Genetic Structure of World Animal Populations

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 55765

Special Issue Editors


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Guest Editor
Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska st. 33, 60-637 Poznan, Poland
Interests: statistical animal genetics and genomics; conservation of animal genetic resources; Bayesian methods; information theory.

E-Mail Website
Guest Editor
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy
Interests: dairy cattle; economic values; genetic improvement; animal products; livestock biodiversity; genetic traceability

Special Issue Information

There are over 15,000 species of mammals and birds around the world. They are a huge wealth for our civilization. The majority of them are free-living, subject to various threats from the natural environment, such as climate change, urbanization, etc. Sometimes, zoos  are their only asylum, due to implemented conservation programs.

Although only a small percentage of animal species are considered farm animals, their numbers are much greater than those of animals living in the wild. The results of applied  genetic-improvement programs  (based on selection and crossbreeding) are many breeds, varieties, and commercial lines. Over the last decades, the advancing globalization of animal husbandry has led to a significant reduction in local populations, and consequently many species have been included in genetic resources conservation programs. However, new and often endangered populations are still being discovered, especially in developing countries.

The genetic structure of livestock and wild animal populations will be the topic of a Special Issue of Genes. We invite you to submit review articles, original papers, and short communications on genetic variation within and between animal populations. We hope that this Special Issue will be a valuable compendium of knowledge concerning not only biodiversity but also modern methods of molecular and statistical data analysis.

Prof. Dr. Tomasz Szwaczkowski
Prof. Dr. Martino Cassandro
Guest Editors

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Keywords

  • Conservation programs
  • Genetic diversity
  • Molecular markers
  • Local breeds
  • Pedigree analysis
  • Wild animal populations
  • Zoos

Published Papers (18 papers)

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Research

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16 pages, 1039 KiB  
Article
Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds
by Felipe Avila, Shayne S. Hughes, K. Gary Magdesian, Maria Cecilia Torres Penedo and Rebecca R. Bellone
Genes 2022, 13(9), 1641; https://doi.org/10.3390/genes13091641 - 13 Sep 2022
Cited by 9 | Viewed by 6222
Abstract
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. [...] Read more.
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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10 pages, 1748 KiB  
Article
Evaluation of the Impact of the Peregrine Falcon (Falco peregrinus peregrinus) Reintroduction Process on Captive-Bred Population
by Karol O. Puchała, Zuzanna Nowak-Życzyńska, Sławomir Sielicki and Wanda Olech
Genes 2022, 13(8), 1487; https://doi.org/10.3390/genes13081487 - 20 Aug 2022
Viewed by 1964
Abstract
The main objective of this study was to determine the impact of increased demand for peregrine falcons via breeding (mainly Polish, Czech, German and Slovak) on the genetic structure of the birds. In the analysis, 374 specimens from six countries were sampled in [...] Read more.
The main objective of this study was to determine the impact of increased demand for peregrine falcons via breeding (mainly Polish, Czech, German and Slovak) on the genetic structure of the birds. In the analysis, 374 specimens from six countries were sampled in 2008–2019 (omitting 2009), and all the birds analyzed were released into the wild as part of the Polish reintroduction program. The assessment of genetic variation was based on a well-known panel of 10 microsatellite markers described for the species. We calculated a fixation index for the samples from each year, and based on this, we determined the level of inbreeding. We also performed an analysis using the Bayesian cluster method, assuming that 1–19 hypothetical populations would define the division that best fit the samples. The most probable division was into two groups; in the first group, the samples from individuals delivered in 2013 were most often segregated; moreover, in this year, a jump in inbreeding, expressed by the fixation index, was observed. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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33 pages, 6276 KiB  
Article
Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds
by Yousra Ben Sassi-Zaidy, Aziza Mohamed-Brahmi, Melek Chaouch, Fabio Maretto, Filippo Cendron, Faouzia Charfi-Cheikhrouha, Souha Ben Abderrazak, Mnaour Djemali and Martino Cassandro
Genes 2022, 13(8), 1421; https://doi.org/10.3390/genes13081421 - 10 Aug 2022
Cited by 4 | Viewed by 2234
Abstract
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), [...] Read more.
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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10 pages, 1297 KiB  
Article
Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)
by Alejandra M. Toro-Ospina, Ana C. Herrera Rios, Gustavo Pimenta Schettini, Viviana H. Vallejo Aristizabal, Wellington Bizarria dos Santos, Cesar A. Zapata and Edna Gicela Ortiz Morea
Genes 2022, 13(7), 1232; https://doi.org/10.3390/genes13071232 - 12 Jul 2022
Cited by 5 | Viewed by 2642
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs [...] Read more.
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4–8 Mb, 8–16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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13 pages, 2525 KiB  
Article
Genetic Structure of Racing Pigeons (Columba livia) Kept in Poland Based on Microsatellite Markers
by Angelika Podbielska and Anna Radko
Genes 2022, 13(7), 1175; https://doi.org/10.3390/genes13071175 - 29 Jun 2022
Viewed by 3143
Abstract
Pigeons played a major role in communication before the invention of the telephone and the telegraph, as well as in wars, where they were used to carry information and orders over long distances. Currently, numerous sports competitions and races are held with their [...] Read more.
Pigeons played a major role in communication before the invention of the telephone and the telegraph, as well as in wars, where they were used to carry information and orders over long distances. Currently, numerous sports competitions and races are held with their participation, and their breeding is demanding not only for breeders, but also for the birds themselves. Therefore, an analysis of the genetic structure of racing pigeons kept in Poland was undertaken on the basis of 16 microsatellite markers, as well as the evaluation of the microsatellite panel recommended by ISAG. For this purpose, Bayesian clustering, a dendrogram, and Principal Coordinate Analysis were conducted. In addition, statistical analysis was performed. Based on this research, it was observed that racing pigeons are genetically mixed, regardless of their place of origin. Moreover, genetic diversity was estimated at a relatively satisfactory level (Ho = 0.623, He = 0.684), and no alarmingly high inbreeding coefficient was observed (F = 0.088). Moreover, it was found that the panel recommended by ISAG can be successfully used in Poland for individual identification and parentage testing (PIC = 0.639, CE-1P = 0.9987233, CE-2P = 0.9999872, CE-PP = 0.99999999). Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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13 pages, 668 KiB  
Article
Analysis of Complementary Sex-Determiner (csd) Allele Diversity in Different Honeybee Subspecies from Italy Based on NGS Data
by Gianluigi Paolillo, Maria Grazia De Iorio, Joel F. Soares Filipe, Federica Riva, Alessandra Stella, Gustavo Gandini, Giulio Pagnacco, Barbara Lazzari and Giulietta Minozzi
Genes 2022, 13(6), 991; https://doi.org/10.3390/genes13060991 - 31 May 2022
Cited by 3 | Viewed by 1919
Abstract
Sexual regulation in Apis mellifera is controlled by the complementary sex-determiner (csd) gene: females (queens and workers) are heterozygous at this locus and males (drones) are hemizygous. When homozygous diploid drones develop, they are eaten by worker bees. High csd allelic diversity in [...] Read more.
Sexual regulation in Apis mellifera is controlled by the complementary sex-determiner (csd) gene: females (queens and workers) are heterozygous at this locus and males (drones) are hemizygous. When homozygous diploid drones develop, they are eaten by worker bees. High csd allelic diversity in honeybee populations is a priority for colony survival. The focus of this study is to investigate csd variability in the genomic sequence of the hypervariable region (HVR) of the csd gene in honeybee subspecies sampled in Italy. During the summer of 2017 and 2018, worker bees belonging to 125 colonies were sampled. The honeybees belonged to seven different A. mellifera subspecies: A. m. ligustica, A. m. sicula, A. m cecropia, A. m. carnica, A. m. mellifera, Buckfast and hybrid Carnica. Illumina genomic resequencing of all samples was performed and used for the characterization of global variability among colonies. In this work, a pipeline using existing resequencing data to explore the csd gene allelic variants present in the subspecies collection, based on de novo assembly of sequences falling within the HVR region, is described. On the whole, 138 allelic sequences were successfully reconstructed. Among these, 88 different alleles were identified, 68 of which match with csd alleles present in the NCBI GenBank database. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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14 pages, 2873 KiB  
Article
Genetic Structure of the Root Vole Microtus oeconomus: Resistance of the Habitat Specialist to the Natural Fragmentation of Preferred Moist Habitats
by Rafał Łopucki, Iwona Mróz, Zuzanna Nowak-Życzyńska, Magdalena Perlińska-Teresiak, Edyta Owadowska-Cornil and Daniel Klich
Genes 2022, 13(3), 434; https://doi.org/10.3390/genes13030434 - 27 Feb 2022
Cited by 3 | Viewed by 2590
Abstract
Climate-related changes have a severe impact on wetland ecosystems and pose a serious challenge for wetland-dependent animals as their preferred habitats decline, lose spatial continuity, and appear as isolated islands in the landscape. In this paper, we studied the effects of long-term habitat [...] Read more.
Climate-related changes have a severe impact on wetland ecosystems and pose a serious challenge for wetland-dependent animals as their preferred habitats decline, lose spatial continuity, and appear as isolated islands in the landscape. In this paper, we studied the effects of long-term habitat changes (drying out and fragmentation of wet non-forest habitats) on the genetic structure of the population of the root vole Microtus oeconomus, a species preferring moist habitats. We intended to check what barriers and what distances affected its genetic isolation on a local scale. The study was conducted in the area of Kampinoski National Park in central Poland (Europe). DNA variability of 218 root vole individuals was assessed by genotyping nine microsatellite loci. Despite its spatial fragmentation, the studied population did not seem to be highly structured, and isolation through distance was the main differentiating factor. Even a distance of several kilometres of unfavourable natural habitats and unfavourable terrain did not exclude the exchange of genes between subpopulations. Our results suggest that the genetic effects of the fragmentation of wetlands have been considerably compensated (delayed) due to the migratory abilities of this species. Our study does not provide clear results on the impact of anthropogenic barriers but suggests that such barriers may have a much stronger effect than natural barriers. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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13 pages, 1472 KiB  
Article
Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis
by Yousra Ben Sassi-Zaidy, Aziza Mohamed-Brahmi, Ghada Nouairia, Faouzia Charfi-Cheikhrouha, M’Naouer Djemali and Martino Cassandro
Genes 2022, 13(2), 304; https://doi.org/10.3390/genes13020304 - 5 Feb 2022
Cited by 8 | Viewed by 2201
Abstract
This study analyzed the genetic variability, inbreeding and population structure of the Tunisian–North African dairy sheep breed, the Sicilo-Sarde (SS), created by crossing the Sarda and Comisana dairy breeds. The level of variability in the SS, considered as an endangered breed after a [...] Read more.
This study analyzed the genetic variability, inbreeding and population structure of the Tunisian–North African dairy sheep breed, the Sicilo-Sarde (SS), created by crossing the Sarda and Comisana dairy breeds. The level of variability in the SS, considered as an endangered breed after a dramatic decrease, was assessed using 17 microsatellite markers by analyzing the two breed populations sampled from their respective cradles: SS of Beja (SSB, n = 27) and SS of Mateur (SSM, n = 25). High levels of genetic diversity in SS were revealed, with a total of 212 alleles, a high mean number of alleles (12.47 ± 4.17) and a high average polymorphism information content (PIC) (0.81 ± 0.10). The observed heterozygosity was considerable in SSB and SSM (0.795 and 0.785, respectively). The inbreeding level measured by the population inbreeding coefficient FIS is higher in the SSM population (0.121) than in the SSB population (0.090). The higher genetic diversity level detected in SSB reflected the effect of new Italian Sarda genes introduced by intra-uterine artificial insemination recently practiced in this population. The Wilcoxon test and the mode-shift distribution indicated that the SS breed is a non-bottlenecked population. The structural analysis reflected the historical miscegenation practiced during the breed creation and highlighted further ancient miscegenation, which could date back to the first waves of sheep introduction to the western Mediterranean region. Microsatellite markers were successfully applied in the assessment of the genetic variability of SS and should be used in monitoring this variability during the application of conservation strategies. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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18 pages, 2542 KiB  
Article
Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin
by Nina Moravčíková, Radovan Kasarda, Radoslav Židek, Luboš Vostrý, Hana Vostrá-Vydrová, Jakub Vašek and Daniela Čílová
Genes 2021, 12(6), 832; https://doi.org/10.3390/genes12060832 - 28 May 2021
Cited by 4 | Viewed by 3402
Abstract
This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the [...] Read more.
This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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11 pages, 1846 KiB  
Article
Assessment of the Genetic Potential of the Peregrine Falcon (Falco peregrinus peregrinus) Population Used in the Reintroduction Program in Poland
by Karol O. Puchała, Zuzanna Nowak-Życzyńska, Sławomir Sielicki and Wanda Olech
Genes 2021, 12(5), 666; https://doi.org/10.3390/genes12050666 - 29 Apr 2021
Cited by 3 | Viewed by 2320
Abstract
Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for [...] Read more.
Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1–15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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27 pages, 4145 KiB  
Article
Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes
by Katarzyna Kozyra, Tomasz M. Zając, Hermann Ansorge, Heliodor Wierzbicki, Magdalena Moska, Michal Stanko and Pavel Stopka
Genes 2021, 12(5), 642; https://doi.org/10.3390/genes12050642 - 26 Apr 2021
Cited by 7 | Viewed by 3540
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained [...] Read more.
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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16 pages, 1571 KiB  
Article
Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes
by Heliodor Wierzbicki, Magdalena Zatoń-Dobrowolska, Anna Mucha and Magdalena Moska
Genes 2021, 12(5), 637; https://doi.org/10.3390/genes12050637 - 25 Apr 2021
Cited by 3 | Viewed by 2258
Abstract
In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated [...] Read more.
In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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10 pages, 624 KiB  
Communication
Microsatellite DNA Analysis for Diversity Study, Individual Identification and Parentage Control in Pig Breeds in Poland
by Anna Radko, Grzegorz Smołucha and Anna Koseniuk
Genes 2021, 12(4), 595; https://doi.org/10.3390/genes12040595 - 19 Apr 2021
Cited by 6 | Viewed by 2642
Abstract
Swine DNA profiling is of high importance for animal identification and parentage verification. The aim of this study was to test a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in Polish Landrace (PL, n = 900), Polish Large [...] Read more.
Swine DNA profiling is of high importance for animal identification and parentage verification. The aim of this study was to test a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in Polish Landrace (PL, n = 900), Polish Large White (PLW, n = 482), Pulawska (PUL, n = 127), and Duroc pigs (DU n = 108). The studied breeds showed a medium level of genetic differentiation. The average value of heterozygosity and degree of polymorphism (PIC) were above 0.5 for the studied breeds, except for the DU breed (PIC = 0.477). The population inbreeding coefficient indicates an absence of inbreeding in the studied breeds (an average value of FIS = 0.007). The cumulative power of discrimination for all breeds reached high values close to 1.0, while the probability of identity (PID) was low, with PID values ranging between 10−9 (for DU) and 10−12 (for PLW). The cumulative exclusion probability for PE1 and PE2 showed that the parentage can be confirmed with a probability of from 92.75% to 99.01% and from 99.49% to 99.97%, respectively. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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9 pages, 1363 KiB  
Article
Genetic Variability and Population Structure of Polish Konik Horse Maternal Lines Based on Microsatellite Markers
by Agnieszka Fornal, Katarzyna Kowalska, Tomasz Zabek, Agata Piestrzynska-Kajtoch, Adrianna D. Musiał and Katarzyna Ropka-Molik
Genes 2021, 12(4), 546; https://doi.org/10.3390/genes12040546 - 9 Apr 2021
Cited by 6 | Viewed by 2295
Abstract
The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines [...] Read more.
The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines as possible. The Polish Konik, a native Polish primitive-type horse breed and is one of the breeds included in such a programme in Poland. Presently, there are only 16 (of the 35 maternal lines known in 1962), some of which are endangered. We examined the genetic variability and structure of the Polish Konik maternal lines (176 individuals) on the basis of the pedigree data and 17 microsatellite markers (STRs) from parentage testing. The overall mean number of alleles was 7.647 (±0.411), the effective number of alleles was 3.935 (±0.271), the mean number of alleles for which the frequency was equal to or lower than 5% was 4.471 (±0.286), and the mean information index was 1.506 (±0.087). The structure of the population and admixture patterns were calculated with the Structure and Structure Harvester software. The structural analysis indicated three likely genetic clusters; as the most optimal K value was estimated as 3, with ∆K of 15.4188. The F-statistics results indicated a low level of inbreeding (average inbreeding coefficient FIT was 0.0188, coefficient of differentiation FST was 0.0304, and mean inbreeding index value FIS was −0.0119). Variability monitoring should be carried out in order to avoid inbreeding depression, while breeding strategies should be designed to prevent the decrease of genetic variability in the Polish horse breed and to sustain the active female lines. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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11 pages, 1165 KiB  
Article
Microsatellite DNA Analysis of Genetic Diversity and Parentage Testing in the Popular Dog Breeds in Poland
by Anna Radko and Angelika Podbielska
Genes 2021, 12(4), 485; https://doi.org/10.3390/genes12040485 - 26 Mar 2021
Cited by 12 | Viewed by 4094
Abstract
There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in [...] Read more.
There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in Poland and evaluated the effectiveness of a 21-microsatellite (STR) panel recommended by the International Society for Animal Genetics (ISAG) for parent verification. The following breeds were characterized: German Shepherd, Maltese, Irish Wolfhound, Yorkshire Terrier, Biewer Yorkshire Terrier, Golden Retriever, Labrador Retriever, and French Bulldog. STRUCTURE analysis showed breed distinctiveness among all the dog breeds under study. Reynold’s distance ranged between θw = 0.634 and θw = 0.260. The studied breeds showed a medium level of genetic differentiation; the mean number of alleles per locus ranged from 3.4 to 6.6, and the effective number of alleles from 2.1 to 3.5. The mean degree of heterozygosity varied from 49% to 69% and from 47% to 68% for HO and HE, respectively. The population inbreeding coefficient (FIS) indicated an absence of inbreeding in the studied breeds. The average polymorphism information content (PIC) values for most of the breeds were higher than 0.5. The cumulative power of discrimination (PD) for all the markers in all breeds reached high values (close to 1.0), while the probability of identity (PID) was low, ranging between 10−11 and 10−19. The cumulative exclusion probability when the genotypes of one (PE1) and both parents (PE2) are known and showed that the parentage can be confirmed with a probability of 94.92% to 99.95% and 99.78% to 99.9999%, respectively. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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18 pages, 5423 KiB  
Article
Waves Out of the Korean Peninsula and Inter- and Intra-Species Replacements in Freshwater Fishes in Japan
by Shoji Taniguchi, Johanna Bertl, Andreas Futschik, Hirohisa Kishino and Toshio Okazaki
Genes 2021, 12(2), 303; https://doi.org/10.3390/genes12020303 - 21 Feb 2021
Cited by 8 | Viewed by 4292
Abstract
The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia by about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated [...] Read more.
The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia by about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated by lowered sea level. As the Korean Peninsula and Japanese archipelago were not covered by an ice sheet during glacial periods, phylogeographical analyses in this region can trace the history of biota that were, for a long time, beyond the last glacial maximum. In this study, we analyzed the phylogeography of four freshwater fish taxa, Hemibarbus longirostris, dark chub Nipponocypris temminckii, Tanakia ssp. and Carassius ssp., whose distributions include both the Korean Peninsula and Western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. The replacements of indigenous populations by succeeding migrants may have also influenced the phylogeography. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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Review

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14 pages, 2573 KiB  
Review
Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes
by Karolína Machová, Anežka Málková and Luboš Vostrý
Genes 2022, 13(4), 613; https://doi.org/10.3390/genes13040613 - 29 Mar 2022
Cited by 10 | Viewed by 3437
Abstract
Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated [...] Read more.
Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes. Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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Other

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9 pages, 2949 KiB  
Case Report
Mitochondrial Markers for the Detection of Duck Breeds Using Polymerase Chain Reaction
by Małgorzata Natonek-Wiśniewska, Piotr Krzyścin and Dominika Rubiś
Genes 2021, 12(6), 857; https://doi.org/10.3390/genes12060857 - 3 Jun 2021
Cited by 3 | Viewed by 2002
Abstract
Species identification of the components of various duck breeds has revealed that the lowest identifiable number of components depends on the breed. The results (shown on the agarose gel) of a species-specific PCR reaction for Rouen ducks were less intense than the results [...] Read more.
Species identification of the components of various duck breeds has revealed that the lowest identifiable number of components depends on the breed. The results (shown on the agarose gel) of a species-specific PCR reaction for Rouen ducks were less intense than the results for the same amount of components from other popular duck breeds, suggesting differences in the Rouen duck genome. Therefore, the present study aimed to identify part of the Rouen duck’s gene sequences and to develop two new primer pairs. The first pair enables breed-independent identification of duck DNA, and the second distinguishes Rouen ducks from Chinese and Indian Runner ducks. The sequencing reaction yielded sequences of 1386 bp in length, and the identified sequence differs by around 7% from the sequences of Chinese duck species. The detected sequence contributes to improving species identification methods for duck DNA. On its basis, two primers for the identification of duck DNA were designed. The first allows for DNA amplification with the same sensitivity regardless of duck breed. The second primer’s pair is breed specific, and it distinguishes Rouen ducks from Chinese and Indian Runner ducks. Both methods are very sensitive (0.05%). Full article
(This article belongs to the Special Issue Genetic Structure of World Animal Populations)
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