scholarly journals A new genetic distance with application to constrained variation at microsatellite loci

1999 ◽  
Vol 16 (4) ◽  
pp. 467-471 ◽  
Author(s):  
L. A. Zhivotovsky
Keyword(s):  
Genetic Distance ◽  
Microsatellite Loci ◽  
Constrained Variation

scholarly journals Genetic variability of the fifth generation of nile tilapia Oreochromis niloticus using microsatellite DNA markers

2015 ◽  
Vol 10 (2) ◽  
pp. 124
Author(s):  
Gloria Ika Satriani ◽  
Dinar Tri Soelistyowati ◽  
Dian Hardianto ◽  
Ratu Siti Aliah
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Dna Markers ◽  
Microsatellite Loci ◽  
Microsatellite Dna ◽  
Nile Tilapia ◽  
Fifth Generation ◽  
Freshwater Aquaculture ◽  
Microsatellite Dna Markers ◽  
Aquaculture Development

<p>ABSTRACT</p><p><br />Fifth generations of Nile tilapia from several strains have been produced by using selective breeding program in Main Centre for Freshwater Aquaculture Development (MCFAD) Sukabumi, West Java. This research was aimed to evaluate the impact of family selection program of some highly economic traits on its genetic variability using microsatellite DNA markers. The total of 180 specimens have been collected from fifth generation of nine reciprocal mating between three families selected from fourth generation of Nile tilapia and were screened for genetic variability at three microsatellite loci (UNH 123*, UNH 172*, UNH 216*). The results showed that the amount of genetic variability on fifth generations of Nile tilapia from three strains was ranged between 33 to 100% and the highest genetic distance relationship between families was 0.3875. This research approved that females and males issued from the family which have more amount of genetic variability and higher distance to others could be considered as genetic materials to produce the next generation.</p><p><br />Keywords: microsatellite DNA, genotype, genetic variability, genetic distance, Oreochromis nilotiocus</p><p><br /> ABSTRAK</p><p><br />Beberapa strain ikan nila generasi kelima telah dihasilkan dalam program pemuliaan di Main Centre untuk Freshwater Aquaculture Development (MCFAD) Sukabumi, Barat Jawa. Riset ini bertujuan untuk mengevaluasi pengaruh seleksi famili terhadap performa karakter ekonomis penting berdasarkan keragaman genetiknya menggunakan penanda microsatellite DNA. Spesimen dari 180 individu generasi kelima hasil persilangan resiprokal antara tiga famili generasi keempat dianalisis dengan penanda tiga microsatellite loci (UNH 123*, UNH 172*, UNH 216*). Hasil penelitian menunjukkan bahwa keragaman genetik ikan nila generasi kelima berkisar antara 33 sampai 100% dan hubungan kekerabatan genetik antar famili yang paling jauh adalah 0,3875. Individu betina dan jantan yang berasal dari famili dengan tingkat keragaman genetik dan kekerabatan yang lebih tinggi dapat dipertimbangkan sebagai sumber genetik berkualitas untuk menghasilkan generasi berikutnya.<br />Kata kunci: microsatellite DNA, genotipe, keragaman genetik, jarak genetik, Oreochromis nilotiocus</p>

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

Genetic analysis of ten sheep breeds using microsatellite markers

2000 ◽  
Vol 80 (1) ◽  
pp. 9-17 ◽  
Author(s):  
A. Farid ◽  
E. O'Reilly ◽  
C. Dollard ◽  
C.R. Kelsey Jr.
Keyword(s):  
North America ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Narrow Range ◽  
The Other ◽  
The North ◽  
Expected Heterozygosity

The genetic variability of 257 sheep from 10 breeds; North Country Cheviot (NCC), Cheviot (CHE), Dorset (DOR), Suffolk (SUF), Scottish Blackface (SBF), Texel (TEX), Romanov (ROM), Finnish Landrace (FIN), Icelandic (ICE) and Red Masai (MAS) was assessed using 10 microsatellite loci. The average number of alleles per locus was 4.3 in ROM, 5.0 in MAS, and spanned a narrow range (5.4 to 6.0) in the other breeds. Estimates of expected heterozygosity (HE) of the breeds varied within 0.05 point of each other (0.62 in FIN to 0.67 in CHE), except for ROM (0.53) which was lower (P < 0.05) than those of the other breeds, and in MAS (0.57), which was lower (P < 0.05) than those of NCC, CHE and SBF. Estimates of observed heterozygosity (HO) of the breeds were the lowest in MAS, ROM and SUF (0.50 to 0.53) and the highest in NCC and CHE (0.64 and 0.67). The HE was greater (P < 0.01) than HO only in SUF. The results suggest that there have not been drastic losses of genetic variability in the intensely selected breeds. The low genetic variability of ROM was probably due to a small number of animals imported to North America. The British breeds (NCC, CHE, SUF, DOR, SBF) were genetically close to each other, as were the North European breeds (ROM, ICE, FIN). MAS was remotely related to the British breeds, but it was surprisingly close to the North European breeds. TEX was more closely related to the British breeds than to the North European breeds. More than 90% of 1000 simulated individuals from each breed were assigned to the correct breed, indicating that this panel of markers is useful for the identification of breed membership of individual animals, and could be used to protect the integrity of registered breeds. Key words: Sheep, genetic variability, genetic distance, microsatellites

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 Dynamics of Repeat Polymorphisms Under a Forward-Backward Mutation Model: Within- and Between-Population Variability at Microsatellite Loci

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 549-555 ◽  
Author(s):  
Marek Kimmel ◽  
Ranajit Chakraborty ◽  
David N Stivers ◽  
Ranjan Deka
Keyword(s):  
Genetic Distance ◽  
Microsatellite Loci ◽  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Distance Measure ◽  
Divergence Time ◽  
Human Populations ◽  
Mathematical Basis ◽  
Microsatellite Variation ◽  
Components Of Variance

Abstract Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite loci evolve via some form of forward-backward mutation. We provide a mathematical basis for suggesting a measure of genetic distance between populations based on microsatellite variation. Our results indicate that such a genetic distance measure can remain proportional to the divergence time of populations even when the forward-backward mutations produce variable and/or directionally biased alleles size changes. If the population size and the rate of mutation remain constant, then the measure will be proportional to the time of divergence of populations. This genetic distance is expressed in terms of a ratio of components of variance of allele sizes, based on expressions developed for studying population dynamics of quantitative traits. Application of this measure to data on 18 microsatellite loci in nine human populations leads to evolutionary trees consistent with the known ethnohistory of the populations.

The isolation and characterization of 18 equine microsatellite loci, TKY272–TKY289

2000 ◽  
Vol 31 (2) ◽  
pp. 149-149 ◽  
Author(s):  
T Tozaki ◽  
H Kakoi ◽  
S Mashima ◽  
K Hirota ◽  
T Hasegawa ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Isolation And Characterization
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