scholarly journals Monitoring for the genetic structure of Mezen breed of horses in terms of DNA microsatellites

2021 ◽  
Vol 25 (2) ◽  
pp. 202-207
Author(s):  
N. V. Vdovina ◽  
I. B. Yuryeva
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Gene Pool ◽  
Nuclear Dna ◽  
Small Population ◽  
Dna Microsatellites ◽  
Time Intervals ◽  
Average Value ◽  
Far North ◽  
Northern Territories

Mezenskaya horse (Mezenka) is Russia’s aboriginal breed. It is a domestic selection in the northern territories of Arkhangelsk region. The breed is perfectly adapted to the conditions of the Far North, and has a number of valuable economic and biological qualities. At present, it has a limited gene pool and is bred only in the Mezensky district, where one gene pool-breeding farm is operating and so is a number of basic farms, where selection and breeding activities take place with the breed. Due to a small population of Mezen horses, the challenge of preserving its intra-breed diversity is very urgent. To determine the degree of genetic variability in the Mezen population, the alleles-fond was monitored. A comparative analysis of the genetic structure of the breed was done on DNA microsatellites at time-intervals of 10 years (2000, 2010 and 2020). Crista samples of 198 horses were studied in specialized laboratories. It was established that the breed has wide genetic diversity in 17 loci of nuclear DNA. The population’s alleles-fond includes from 128, 139, and 133 alleles respectively (with an average value of 7.53, 8.18, and 7.82 alleles per locus). The most common alleles are AHT4O, AHT5N, ASB2K, ASB23S, CA425N, HMS1J, HMS1M, HMS2H, HMS3M, HMS7L, HTG4M, HTG6O, HTG7K, HTG7O and LEX3M. Mezen horses revealed 6 rare, lowfrequency (0.004–0.056) alleles not found in the horse populations of domestic selection. The average value of the polymorphic level (Ae) in the breed over the years is 4.16, 4.21 and 4.06, respectively. The highest polymorphism is found in locus ASB17 (6.49–6.90–6.76); the lowest, in locus HTG6 (1.71–1.66–1.67) and HMS7 (1.77–1.95–1.77). A slight deficit of heterozygous genotypes (Fis = 0.003) was observed in Mezen horses in 2010. In 2000 and 2020, the observed heterozygosity (Ho) exceeds the expected value (He), which indicates the absence of intra-population inbreeding (Fis = –0.014 and –0.011, respectively). The results obtained testify to the effectiveness of breeding activities carried out to preserve, improve and maintain genetic diversity in the population.

scholarly journals Genetic diversity in portuguese native Vitis vinifera L. ssp. vinifera and ssp. sylvestris

2010 ◽  
Vol 46 (Special Issue) ◽  
pp. S54-S56 ◽  
Author(s):  
J. Cunha ◽  
M. Teixeira Santos ◽  
J. Brazăo ◽  
L.C. Carneiro ◽  
M. Veloso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Vitis Vinifera ◽  
Gene Pool ◽  
Western Europe ◽  
Eastern European ◽  
Starting Point ◽  
Probable Origin ◽  
Different Origins

To assess the different origins of Portuguese grapevine varieties, we used six nuclear and four chloroplastidal microsatellites as molecular markers, in order to compare the genetic structure of native wild-vines with native grapevine varieties. Both native subspecies have a great diversity, and a high interrelationship across the six nuclear microsatellites. Although identical numbers of alleles were found in each population, their distribution was different in the <I>vinifera </I>and <I>sylvestris </I>subspecies. Portuguese wild-vines have only chlorotypes A and B; A being the most frequent. The fifty-seven analysed Portuguese varieties have chlorotypes A, B, C, and D. The most frequent was the chlorotype A (75%), followed by D (21%). The results obtained reinforced the idea of Western Europe as having been one of the domestication centres for the grapevine, with contributions from the Eastern European gene pool. The observed genetic structure is a starting point from which to clarify the high number of native cultivars found in Portugal, and reinforces their probable origin in the Iberian Peninsula.

scholarly journals Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

2015 ◽  
Vol 2 (8) ◽  
pp. 140255 ◽  
Author(s):  
Claire C. Keely ◽  
Joshua M. Hale ◽  
Geoffrey W. Heard ◽  
Kirsten M. Parris ◽  
Joanna Sumner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Urban Expansion ◽  
Nuclear Gene ◽  
Management Approach ◽  
Natural Habitats ◽  
High Genetic Diversity ◽  
Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

scholarly journals Analysis of the genetic structure of a population of Lebedyn cattle by microsatellite markers

2019 ◽  
Vol 10 (1) ◽  
pp. 45-49
Author(s):  
V. І. Ladyka ◽  
L. M. Khmelnychyi ◽  
Y. V. Lyashenko ◽  
R. O. Kulibaba
Keyword(s):  
Genetic Structure ◽  
Microsatellite Markers ◽  
Gene Pool ◽  
Population Genetic ◽  
Molecular Genetic ◽  
Cattle Breed ◽  
Fixation Index ◽  
Experimental Population ◽  
Negative Effects ◽  
Average Value

Microsatellites – a separate class of molecular genetic markers, are widely used for the study of genetic variability, in particular in populations of animals bred by artificial selection under the influence of microevolutionary processes. The object of study is the gene pool of a population of animals of the Lebedyn cattle breed, which is under threat of extinction. The sample comprised 30 individuals from the farm "Komyshans'ke" in Sumy region. The analysis of population genetic structure was performed using 10 microsatellite loci recommended by FAO-ISAG: ETH225, BM2113, ETH3, BM1818, BM1824, ILSTS006, INRA023, TAGLA053, TAGLA12, ETH10. Amplification products were separated in polyacrylamide gels of different concentrations (5–8%), both native and denaturing. All studied loci were polymorphic. The number of detected alleles per locus ranged from 4 to 8 (on average 5 alleles per locus), the size of which ranged from 115 bp (ETH3) to 307 bp (ILSTS006). The majority of the investigated loci (except ETH3) belonged to valuable informative markers (PIC > 0.5). The most polymorphic TGLA053 (8 alleles), BM2113 (6) and ETH3 (6) loci have been identified. In general, the minimum number of alleles (4) was fixed in 50% loci. The main population genetic parameters for the studied loci have been calculated. The highest values of heterozygosity (He), and effective number of alleles (ne) was characterized for loci BM2113, ILSTS006, TGLA053 and ETH225. With the exception of ETH3 and VM1818 loci, the experimental group of animals is in a state of genetic equilibrium. The average value of the Wright fixation index indicates a tendency to increase in the number of homozygous individuals (inbreeding). Comparative analysis of genetic structure of breeds that have a common origin (Lebedyn (PJSC "Mykhaylivka"), Ukrainian grey (DPDG "Polyvanivka"), Red steppe (DPPR "Stepne"), etc.) has been carried out. The obtained results give grounds to assert that in the experimental population of the Lebedyn breed there are processes that lead to a decrease in genetic diversity. In order to overcome the negative effects of artificial reproduction in the gene pool of small populations of cattle, which include Lebedyn cattle, it is appropriate to use microsatellite markers in the selection and breeding work.

Genetic Diversity and Population Genetic Structure in the Rare Chittering Grass Wattle, Acacia anomala Court

1988 ◽  
Vol 36 (3) ◽  
pp. 273 ◽  
Author(s):  
DJ Coates
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Genetic System ◽  
Small Population ◽  
Vegetative Multiplication ◽  
The Mean ◽  
Allozyme Loci

There are 10 known populations of Acacia anomala occurring in two small disjunct groups some 30 km apart. The Chittering populations reproduce sexually whereas the Kalamunda populations appear to reproduce almost exclusively by vegetative multiplication. The level and distribution of genetic variation were studied at 15 allozyme loci. Two loci were monomorphic in all populations. In the Chittering populations the mean number of alleles per locus was 2.0 and the expected panmictic heterozygosity (genetic diversity) 0.209. In the Kalamunda populations the mean number of alleles per locus was 1.15 and the expected panmictic heterozygosity 0.079, although the observed heterozygosity of 0.150 was only marginally less than the Chittering populations (0.177). These data support the contention that the Chittering populations are primarily outcrossing whereas the Kalamunda populations are clonal, with each population consisting of individuals with identical and, in three of the four populations, heterozygous, multilocus genotypes. The level of genetic diversity within the Chittering populations is high for plants in general even though most populations are relatively smsll and isolated. It is proposed that either the length of time these populations have been reduced in size and isolated is insufficient for genetic diversity to be reduced or the genetic system of this species is adapted to small population conditions. Strategies for the adequate conservation of the genetic resources of Acacia anomala are discussed.

scholarly journals Genetic Structure and Diversity Among Maize Inbred Lines as Inferred From DNA Microsatellites

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2117-2128 ◽  
Author(s):  
Kejun Liu ◽  
Major Goodman ◽  
Spencer Muse ◽  
J Stephen Smith ◽  
Ed Buckler ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Gene Pool ◽  
Gene Diversity ◽  
Inbred Lines ◽  
Pedigree Information ◽  
Maize Inbred Lines ◽  
Core Sets ◽  
Maize Inbreds ◽  
Genetic Structure And Diversity

AbstractTwo hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A “phylogenetic” tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture &lt;80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.

Population genetic structure andWolbachiainfection in an endangered butterfly,Zizina emelina(Lepidoptera, Lycaenidae), in Japan

2014 ◽  
Vol 105 (2) ◽  
pp. 152-165 ◽  
Author(s):  
Y. Sakamoto ◽  
N. Hirai ◽  
T. Tanikawa ◽  
M. Yago ◽  
M. Ishii
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Nuclear Dna ◽  
Geographic Distance ◽  
Fixation Index ◽  
Migratory Activity ◽  
Dna Analyses ◽  
Mitochondrial Haplotypes ◽  
Male Killer

AbstractZizina emelina(de l'Orza) is listed on Japan's Red Data List as an endangered species because of loss of its principal food plant and habitat. We compared parts of the mitochondrial and nuclear genes of this species to investigate the level of genetic differentiation among the 14 extant populations. We also examined infection of the butterfly with the bacteriumWolbachiato clarify the bacterium's effects on the host population's genetic structure. Mitochondrial and nuclear DNA analyses revealed that haplotype composition differed significantly among most of the populations, and the fixation indexFSTwas positively correlated with geographic distance. In addition, we found three strains ofWolbachia, one of which was a male killer; these strains were prevalent in several populations. There was linkage between some host mitochondrial haplotypes and the threeWolbachiastrains, although no significant differences were found in a comparison of host mitochondrial genetic diversity with nuclear genetic diversity inWolbachia-infected or -uninfected populations. These genetic analyses andWolbachiainfection findings show thatZ. emelinahas little migratory activity and that little gene flow occurs among the current populations.

scholarly journals Fine-Scale Spatial Patterns of the Genetic Diversity of European Beech (Fagus sylvatica L.) around a Mountainous Glacial Refugium in the SW Balkans

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 725
Author(s):  
Olympia Tsipidou ◽  
Ludger Leinemann ◽  
Georgios Korakis ◽  
Reiner Finkeldey ◽  
Oliver Gailing ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fagus Sylvatica ◽  
Nuclear Dna ◽  
European Beech ◽  
Glacial Refugia ◽  
Glacial Refugium ◽  
Fine Scale ◽  
Dna Microsatellites ◽  
Gene Markers ◽  
Fagus Sylvatica L

Beech (Fagus sylvatica L.) is one of the most important forest trees in Europe and its current broad expanse over the continent is believed to be the outcome of the Holocene postglacial expansion of lineages originating from different glacial refugia. Studies using gene markers, pollen profiles and fossils suggest the main locations of glacial refugia in Southern Europe. In this study, we conduct a fine-scale genetic study on the beech populations surrounding the Almopia basin, an area that is said to have hosted one of the main European glacial refugia for several plant and animal species during the Pleistocene Epoch. We test the hypothesis of the existence of a local refugium in the study area for beech to understand the spatial genetic pattern of the putative refugial beech populations in the area and to investigate possible genetic connections between the local beech populations and the European expansion of the species. The genetic diversity of 100 sampled trees in 20 plots representing the expansion of beech in the area was studied using chloroplast and nuclear DNA microsatellites (cpSSR and nSSR, respectively). All three cpSSR regions were polymorphic, resulting in eight haplotypes, separated spatially in two distinct groups (one on the western and the other on the eastern part of the Almopia basin) that correspond to two different postglacial beech lineages. Furthermore, the cpSSR sequences of the eastern lineage are genetically identical to those of beech populations extending over central and northern Europe. The nSSR markers were highly polymorphic, and the trees studied were separated into two genetic groups that coincided with the cpSSR ones in locations where the topography is more pronounced. These results indicated that the Almopia region was indeed a major refugium for beech that possibly produced two main postglacial lineages for Europe, one of which is connected with the majority of beech populations growing on the continent. These southern refugial populations are important diversity centers that need to be the subject of special management and conservation.

scholarly journals Genetic diversity of the Andean tetraploid cultivated potato (Solanum tuberosum L. subsp. andigena Hawkes) evaluated by chloroplast and nuclear DNA markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Thitaporn Sukhotu ◽  
Osamu Kamijima ◽  
Kazuyoshi Hosaka
Keyword(s):  
Genetic Diversity ◽  
Solanum Tuberosum ◽  
Chloroplast Dna ◽  
Gene Pool ◽  
Nuclear Dna ◽  
Solanum Tuberosum L ◽  
Diploid Species ◽  
Distribution Area ◽  
Rflp Markers ◽  
Long Distance

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are native farmer-selected important cultivars that form a primary gene pool of the common potato (Solanum tuberosum L. subsp. tuberosum). The genetic diversity of 185 Andigena accessions and 6 Chilean native potatoes (S. tuberosum subsp. tuberosum) was studied using chloroplast DNA (ctDNA) microsatellites and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Andigena potatoes had 14 ctDNA haplotypes and showed higher variability in the central Andes, particularly in Bolivia, whereas those in the northern regions of the distribution area were remarkably uniform with A1 ctDNA and Chilean subsp. tuberosum with T ctDNA. Most of 123 clearly scored RFLP bands using 30 single-copy probes were randomly distributed throughout the distribution area and proved the same gene pool shared among these widely collected accessions. Nevertheless, the geographic trend of the nDNA differentiation from north to south along the Andes and the correlated differentiation between nDNA and ctDNA (r = 0.120) could also be revealed by canonical variates analysis. These results suggest that the genetic diversity in Andigena was brought about primarily from cultivated diploid species but considerably modified through sexual polyploidization and intervarietal and (or) introgressive hybridization and long-distance dispersal of seed tubers by humans.Key words: Andigena, chloroplast DNA, nuclear DNA, RFLP, geographic trend, diversity.

scholarly journals Demographic decline and lineage-specific adaptations characterize New Zealand kiwi

2021 ◽  
Vol 288 (1965) ◽  
Author(s):  
Jordan B. Bemmels ◽  
Else K. Mikkelsen ◽  
Oliver Haddrath ◽  
Rogan M. Colbourne ◽  
Hugh A. Robertson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Size ◽  
Genetic Drift ◽  
Demographic History ◽  
Small Population ◽  
Population Declines ◽  
Demographic Stochasticity ◽  
Fragmented Populations ◽  
Low Genetic Diversity

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

scholarly journals Analysis of Genetic Structure of Huchen (Hucho Hucho) in Serbia Inferred From Mitochondrial and Nuclear DNA

2014 ◽  
Vol 64 (2) ◽  
pp. 236-244 ◽  
Author(s):  
Saša Marić ◽  
Andrej Razpet ◽  
Vera Nikolić ◽  
Aleš Snoj ◽  
Predrag Simonović
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Control Region ◽  
Nuclear Dna ◽  
Microsatellite Data ◽  
Danube Basin ◽  
Mitochondrial Dna Control Region ◽  
Species Management ◽  
Conservation And Management

Abstract The purpose of this study was to assess the genetic diversity of Serbian huchen and provide guidelines for conservation and management. Fourteen huchen individuals were collected from six localities. For all individuals the mitochondrial DNA control region and the NADH1 gene were sequenced, and two microsatellite loci were genotyped. Sequencing of two mtDNA loci showed the presence of the same haplotypes (Hh_CR_1 and Hh_ND1_1) in all investigated specimens and the complete absence of genetic variability at inter- and intra-populational level. However, analyzed individuals from Serbia have the largest number of control region repeats (average 8.7) compared to all other huchen populations from the Danube basin. Microsatellite data show that the most of Serbian huchens were placed in the “eastern” cluster except one individual from the Drina River which clustered with “western” samples, most likely a consequence of stocking. In spite of only two loci used, four unique alleles found in the studied Serbian and Drina basin population indicate that the Danube basin may possess more region specific alleles than previously thought, which could be of great importance for efficient species management in the future.

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