scholarly journals Evaluation of genetic diversity and relationships among eight Russian and Ukrainian cattle breeds based on microsatellite markers

2019 ◽  
Vol 10 (4) ◽  
pp. 388-393
Author(s):  
E. A. Snegin ◽  
A. S. Kramarenko ◽  
E. A. Snegina ◽  
S. S. Kramarenko
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphism ◽  
Russian Federation ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Effective Population ◽  
Very High Frequency ◽  
Cattle Breeds ◽  
The Russian Federation ◽  
Very High

In recent years, special attention has been paid both to the preservation of the genetic diversity of cattle breeds in the Russian Federation and Ukraine, and to the evaluation of the breeds’ ‘purity’, especially in relation to undesirable recessive lethal mutations. The main goal of our work was to assess the genetic diversity of the main cattle breeds bred in the Russian Federation and Ukraine using microsatellite DNA loci, as well as to evaluate the phylogenetic relationships between them. An analysis of molecular genetic diversity was carried out in different cattle breeds represented both in the Russian Federation and Ukraine. A total of 752 individuals, which belonged to eight breeds of the dairy and meat productivity directions were studied. Ten microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (ETH3, INRA023, TGLA227, BM1818, TGLA122, SPS115, TGLA53, BM2113, BM1824 and ETH10) were used as DNA markers. Some alleles were found with a very high frequency in most of the studied cattle breeds and, thus, they can be considered as species-specific for the species Bos taurus as a whole. These were alleles 262 and 266 bp (for BM1818), 180 and 188 bp (for BM1824), 125-127 and 133-135 bp (for BM2113), 217-219 bp (for ETH10), 248 and 252 bp (for SPS115). All breeds included in the analysis are characterized by a very high genetic uniqueness based on microsatellite loci; the accuracy of assigning the studied individuals to their own population varied within the range of 95–100%. In general, all breeds studied are grouped into two clusters. Cluster No. 1 contains genetic groups originating from Holstein, and cluster No. 2 contains the remaining breeds. Three breeds (Ayrshire, Simmental and Russian Red Pied) are characterized by very low estimates of the effective population size (less than 50 animals), which may lead to the loss of their genetic uniqueness in the future. In the study of eight dairy and meat cattle breeds that are bred in the Russian Federation and Ukraine, we found that the breeds differ significantly in the genetic polymorphism indicators over ten MS-DNA loci used. Moreover, the level of allelic diversity for the studied breeds was determined, primarily, by the presence and number of rare (and/or “private”) alleles. This may be due to the manifestation of different mechanisms of the formation and maintenance of genetic polymorphism in breeds, based on productivity direction.

scholarly journals Genetic polymorphism of mountain-taiga populations of siberian stone pine in Kusnetsky Alatau

2021 ◽  
Vol 28 ◽  
pp. 30-35
Author(s):  
N. V. Oreshkova ◽  
t. S. Sedelnikova ◽  
S. P. Efremov ◽  
A. V. Pimenov
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphism ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Individual Growth ◽  
Pinus Sibirica ◽  
Stone Pine ◽  
Siberian Stone Pine ◽  
Siberian Stone ◽  
Nuclear Microsatellite

Aim. Study of DNA polymorphism of 7 coenopopulations of Siberian stone pine (Pinus sibirica) growing in theKuznetsk Alatau. Methods. Nuclear microsatellite loci developed for P. sibirica were used as genetic markers. Results. 44 allelic variants were identified from 11 nuclear microsatellite loci, which significantly differ in the composition and frequency of occurrence of the studied P. sibirica coenopopulations. The highest level of allelic diversity is found in loci Ps_80612 and Ps_1502048, where 8 and 7 alleles were identified, respectively. The calculation of the main parameters of genetic diversity showed a relatively low level of polymorphism in the studied samples (NA = 3.078; NE = 1.877; HE = 0.445; HO = 0.401). The assessment of the degree of genetic differences between populations using the Nei genetic distance (DN) showed that, despite the low genetic differentiation (DN varies from 0.019 to 0.061), the differences between them can be traced quite clearly. Conclusions. Differences in the level of genetic polymorphism of P. sibirica is defined by the presence of orographic and phytocoenotic barriers between coenopopulations, as well as a high degree of ecological and anthropogenic extremity of individual growth sites. Keywords: Pinus sibirica, Kuznetsk Alatau, microsatellites, genetic diversity, heterozygosity.

Genetic diversity and forensic parameters of 12 X-STR included in Argus X-12® marker panel in the population of the Russian Federation

2021 ◽  
pp. 1-13
Author(s):  
Andrei Semikhodskii ◽  
Yevgeniy Krassotkin ◽  
Tatiana Makarova ◽  
Vladislav Zavarin ◽  
Viktoria Ilina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Russian Federation ◽  
Marker Panel ◽  
The Russian Federation ◽  
Forensic Parameters

scholarly journals Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals GENETIC DIVERSITY OF THE MITOCHONDRIAL GENOME OF LANDRACE PIGS

PIG-BREEDING ◽  
2021 ◽  
pp. 13-15
Author(s):  
BAKOEV N.F. ◽  
◽  
GETMANTSEVA L.V. ◽  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Genome ◽  
Russian Federation ◽  
Loop Area ◽  
D Loop ◽  
The Russian Federation ◽  
Breeding Farms

The paper presents the results of a study of the D-loop area in Landrace pigs (n=49). Amplification of the mtDNA D-loop fragment was performed according to Sanger's method. The experiments showed that modern Landrace pigs in the breeding farms of the Russian Federation are distinguished by a sufficient intra-breed diversity and have different haplotypes that belong to both the European and Asian haplogroups.

scholarly journals Features of the Epidemiological Situation on Siberian Tick Typhus and other Tick-Borne Ricketsioses in the Russian Federation, Prognosis for 2019

2019 ◽  
pp. 89-97 ◽  
Author(s):  
N. V. Rudakov ◽  
S. N. Shpynov ◽  
D. V. Trankvilevsky ◽  
N. D. Pakskina ◽  
D. A. Savel’ev ◽  
...  
Keyword(s):  
Russian Federation ◽  
Far East ◽  
Laboratory Diagnostics ◽  
The Far East ◽  
Natural Foci ◽  
Causative Agents ◽  
Risk Areas ◽  
The Russian Federation ◽  
Very High ◽  
Epidemiological Situation

The review presents an analysis of the epidemic situation on infections of rickettsial etiology, the causative agents of which are transmitted by Ixodidae ticks in the territory of the Russian Federation. The data obtained through molecular-biological verification allow to unite under the name of “tick-borne ricketsioses” a group of infections caused by R. sibirica subsp. sibirica, R. conorii, R. heilongjiangensis and other species of rickettsiae circulating in natural foci of various regions of Russia. Cases of tick-borne rickettsioses in Siberia and the Far East, caused by various species of rickettsiae, are registered under the name of “Siberian tick-borne typhus” due to the lack of available methods of differential laboratory diagnostics. The paper presents the assessment of the incidence of Siberian tick-borne typhus, indicating not only the varying degrees of epidemic hazard of endemic regions, but also changes in the distribution of risk areas, including the identification of new, epidemically significant foci. In accordance with the risk-oriented approach to prophylaxis, forecasting of epidemic situation on tick-borne rickettsioses was given and differentiation of the endemic territories of the Russian Federation as regards Siberian tick-borne typhus was carried out with distinguishing of epidemiological zones of low, medium, above average, high and very high risk of population infection.

scholarly journals NG-MAST GENOTYPING OF NEISSERIA GONORRHOEAE STRAINS ISOLATED IN RUSSIAN FEDERATION IN 2012 - 2015

2016 ◽  
pp. 42-51 ◽  
Author(s):  
D. V. Vorobiev ◽  
V. S. Solomka ◽  
K. I. Plakhova ◽  
D. G. Deryabin ◽  
A. A. Kubanov
Keyword(s):  
Genetic Diversity ◽  
Neisseria Gonorrhoeae ◽  
Russian Federation ◽  
Variable Regions ◽  
The Russian Federation ◽  
First Time ◽  
Sequence Types

Aim. Characteristics of contemporary strains of N. gonorrhoeae using NG-MAST genotyping (.Neisseria gonorrhoeae multi-antigen sequence typing), isolation of dominating variants and analysis of their territorial distribution. Materials and methods. 440 strains of N. gonorrhoeae isolated in 2012 - 2015 in 19 subjects of the Russian Federation were used in the study. Genotyping was carried out based on sequencing of variable regions of porB and tbpB genes. Identification of alleles and sequence-types was carried out according to http://www.ng-mast.net. Results. 172 NG-MAST genotypes were identified, 100 of which -were described for the first time. 807,1152, 1544,5714 and 5941 were predominating sequence-types, typical for several subjects of the Russian Federation and some neighboring countries, as well as sequence-types 8583 and 9476 described for the first time, that were exclusively distributed in the regions of their emergence. Sequence-types 225, 1407 and 2992, that are epidemically significant in distant countries, were represented by single isolates in this study. Conclusion. A peculiar and significant genetic diversity of N. gonorrhoeae strains, circulating in the Russian Federation, with characteristic bond of several NG-MAST genotypes to one or several regions, was shown.

scholarly journals Genetic diversity in natural populations of Hancornia speciosa Gomes: Implications for conservation of genetic resources

2018 ◽  
Vol 42 (6) ◽  
pp. 623-630
Author(s):  
Cristiane Gouvêa Fajardo ◽  
Daniel Ferreira da Costa ◽  
Kyvia Pontes Teixeira das Chagas ◽  
Fábio de Almeida Vieira
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Allelic Diversity ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Effective Population ◽  
Infinite Allele Model ◽  
Hancornia Speciosa

ABSTRACT The continuing fragmentation of forests has been a threat to the maintenance of genetic resources. Genetic diversity is fundamental to the survival of species in natural environments in the long term, as well as being the basis for genetic improvement. The objective of this study was to evaluate the genetic diversity in natural populations of Hancornia speciosa and to contribute to the development of conservation strategies. We sampled 105 individuals of H. speciosa, distributed in seven populations. The ISSR (Inter-Simple Sequence Repeat) markers provided 70 loci, of which 81% were polymorphic. The mean genetic diversity of Nei (h) was 0.19, and the Shannon index (I) was 0.27. The h and I diversity indices ranged respectively from 0.16 to 0.24 in the PAD (Parque das Dunas) population and from 0.21 to 0.29 in MAC (Macaíba) population. Resulting from a Bayesian analysis, the genotypes were divided into four groups (K = 4). The allelic diversity patterns observed indicated the occurrence of the genetic bottleneck in all populations, according to the stepwise mutation model (SMM). The infinite allele model (IAM) revealed an imbalance between mutation and genetic drift only in the PAD population. Genetic conservation strategies for H. speciosa should cover each genetic group that was differentially structured. We recommend in situ conservation and the creation of germplasm banks, especially with the PAD population which demonstrated the lower genetic diversity and decreased effective population size according to the two mutational models.

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