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Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
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Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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Novosel D, Brajković V, Simčič M, Zorc M, Svara T, Cakanic KB, Jungić A, Logar B, Cubric-Curik V, Dovc P, Curik I. The Consequences of Mitochondrial T10432C Mutation in Cika Cattle: A “Potential” Model for Leber’s Hereditary Optic Neuropathy. Int J Mol Sci 2022; 23:ijms23116335. [PMID: 35683014 PMCID: PMC9181260 DOI: 10.3390/ijms23116335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 12/04/2022] Open
Abstract
While mitogenome mutations leading to pathological manifestations are rare, more than 200 such mutations have been described in humans. In contrast, pathogenic mitogenome mutations are rare in domestic animals and have not been described at all in cattle. In the small local Slovenian cattle breed Cika, we identified (next-generation sequencing) two cows with the T10432C mitogenome mutation in the ND4L gene, which corresponds to the human T10663C mutation known to cause Leber’s hereditary optic neuropathy (LHON). Pedigree analysis revealed that the cows in which the mutation was identified belong to two different maternal lineages with 217 individual cows born between 1997 and 2020. The identified mutation and its maternal inheritance were confirmed by Sanger sequencing across multiple generations, whereas no single analysis revealed evidence of heteroplasmy. A closer clinical examination of one cow with the T10432C mutation revealed exophthalmos, whereas histopathological examination revealed retinal ablations, subretinal oedema, and haemorrhage. The results of these analyses confirm the presence of mitochondrial mutation T10432C with homoplasmic maternal inheritance as well as clinical and histopathological signs similar to LHON in humans. Live animals with the mutation could be used as a suitable animal model that can improve our understanding of the pathogenesis of LHON and other mitochondriopathies.
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Affiliation(s)
- Dinko Novosel
- Department of Pathology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.B.); (V.C.-C.)
- Correspondence: (D.N.); (I.C.); Tel.: +385-91-5179431 (D.N.); +385-98-474406 (I.C.)
| | - Vladimir Brajković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.B.); (V.C.-C.)
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.S.); (M.Z.); (P.D.)
| | - Minja Zorc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.S.); (M.Z.); (P.D.)
| | - Tanja Svara
- Institute of Pathology, Wild Animals, Fish and Bees, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | | | - Andreja Jungić
- Department of Virology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Betka Logar
- Agricultural Institute of Slovenia, 1000 Ljubljana, Slovenia;
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.B.); (V.C.-C.)
| | - Peter Dovc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.S.); (M.Z.); (P.D.)
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.B.); (V.C.-C.)
- Correspondence: (D.N.); (I.C.); Tel.: +385-91-5179431 (D.N.); +385-98-474406 (I.C.)
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Simčič M, Luštrek B, Štepec M, Logar B, Potočnik K. Estimation of Genetic Parameters of Type Traits in First Parity Cows of the Autochthonous Cika Cattle in Slovenia. Front Genet 2021; 12:724058. [PMID: 34880898 PMCID: PMC8646033 DOI: 10.3389/fgene.2021.724058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of this study was to estimate genetic parameters of 26 individual and four composite type traits in first parity Cika cows. An analysis of variance was performed with the generalized linear model procedure of the SAS/STAT statistical package, where the fixed effects of year of recording, cow's age at recording and days after calving as a linear regression were included in the model. The variance components for the direct additive genetic effect and the herd effect in all type traits were estimated using the REML method in the VCE-6 software package. The estimated heritabilities ranged from 0.42 to 0.67 for the measured body frame traits, from 0.36 to 0.80 for the scored autochthonous traits, from 0.11 to 0.61 for the scored body frame traits, and from 0.20 to 0.47 for the scored udder traits. The estimated heritabilities for the composite traits called "autochthonous characteristics", "muscularity", "body frame" and "udder" were 0.55, 0.19, 0.19, and 0.26, respectively. The estimated genetic correlations among the measured body frame traits were positive and high, while the majority of them among the scored body frame traits were low to moderate. The estimated proportions of variance explained by the herd effect for the composite traits "autochthonous characteristics," "muscularity," "body frame" and "udder" were 0.09, 0.28, 0.14, and 0.10, respectively. The estimated heritabilities for the type traits of first parity Cika cows were similar to those reported for other breeds where breeding values have been routinely predicted for a long time. All estimated genetic parameters are already used for breeding value prediction in the Cika cattle population.
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Affiliation(s)
- Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Luštrek
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Miran Štepec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Betka Logar
- Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Klemen Potočnik
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Pogorevc N, Simčič M, Khayatzadeh N, Sölkner J, Berger B, Bojkovski D, Zorc M, Dovč P, Medugorac I, Horvat S. Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds. BMC Genomics 2021; 22:546. [PMID: 34273960 PMCID: PMC8285797 DOI: 10.1186/s12864-021-07802-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/13/2021] [Indexed: 12/05/2022] Open
Abstract
Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07802-z.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Mojca Simčič
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Negar Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Beate Berger
- Department Animal Genetic Resources, AREC Raumberg-Gumpenstein, Institute of Organic Farming and Biodiversity of Farm Animals, 4601 Thalheim b., Wels, Austria
| | - Danijela Bojkovski
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Minja Zorc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Lena-Christ-Straβe 48, 8215, Martinsried/Planegg, Germany
| | - Simon Horvat
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Silva JPD, Caetano AR. Determining minimum numbers of di-allelic diagnostic markers required to identify introgressions in diploid cross-species hybrid individuals from different types of inter- and backcross populations. Genet Mol Biol 2020; 43:e20190324. [PMID: 32870232 PMCID: PMC7445936 DOI: 10.1590/1678-4685-gmb-2019-0324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/28/2020] [Indexed: 08/21/2023] Open
Abstract
Cross-species hybridizations have been extensively used to generate animals and plants better suited for draft and food and fiber production since Roman times, and are still important in current agricultural practices with growing uses especially in aquaculture. Diagnostic tools based on marker panels with sufficient numbers of markers for accurate identification of cross-species hybrid individuals from intercrossed and backcrossed populations are increasingly necessary for practical, accurate species-purity certification and management of commercial broodstocks. Minimal numbers of di-allelic markers with species-specific alleles required to accurately identify hybrid individuals in intercrossed and advanced backcrossed populations were estimated using power analysis, and ranged from 5 to 191 (α = .05), and from 7 to 293 (α = .01), considering backcross 1 (BC1) to BC6 populations, respectively. Numbers of markers required for accurate hybrid identification observed in simulated BC1 to BC6 populations ranged from 5 to 1,131 and 7 to 8,065, considering error rates ≤ 5% and ≤ 1%, respectively. Estimated and observed numbers of diagnostic markers required for accurate hybrid identification up to four generations of backcrossing fall within practical operational limits of most commercial platforms currently available for genotyping low-density SNP marker panels. Therefore, cost-effective assay panels could be developed to provide practical tools for accurate species-purity certification.
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Papachristou D, Koutsouli P, Laliotis GP, Kunz E, Upadhyay M, Seichter D, Russ I, Gjoko B, Kostaras N, Bizelis I, Medugorac I. Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genet Sel Evol 2020; 52:43. [PMID: 32727375 PMCID: PMC7391618 DOI: 10.1186/s12711-020-00560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
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Affiliation(s)
- Dimitris Papachristou
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - George P Laliotis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Bunevski Gjoko
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, 16-ta Makedonska Brigada 3, 1000, Skopje, North Macedonia
| | - Nikolaos Kostaras
- AMALTHIA, Network for the Protection of Greek Indigenous Farm Animals, 51 Argyrokastrou, 15669, Athens, Greece
| | - Iosif Bizelis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
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Senczuk G, Mastrangelo S, Ciani E, Battaglini L, Cendron F, Ciampolini R, Crepaldi P, Mantovani R, Bongioni G, Pagnacco G, Portolano B, Rossoni A, Pilla F, Cassandro M. The genetic heritage of Alpine local cattle breeds using genomic SNP data. Genet Sel Evol 2020; 52:40. [PMID: 32664855 PMCID: PMC7362560 DOI: 10.1186/s12711-020-00559-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/09/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. RESULTS After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. CONCLUSIONS This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.
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Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124 Bari, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095 Grugliasco, Italy
| | - Filippo Cendron
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100 Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie ed Ambientali - Produzione, Territorio, Agroenergia, University of Milano, 20133 Milan, Italy
| | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
| | - Graziella Bongioni
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027 Rivolta d’Adda, CR Italy
| | - Giulio Pagnacco
- Istituto di Biologia e Biotecnologia Agraria (IBBA), CNR, 20133 Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Attilio Rossoni
- Italian Brown Cattle Breeders’ Association, Loc. Ferlina 204, 37012 Bussolengo, VR Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
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Ramljak J, Bunevski G, Bytyqi H, Marković B, Brka M, Ivanković A, Kume K, Stojanović S, Nikolov V, Simčič M, Sölkner J, Kunz E, Rothammer S, Seichter D, Grünenfelder HP, Broxham ET, Kugler W, Medugorac I. Conservation of a domestic metapopulation structured into related and partly admixed strains. Mol Ecol 2018; 27:1633-1650. [PMID: 29575253 DOI: 10.1111/mec.14555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 01/31/2023]
Abstract
Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.
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Affiliation(s)
- Jelena Ramljak
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,Department of Animal Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Gjoko Bunevski
- Faculty of Agricultural Sciences and Food, University Ss. Cyril and Methodius, Skopje, Macedonia
| | - Hysen Bytyqi
- Department of Animal Science, Faculty of Agriculture and Veterinary, University of Prishtina, Prishtina, Kosovo-UNMIC
| | - Božidarka Marković
- Department of Livestock Science, Biotechnical Faculty, University of Montenegro, Podgorica, Montenegro
| | - Muhamed Brka
- Institute of Animal Sciences, Faculty of Agriculture, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Ante Ivanković
- Department of Animal Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management, Beograd, Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding, Sofia, Bulgaria
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Johann Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Sophie Rothammer
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | | | | | | | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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10
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Simčič M, Čepon M, Žgur S. Carcass and meat quality of young Cika and Simmental bulls finished under similar conditions. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an15745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Twenty indigenous Cika and 20 young Simmental bulls (slaughtered at 560–718 days) were finished on two diets (extensive vs semi-intensive). When fed similar rations, Cika bulls at a ‘suitable’ finished level, had a significantly higher dressing percentage (+2.5%), more total fat (+13.7%), a lower percentage of tendons (–22.7%) and bones (–7.7%), a higher lean meat to bones ratio (+8.1%) and a greater percentage of intramuscular fat (+45.9%) than the Simmental bulls. Their meat also had a significantly lower pH (–4.0%), higher redness (+13.74%), yellowness (+15.0%) and drip loss (after 2 days, +28.3%) and a more intense flavour (+6.1%). Cika fat contained higher proportions of saturated fatty acids (+6.86%) and less polyunsaturated fatty acids (–30.8%) than Simmental fat. However, it appears that the main difference between these two breeds were the slower growth rate of the Cika and their lower weight but greater age when a finished state was reached relative to the Simmental.
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11
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Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0935-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Medugorac I, Graf A, Grohs C, Rothammer S, Zagdsuren Y, Gladyr E, Zinovieva N, Barbieri J, Seichter D, Russ I, Eggen A, Hellenthal G, Brem G, Blum H, Krebs S, Capitan A. Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks. Nat Genet 2017; 49:470-475. [PMID: 28135247 DOI: 10.1038/ng.3775] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/23/2016] [Indexed: 12/16/2022]
Abstract
The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak's hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ∼1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding.
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Affiliation(s)
- Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig Maximilians University Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Rothammer
- Chair of Animal Genetics and Husbandry, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Elena Gladyr
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry, Moscow region, Russian Federation
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry, Moscow region, Russian Federation
| | - Johanna Barbieri
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage GeT-PlaGe Genomic Facility, Castanet-Tolosan, France.,Université de Toulouse, INPT, ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France
| | | | - Ingolf Russ
- Tierzuchtforschung e.V. München, Grub, Germany
| | - André Eggen
- AgriGenomics, Illumina, San Diego, California, USA
| | - Garrett Hellenthal
- Genetics Institute, Faculty of Life Sciences, University College London, London, UK
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,ALLICE, Paris, France
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13
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Sánchez-Molano E, Tsiokos D, Chatziplis D, Jorjani H, Degano L, Diaz C, Rossoni A, Schwarzenbacher H, Seefried F, Varona L, Vicario D, Nicolazzi EL, Banos G. A practical approach to detect ancestral haplotypes in livestock populations. BMC Genet 2016; 17:91. [PMID: 27342071 PMCID: PMC4921009 DOI: 10.1186/s12863-016-0405-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/21/2016] [Indexed: 12/04/2022] Open
Abstract
Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0405-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Sánchez-Molano
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Dimitrios Tsiokos
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece
| | | | - Lorenzo Degano
- Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy
| | - Clara Diaz
- Departamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain
| | - Attilio Rossoni
- Associazione Nazionale Allevatori Bovini della Razza Bruna, Verona, Italy
| | | | | | - Luis Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, Zaragoza, 50013, Spain.,Instituto Agroalimentario de Aragón (IA2), Zaragoza, 50013, Spain
| | - Daniele Vicario
- Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy
| | - Ezequiel L Nicolazzi
- Bioinformatics core facility, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. CascinaCodazza, Lodi, 26900, Italy
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.,SRUC,The Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, Edinburgh, UK.,School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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14
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Grueber CE. Comparative genomics for biodiversity conservation. Comput Struct Biotechnol J 2015; 13:370-5. [PMID: 26106461 PMCID: PMC4475778 DOI: 10.1016/j.csbj.2015.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/13/2015] [Accepted: 05/15/2015] [Indexed: 12/31/2022] Open
Abstract
Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.
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