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Drzaic I, Curik I, Lukic B, Shihabi M, Li MH, Kantanen J, Mastrangelo S, Ciani E, Lenstra JA, Cubric-Curik V. High-Density Genomic Characterization of Native Croatian Sheep Breeds. Front Genet 2022; 13:940736. [PMID: 35910220 PMCID: PMC9337876 DOI: 10.3389/fgene.2022.940736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.
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Affiliation(s)
- Ivana Drzaic
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
| | - Ino Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Boris Lukic
- Department of Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, Chair for Domestic Animal Breeding and Genetics, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Universita Degli Studi di Bari “Aldo Moro”, Bari, Italy
| | | | - Vlatka Cubric-Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
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Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites. Animal 2014; 8:200-7. [PMID: 24433957 DOI: 10.1017/s1751731113002243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear genetic diversity and differentiation of 341 sheep belonging to 12 sheep breeds from Croatia and Bosnia and Herzegovina were examined. The aim of the study was to provide the understanding of the genetic structure and variability of the analysed pramenka sheep populations, and to give indications for conservation strategies based on the population diversity and structure information. The genetic variation of the sheep populations, examined at the nuclear level using 27 microsatellite loci, revealed considerable levels of genetic diversity, similar to the diversity found in other European indigenous low-production sheep breeds. Population-specific alleles were detected at most loci and in breeds analysed. The observed heterozygosity ranged from 0.643 (in Lika pramenka) to 0.743 (in Vlasic pramenka), and the expected heterozygosity ranged from 0.646 (in Lika pramenka) to 0.756 (in Dalmatian pramenka). Significant inbreeding coefficients were found for half of the populations studied and ranged from 0.040 (Pag island sheep) to 0.091 (Kupres pramenka). Moderate genetic differentiation was found between the studied sheep populations. The total genetic variability observed between different populations was 5.29%, whereas 94.71% of the variation was found within populations. Cres island sheep, Lika pramenka and Istrian sheep were identified as the most distinct populations, which was confirmed by the factorial analysis of correspondence and supported through a bootstrapping adjustment to correct for the difference in the sample sizes. The population structure analysis distinguished 12 clusters for the 12 sheep breeds analysed. However, the cluster differentiation was low for Dalmatian, Vlasic, Stolac and Krk pramenka. This systematic study identified Lika pramenka and Rab island sheep as those with the lowest diversity, whereas Istrian sheep and Pag island sheep had the highest. Conservation actions are proposed for Istrian, Rab and Cres island sheep, Lika and Kupres pramenka because of high estimated coefficients of inbreeding.
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Kusza S, Ivankovic A, Ramljak J, Nagy I, Jávor A, Kukovics S. Genetic structure of Tsigai, Ruda, Pramenka and other local sheep in Southern and Eastern Europe. Small Rumin Res 2011. [DOI: 10.1016/j.smallrumres.2011.03.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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DNA microsatellites to ascertain pedigree-recorded information in a selecting nucleus of Murciano-Granadina dairy goats. Small Rumin Res 2006. [DOI: 10.1016/j.smallrumres.2005.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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