Publications by authors named "Szilvia Kusza"

26 Publications

  • Page 1 of 1

Mitochondrial DNA Suggests the Introduction of Honeybees of African Ancestry to East-Central Europe.

Insects 2021 May 2;12(5). Epub 2021 May 2.

Department of Zoology and Animal Welfare, University of Agriculture in Krakow, Adama Mickiewicza 24/28, 30-059 Kraków, Poland.

In Europe, protecting the genetic diversity of is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66-3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/insects12050410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8147603PMC
May 2021

Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa.

Genome Biol Evol 2021 May 1. Epub 2021 May 1.

Department of Zoology, National Museums of Kenya, Nairobi, Kenya.

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evab090DOI Listing
May 2021

Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe.

Sci Rep 2021 May 6;11(1):9680. Epub 2021 May 6.

Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland.

The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-88991-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102581PMC
May 2021

Genetic Diversity and Structure of Common Carp ( L.) in the Centre of Carpathian Basin: Implications for Conservation.

Genes (Basel) 2020 10 28;11(11). Epub 2020 Oct 28.

Animal Genetics Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.

Hungary is one of the largest common carp-production countries in Europe and now, there is a large number of local breeds and strains in the country. For proper maintenance of the animal genetic resources, information on their genetic diversity and structure is essential. At present, few data are available on the genetic purity and variability of the Hungarian common carp. In this study, we genetically analyzed 13 strains in Hungary and, in addition, the Amur wild carp, using 12 microsatellite markers. A total of 117 unique alleles were detected in 630 individuals. Low levels of genetic differentiation (F and Cavalli-Sforza and Edwards distance) were estimated among strains. The AMOVA showed the low but significant level of genetic differentiation among strains (3.79%). Bayesian clustering analysis using STRUCTURE classified the strains into 14 different clusters. The assignment test showed that 93.64% of the individuals could be assigned correctly into their original strain. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of threatened strains of common carp.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11111268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693397PMC
October 2020

Population Genetic Structure of the Wild Boar () in the Carpathian Basin.

Genes (Basel) 2020 10 14;11(10). Epub 2020 Oct 14.

NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary.

In the Carpathian Basin the wild boar () belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different ( < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an F value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations' genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces' having been preserved from both the last ice age and the period before the Hungarian water regulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11101194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602151PMC
October 2020

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color.

Genes (Basel) 2020 08 13;11(8). Epub 2020 Aug 13.

Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy.

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort F-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including , , , and , were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11080932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464420PMC
August 2020

863 genomes reveal the origin and domestication of chicken.

Cell Res 2020 08 25;30(8):693-701. Epub 2020 Jun 25.

Department of Animal Science, Iowa State University, Ames, IA, USA.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41422-020-0349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395088PMC
August 2020

Author Correction: Hotspots of recent hybridization between pigs and wild boars in Europe.

Sci Rep 2019 Dec 24;9(1):20187. Epub 2019 Dec 24.

Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-55961-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6930290PMC
December 2019

Maternal genomic variability of the wild boar () reveals the uniqueness of East-Caucasian and Central Italian populations.

Ecol Evol 2019 Sep 27;9(17):9467-9478. Epub 2019 Jul 27.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology Chinese Academy of Sciences Kunming China.

The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian ( = 8), European ( = 64), and North African ( = 5) wild boar. Our analyses provided evidence of unique lineages in the East-Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.5415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745674PMC
September 2019

Hotspots of recent hybridization between pigs and wild boars in Europe.

Sci Rep 2018 11 26;8(1):17372. Epub 2018 Nov 26.

Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark.

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-35865-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255867PMC
November 2018

Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778).

PLoS One 2018 4;13(10):e0204653. Epub 2018 Oct 4.

Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary.

European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204653PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171851PMC
March 2019

Genetic characterization of indigenous goat breeds in Romania and Hungary with a special focus on genetic resistance to mastitis and gastrointestinal parasitism based on 40 SNPs.

PLoS One 2018 9;13(5):e0197051. Epub 2018 May 9.

Department of Research, Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania.

Goat breeding has become an important sector in Eastern Europe, with Romania and Hungary being among the major producer countries. Given the limited number of research done up-to-date concerning genetic studies of indigenous goat breeds reared in Romania and Hungary, the current preliminary study aimed to analyze the variability of genes related to mastitis and gastrointestinal parasitism by using Kompetitive Allele Specific PCR (KASP™). We studied 52 single nucleotide polymorphisms (SNPs) belonging to 19 genes in indigenous breeds from both countries, namely Banat's White (n = 36), Carpatina (n = 35) from Romania and Hungarian Milking (n = 79) and identified 16 polymorphic SNPs among 10 genes (PTX3, IL6, CLEC4E, IL8, IL1RN, IL15RA, TNFSF13, SOCS3, TNF and TLR3) in 150 animals. Furthermore, the diversity of the studied breeds was investigated. The PIC values ranged from 0.042 to 0.691. The mean values of observed and expected heterozygosity were 0.235 and 0.246 respectively. The highest observed heterozygosity was obtained for IL15RA g.10343904C>T in Banat's White (0.464), IL15RA g.10354813C>T in Carpatina (0.577) and SOCS3 g.52626440T>G in Hungarian Milking (0.588). Pairwise FST values between the Romanian breeds and Romanian and Hungarian breeds were small (0.009 and 0.015), indicating the close relationship among the studied goat populations. From all the polymorphic SNPs identified, the Hungarian Milking breed showed the highest proportion of polymorphisms (100%), whereas the Carpatina breed had the lowest percentage (87.5%). The highest value of MAF was obtained for SOCS3 g.52626440T>G (0.46), IL15RA g.10343904C>T (0.47), IL15RA g.10344025C>T (0.45), and IL15RA g.10354813C>T (0.42). The 16 polymorphic SNPs identified in a panel of 150 unrelated individuals belonging to three Romanian and Hungarian indigenous goat breeds could be used in future genomic based breeding schemes as markers for genetic resistance to mastitis and gastrointestinal parasitism in goat breeds found in Eastern and Central Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197051PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5942826PMC
August 2018

MtDNA genetic diversity and structure of Eurasian Collared Dove (Streptopelia decaocto).

PLoS One 2018 8;13(3):e0193935. Epub 2018 Mar 8.

Animal Genetic Laboratory, University of Debrecen, Debrecen, Hungary.

The Eurasian Collared Dove (Streptopelia decaocto) is one of the most successful biological invaders among terrestrial vertebrates. However, little information is available on the genetic diversity of the species. A total of 134 Eurasian Collared Doves from Europe, Asia and the Caribbean (n = 20) were studied by sequencing a 658-bp length of mitochondrial DNA (mtDNA) cytochrome oxidase I (COI). Fifty-two different haplotypes and relatively high haplotype and nucleotide diversities (Hd±SD = 0.843±0.037 and π±SD = 0.026±0.013) were detected. Haplotype Ht1 was particularly dominant: it included 44.03% of the studied individuals, and contained sequences from 75% of the studied countries. Various analyses (FST, AMOVA, STRUCTURE) distinguished 2 groups on the genetic level, designated 'A' and 'B'. Two groups were also separated in the median-joining network and the maximum likelihood tree. The results of the neutrality tests were negative (Fu FS = -25.914; Tajima D = -2.606) and significantly different from zero (P≤0.001) for group A, whereas both values for group B were positive (Fu FS = 1.811; Tajima D = 0.674) and not significant (P>0.05). Statistically significant positive autocorrelation was revealed among individuals located up to 2000 km apart (r = 0.124; P = 0.001). The present results provide the first information on the genetic diversity and structure of the Eurasian Collared Dove, and can thereby serve as a factual and comparative basis for similar studies in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193935PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843281PMC
July 2018

Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition.

PeerJ 2018 21;6:e4416. Epub 2018 Feb 21.

Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania.

Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine ( = 24) and Saanen ( = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: and . The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) ( < 0.05). The results showed that four SNPs rs671391101 (), rs640582069 () rs635583012 () and rs635969404 () out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the , , , and genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.4416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827040PMC
February 2018

Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing.

PeerJ 2018 31;6:e4198. Epub 2018 Jan 31.

Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary.

Background: The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.

Methods: To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.

Results: One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (  = 0.954 ± 0.004;  = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (  = 0.972 ± 0.002;  = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected.

Discussion: Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from 'ancestrally' different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.4198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797449PMC
January 2018

Preliminary report on β-casein gene Met183QVal183 polymorphism in Romanian indigenous Zackel sheep breeds.

Acta Biochim Pol 2017 17;64(2):339-341. Epub 2017 May 17.

Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, 325400, Caransebes, Romania.

Genetic polymorphisms of the milk protein genes are important because of their effects on quantitative traits and technological properties of milk manufacturing. In the present study we identified the polymorphism of the beta-casein gene in two local sheep breeds (Racka n=98 and Turcana n=111) in Romania. The most studied variants at the ovine beta-casein (CSN2) locus are: A and G variants. Genomic DNA was extracted from hair follicles and beta-casein genotypes were determined by the rapid TaqMan (Applied Biosystems, USA) genotyping assay. Homozygote genotypes GG were not detected in any of the studied breeds. In both, the Racka and Turcana breeds, the A variant had a much higher frequency, 0.98% and 0.97%, respectively. In the current study, the fast DNA tests for genotyping ovine CSN2 were successfully optimized, however, further samples and correlations of genomic results with milk characteristics and production data are needed for the development of future selection schemes of the Romanian indigenous sheep breeds, with the ultimate purpose to produce low allergen level sheep milk and derived dairy products.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18388/abp.2016_1437DOI Listing
August 2017

Genetic polymorphism of CSN2 gene in Banat White and Carpatina goats.

Acta Biochim Pol 2016 6;63(3):577-80. Epub 2016 Jul 6.

Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania.

The main objective of the current study was to obtain preliminary results on genetic polymorhism of A and C variants at the CSN2 locus in indigenous Romanian goat (Banat White, Carpatina) breeds using a rapid and efficient genotyping method, TaqMan assay (Applied Biosystems, USA). Hair follicle samples were taken from 73 Banat White and 82 Carpatina purebred goats from Arad, Caras-Severin and Timis counties. After the optimization of the genotyping assay it was found that the most frequent allele at the CSN2 locus was C in Banat White breed, while CSN2*A and CSN2*C showed similar frequencies in Carpatina breed (0.51 and 0.49, respectively). All three genotypes were detected in the two studied breeds, however, AA was the least frequent, especially in Banat White. The studied polymorphisms are potential markers for milk production in the studied breeds and the results will be useful in future works aimed at identifying possible associations with milk production traits, in order to test the feasibility of producing hypoallergenic organic goat milk.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18388/abp.2016_1266DOI Listing
January 2017

Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers.

PeerJ 2016 2;4:e1894. Epub 2016 May 2.

Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen , Debrecen , Hungary.

The Gidran is a native Hungarian horse breed that has approached extinction several times. Phylogenetic analysis of two mitochondrial markers (D-loop and cytochrome-b) was performed to determine the genetic characterization of the Gidran for the first time as well as to detect errors in the management of the Gidran stud book. Sequencing of 686 bp of CYTB and 202 bp of the D-loop in 260 mares revealed 24 and 32 haplotypes, respectively, among 31 mare families. BLAST analysis revealed six novel CYTB and four D-loop haplotypes that have not been previously reported. The Gidran mares showed high haplotype (CYTB: 0.8735 ± 0.011; D-loop: 0.9136 ± 0.008) and moderate nucleotide (CYTB: 0.00472 ± 0.00017; D-loop: 0.02091 ± 0.00068) diversity. Of the 31 Gidran mare families, only 15 CYTB (48.4%) and 17 D-loop (54.8%) distinct haplotypes were formed using the two markers separately. Merged markers created 24 (77.4%) mare families, which were in agreement with the mare families in the stud book. Our key finding was that the Gidran breed still possesses high genetic diversity despite its history. The obtained haplotypes are mostly consistent with known mare families, particularly when the two mtDNA markers were merged. Our results could facilitate conservation efforts for preserving the genetic diversity of the Gidran.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.1894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860319PMC
May 2016

Association and polymorphism study of seven candidate genes with reproductive traits in three pig breeds in Hungary.

Acta Biochim Pol 2016 26;63(2):359-64. Epub 2016 Apr 26.

Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary.

Seven genes (BF, EGF, ESR, FSHB, H2AFZ, LEP and PRLP) were studied as candidate gene influencing eleven reproduction traits (interval between litters (IBL), percent of litter (PL), number of litters (NL), number of piglets born dead (NBD), number of piglet born alive (NBA), total number born (TNB), mean of born alive (MBA), mean of born dead (MBD), mean of born total (MBT), mean of piglets at 21 days of age (M21D) and growth rate (GR) in three pig breeds (Hungarian Large White (HLW), Duroc and Pietrain) by PCR-RFLP. Based on the observed vs. expected genotypes frequencies populations across loci were in Hardy-Weinberg equilibrium (P>0.05). In case HLW breed ESR and FSHβ genes were in disequilibrium. Association study suggested that only EGF gene showed significant influence on the trait NBA and TNB. The AA genotype are preferable for sows, associated with higher NBA and TNB. The longest IBL, and the highest NL is associated with AB and AA genotype of EGF gene. IBL is significantly shorter in case of pigs with AB and AA alleles than BB alleles of PRLP genes. Selection for these SNPs could improve the reproductivity in the studied breeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18388/abp.2015_1188DOI Listing
January 2017

Population structure of honey bees in the Carpathian Basin (Hungary) confirms introgression from surrounding subspecies.

Ecol Evol 2015 Dec 4;5(23):5456-67. Epub 2015 Nov 4.

Institute of Animal Science Biotechnology and Nature Conservation University of Debrecen 4032 Debrecen Hungary.

Carniolan honey bees (Apis mellifera carnica) are considered as an indigenous subspecies in Hungary adapted to most of the ecological and climatic conditions in this area. However, during the last decades Hungarian beekeepers have recognized morphological signs of the Italian honey bee (Apis mellifera ligustica). As the natural distribution of the honey bee subspecies can be affected by the importation of honey bee queens or by natural gene flow, we aimed at determining the genetic structure and characteristics of the local honey bee population using molecular markers. All together, 48 Hungarian and 84 foreign (Italian, Polish, Spanish, Liberian) pupae and/or workers were used for mitochondrial DNA analysis. Additionally, 53 sequences corresponding to 10 subspecies and the Buckfast hybrid were downloaded from GenBank. For the nuclear analysis, 236 Hungarian and 106 foreign honey bees were genotyped using nine microsatellites. Heterozygosity values, population-specific alleles, FST values, principal coordinate analysis, assignment tests, structure analysis, and dendrograms were calculated. Haplotype and nucleotide diversity values showed moderate values. We found that one haplotype (H9) was dominant in Hungary. The presence of the black honey bee (Apis mellifera mellifera) was negligible, but a few individuals resembling other subspecies were identified. We proved that the Hungarian honey bee population is nearly homogeneous but also demonstrated introgression from the foreign subspecies. Both mitochondrial DNA and microsatellite analyses corroborated the observations of the beekeepers. Molecular analyses suggested that Carniolan honey bee in Hungary is slightly affected by Italian and black honey bee introgression. Genetic differences were detected between Polish and Hungarian Carniolan honey bee populations, suggesting the existence of at least two different gene pools within A. m. carnica.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.1781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813114PMC
December 2015

Microsatellite and Mitochondrial DNA Study of Native Eastern European Cattle Populations: The Case of the Romanian Grey.

PLoS One 2015 23;10(9):e0138736. Epub 2015 Sep 23.

Animal Genetics Laboratory, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary.

The Eastern European Grey cattle are regarded as the direct descendants of the aurochs (Bos taurus primigenius). Nowadays in Romania, less than 100 Grey animals are being reared and included in the national gene reserve. We examined the genetic diversity among Romanian Grey, Brown, Spotted and Black and White cattle breeds, with a particular focus on Romanian Grey through the use of (i) 11 bovine specific microsatellite markers on 83 animals and (ii) 638 bp length of mitochondrial DNA (mtDNA) D-loop region sequence data from a total of 81 animals. Both microsatellite and mtDNA analysis revealed a high level of genetic variation in the studied breeds. In Romanian Grey a total of 100 alleles were found, the mean number of observed alleles per locus was 9.091; the average observed heterozygosity was 0.940; the Wright's fixation index (FIS) was negative (-0.189) and indicates that there is no inbreeding and no selection pressure. MtDNA analysis revealed 52 haplotypes with 67 variable sites among the Romanian cattle breeds without any insertion or deletion. Haplotype diversity was 0.980 ± 0.007 and ranged from 0.883 ± 0.056 (Brown) to 0.990 ± 0.028 (Spotted and Black and White). The highest genetic variability of the mtDNA was recorded in the Grey breed, where 18 haplotypes were identified. The most frequent mtDNA D-loop region belonged to T3 haplogroup (80.247%), which was found across all studied breeds, while T2 haplotypes (16.049%) was only found in Grey, Spotted and Black and White genotypes. The T1 haplotypes (3.704%) were found in the Grey and Spotted. The current results contribute to the general knowledge on genetic diversity found in Eastern European cattle breeds and could prove a valuable tool for the conservation efforts of animal genetic resources (FAnGR).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138736PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580412PMC
June 2016

Mitochondrial DNA variability in Gyimesi Racka and Turcana sheep breeds.

Acta Biochim Pol 2015 22;62(2):273-80. Epub 2015 Jun 22.

Research and Development Station for Sheep and Goats, Caransebes, 325400, Romania.

The current knowledge and documentation on the origins and relationship between Gyimesi Racka reared in Hungary and the Romanian Turcana is rather controversial. Lack of information and scientific reliable proofs for the divergent theories found in the two countries motivated us to implement a trial using molecular methods to assess the genetic distance and diversity in the two breeds. Hair follicles were collected from Gyimesi Racka (2 phenotypes) and from Turcana (6 ecotypes). The 599 bp segment of the D-loop region of the mitochondrial DNA was sequenced. Altogether, 42 haplotypes were identified, while 23 were found in both populations. Populations were highly diverse according to the haplotype and nucleotide diversity indices. AMOVA analysis showed that most of the variation was observed within populations (98%), indicating a weak genetic structure between the two breeds. Animals were grouped into seven groups based on their phenotype; however genetic distances among them were also low. Tajima's D, Fu's Fs, goodness-of-fit statistics, mismatch distribution and network analysis suggested recent demographic expansion. Current comprehensive mtDNA study indicates that there is very low level of genetic differentiation between the Gyimesi Racka and Turcana populations therefore they are de facto one trans-boundary breed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18388/abp.2015_978DOI Listing
April 2016

Preliminary result of a genetic polymorphism of β-lactoglobulin gene and the phylogenetic study of ten balkan and central european indigenous sheep breeds.

Acta Biochim Pol 2015 2;62(1):109-12. Epub 2015 Mar 2.

University of Debrecen, Institute of Animal Science, Biotechnology and Nature Conservation, Hungary.

Genetic polymorphism at the β-lactoglobulin (β-LG) loci in indigenous sheep breeds (Tsigai, Racka, Pramenka) was determined. Altogether 904 sheep were genotyped for the presence of the A, B and C alleles of β-lactoglobulin by PCR-RFLP. The AB genotype was the most common and the β-lactoglobulin A was the most frequent in the Cokanski Tsigai (54%), while the B allele was the most common in the Rusty and the Zomborski Tsigai (59%, 60%). The C allele was found only in one individual from Serbian Cokanski flock. These results differ from those that refer to other native sheep breeds. In the Cokanski Tsigai, deviation from the Hardy-Weinberg equilibrium was detected. Genetic relationship based on β-lactoglobulin polymorphism was the closest between the Rusty and the Cokanski Tsigai among the studied populations and between sheep and goat among the other ruminants. Part of the promoter region (254 bp) of β-LG in studied sheep breeds were sequenced in order to identify polymorphisms, analyze haplotypes, and phylogenetic relationship among them. Sequencing analysis and alignment of the obtained sequences showed one haplotype. Analysis of more samples and longer parts of the promoter region of β-LG are needed to reconstruct a phylogenetic tree.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18388/abp.2014_846DOI Listing
December 2015

Contemporary genetic structure, phylogeography and past demographic processes of wild boar Sus scrofa population in Central and Eastern Europe.

PLoS One 2014 12;9(3):e91401. Epub 2014 Mar 12.

Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland.

The wild boar (Sus scrofa) is one of the most widely distributed mammals in Europe. Its demography was affected by various events in the past and today populations are increasing throughout Europe. We examined genetic diversity, structure and population dynamics of wild boar in Central and Eastern Europe. MtDNA control region (664 bp) was sequenced in 254 wild boar from six countries (Poland, Hungary, Belarus, Ukraine, Moldova and the European part of Russia). We detected 16 haplotypes, all known from previous studies in Europe; 14 of them belonged to European 1 (E1) clade, including 13 haplotypes from E1-C and one from E1-A lineages. Two haplotypes belonged respectively to the East Asian and the Near Eastern clade. Both haplotypes were found in Russia and most probably originated from the documented translocations of wild boar. The studied populations showed moderate haplotype (0.714±0.023) and low nucleotide diversity (0.003±0.002). SAMOVA grouped the genetic structuring of Central and Eastern European wild boar into three subpopulations, comprising of: (1) north-eastern Belarus and the European part of Russia, (2) Poland, Ukraine, Moldova and most of Belarus, and (3) Hungary. The multimodal mismatch distribution, Fu's Fs index, Bayesian skyline plot and the high occurrence of shared haplotypes among populations did not suggest strong demographic fluctuations in wild boar numbers in the Holocene and pre-Holocene times. This study showed relatively weak genetic diversity and structure in Central and Eastern European wild boar populations and underlined gaps in our knowledge on the role of southern refugia and demographic processes shaping genetic diversity of wild boar in this part of Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091401PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951376PMC
May 2015

Microsatellite analysis to estimate genetic relationships among five bulgarian sheep breeds.

Genet Mol Biol 2010 Jan 1;33(1):51-6. Epub 2010 Mar 1.

Institute of Animal Science, University of Debrecen Centre of Agriculture Sciences and Engineering, Debrecen Hungary.

Herein, genetic relationships among five breeds of Bulgarian sheep were estimated using microsatellite markers. The total number of alleles identified was 226 at the 16 loci examined. D(A) distance values were used for phylogenetic tree construction with the UPGMA algorithm. The two Tsigai and two Maritza populations were found to be geneticallvery closely related to each other y (0.198, and 0.258 respectively). The Pleven Black Head population was distinct from the other four. These results could be useful for preserving genes in these breeds, thereby ensuring their preservation in Bulgaria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1590/S1415-47572010005000003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036078PMC
January 2010