofagaceae) is one of the most endangered trees from Chile. Despite its conservation status, few molecular markers are available to study its population genetic, connectivity and to assist reproduction programs. Novel polymorphic microsatellites from the genome of N. alessandrii were isolated and characterized using high-through sequencing. A total of 30 primer pairs were synthesized and 18 microsatellites were amplified correctly. Polymorphism and genetic diversity was evaluated in 58 individuals from three populations of N. alessandrii. Sixteen of them were polymorphic and the number of alleles in the pooled sample ranged from 2 to 14, the mean number of alleles was 4.81. The mean values of observed heterozigosity (HO) and excepted heterozygosity (HE) of the Chanco population were 0.392 and 0.383. The mean values of HO and HE in the population of Empedrado (0.397 and 0.360, respectively) and Fundo el Desprecio (0.397 and 0.395, respectively) were similar. Linkage disequilibrium was found in a few pairs of loci suggesting that most of the markers can be considered as independent. Significant deviations from Hardy- Weinberg equilibrium (P < 0.05) were found in several loci probably due to low sampling size. Transferability to the congeneric N. pumilio was successful in only four out of the sixteen polymorphic markers. The microsatellite markers developed in this study will be useful to study the genetic diversity and structure and to develop integrated managements plans for the conservation on this endangered species.

scholarly journals Molecular Characterization of Lates niloticus (Perciformes, Latidae) Populations from three Nigerian Waterbodies using Random Amplified Polymorphic DNA and Microsatellite Markers

2017 ◽  
Vol 51 (1) ◽  
pp. 31-36
Author(s):  
K. E. Ogbuebunu ◽  
M. O. Awodiran
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Random Amplified Polymorphic Dna ◽  
Population Level ◽  
Effective Number ◽  
Lates Niloticus ◽  
The Mean

Abstract Thirty Lates niloticus (Linnaeus, 1758) from three Nigerian waterbodies were genotyped on six RAPD primers and five microsatellites loci. RAPD revealed that effective number of alleles (AE) at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN) across populations equals 2.000. Characterization on five microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO) was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE) was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of differentiation (FST) within populations was 0.236. Overall gene flow (Nm) among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fish species, especially L. niloticus. Thus, it can be concluded that L. niloticus in the three (3) sampled Nigerian waterbodies is undergoing evolution.

scholarly journals The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

2019 ◽  
Author(s):  
Tanita Wein ◽  
Tal Dagan
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Bottleneck ◽  
Population Bottlenecks ◽  
High Genetic Diversity ◽  
Temperature Regimes ◽  
Consequent Reduction ◽  
History Of

Abstract Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

scholarly journals Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 229 ◽  
Author(s):  
Anouk E. van Breukelen ◽  
Harmen P. Doekes ◽  
Jack J. Windig ◽  
Kor Oldenbroek
Keyword(s):  
Genetic Diversity ◽  
Gene Bank ◽  
Cattle Breeds ◽  
Holstein Friesian ◽  
Native Cattle ◽  
Core Sets ◽  
The Mean ◽  
Mean Similarity

In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. Based on these similarities, most breeds were clearly differentiated, except for two breeds (Deep Red and Improved Red and White) that have recently been derived from the MRY breed, and for the Dutch Friesian and Dutch Friesian Red, which have frequently exchanged bulls. Optimal contribution selection (OCS) was used to construct core sets of bulls with a minimized similarity. The composition of the gene bank appeared to be partly optimized in the semen collection process, i.e., the mean similarity within breeds based on the current number of straws per bull was 0.32% to 1.49% lower than when each bull would have contributed equally. Mean similarity could be further reduced within core sets by 0.34% to 2.79% using OCS. Material not needed for the core sets can be made available for supporting in situ populations and for research. Our findings provide insight in genetic diversity in Dutch cattle breeds and help to prioritize material in gene banking.

scholarly journals Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L

2021 ◽  
Vol 78 (3) ◽  
Author(s):  
Sara Stefanowska ◽  
Katarzyna Meyza ◽  
Grzegorz Iszkuło ◽  
Igor J. Chybicki
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Demographic History ◽  
Genetic Bottleneck ◽  
Tree Age ◽  
Taxus Baccata ◽  
Census Size ◽  
Germplasm Collections ◽  
History Of ◽  
The Mean

Abstract Key message Taxus baccata remnants established recently tend to contribute less to the species’ overall genetic variation than historical populations because they are subjected to a greater impact of the founder effect and genetic isolation. As tree trunk perimeter is a rough indicator of genetic variation in a population, this measure should be considered in conservation programs. Context Genetic variation within Taxus baccata (L.) populations is not associated with the current census size but correlates well with the effective size, suggesting that genetic drift intensity reflects variation in demographic histories. Aims We hypothesize that recently established populations are subjected to greater bottleneck than old remnants. Using the mean trunk perimeter as a surrogate of tree age, we test whether the demographic history and genetic variation are associated with the mean tree age. Methods Using 18 microsatellite markers, we analyze the genetic diversity and demographic history of 11 yew populations in Poland to assess the relationship between the mean trunk perimeter and the inferred genetic parameters. Results Populations reveal significant differences in levels of genetic variation and in the intensity and time of genetic bottleneck. After excluding an apparent outlier, the genetic variation is significantly greater while the bottleneck intensity lower in populations with a greater perimeter. Conclusion Due to continuous species decline and increasing fragmentation, the non-uniform contribution of yew remnants to the overall genetic variation tends to decrease together with the mean tree age. Germplasm collections for the species should take into account tree perimeter as a rough indicator of the genetic variation of a population.

Sign in / Sign up

Export Citation Format

Share Document