Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia
Abstract Background The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2022-04-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-022-00718-6 |
| _version_ | 1811338828353372160 |
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| author | Minja Zorc Dubravko Škorput Kristina Gvozdanović Polona Margeta Danijel Karolyi Zoran Luković Krešimir Salajpal Radomir Savić Maria Muñoz Samuele Bovo Ivona Djurkin Kušec Čedomir Radović Goran Kušec Marjeta Čandek Potokar Peter Dovč |
| author_facet | Minja Zorc Dubravko Škorput Kristina Gvozdanović Polona Margeta Danijel Karolyi Zoran Luković Krešimir Salajpal Radomir Savić Maria Muñoz Samuele Bovo Ivona Djurkin Kušec Čedomir Radović Goran Kušec Marjeta Čandek Potokar Peter Dovč |
| author_sort | Minja Zorc |
| collection | DOAJ |
| description | Abstract Background The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure. |
| first_indexed | 2024-04-13T18:16:22Z |
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| id | doaj.art-c011f24dbec84a1292e781f5942931f2 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-13T18:16:22Z |
| publishDate | 2022-04-01 |
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| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-c011f24dbec84a1292e781f5942931f22022-12-22T02:35:39ZdeuBMCGenetics Selection Evolution1297-96862022-04-0154112310.1186/s12711-022-00718-6Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and SloveniaMinja Zorc0Dubravko Škorput1Kristina Gvozdanović2Polona Margeta3Danijel Karolyi4Zoran Luković5Krešimir Salajpal6Radomir Savić7Maria Muñoz8Samuele Bovo9Ivona Djurkin Kušec10Čedomir Radović11Goran Kušec12Marjeta Čandek Potokar13Peter Dovč14Department of Animal Science, University of Ljubljana, Biotechnical FacultyUniversity of Zagreb, Faculty of AgricultureJosip Juraj Strossmayer University of Osijek, Faculty of Agrobiotechnical Sciences OsijekJosip Juraj Strossmayer University of Osijek, Faculty of Agrobiotechnical Sciences OsijekUniversity of Zagreb, Faculty of AgricultureUniversity of Zagreb, Faculty of AgricultureUniversity of Zagreb, Faculty of AgricultureInstitute of Animal Sciences, University of Belgrade, Faculty of AgricultureDepartamento Mejora Genética Animal, INIADepartment of Agricultural and Food Sciences, Division of Animal Sciences, University of BolognaJosip Juraj Strossmayer University of Osijek, Faculty of Agrobiotechnical Sciences OsijekInstitute for Animal HusbandryJosip Juraj Strossmayer University of Osijek, Faculty of Agrobiotechnical Sciences OsijekAgricultural Institute of SloveniaDepartment of Animal Science, University of Ljubljana, Biotechnical FacultyAbstract Background The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.https://doi.org/10.1186/s12711-022-00718-6 |
| spellingShingle | Minja Zorc Dubravko Škorput Kristina Gvozdanović Polona Margeta Danijel Karolyi Zoran Luković Krešimir Salajpal Radomir Savić Maria Muñoz Samuele Bovo Ivona Djurkin Kušec Čedomir Radović Goran Kušec Marjeta Čandek Potokar Peter Dovč Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia Genetics Selection Evolution |
| title | Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia |
| title_full | Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia |
| title_fullStr | Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia |
| title_full_unstemmed | Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia |
| title_short | Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia |
| title_sort | genetic diversity and population structure of six autochthonous pig breeds from croatia serbia and slovenia |
| url | https://doi.org/10.1186/s12711-022-00718-6 |
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