1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Küttel L, Letko A, Häfliger IM, Signer‐Hasler H, Joller S, Hirsbrunner G, Mészáros G, Sölkner J, Flury C, Leeb T, Drögemüller C. A complex structural variant at the
KIT
locus in cattle with the Pinzgauer spotting pattern. Anim Genet 2019; 50:423-429. [DOI: 10.1111/age.12821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2019] [Indexed: 11/28/2022]
Affiliation(s)
- L. Küttel
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - A. Letko
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - I. M. Häfliger
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - H. Signer‐Hasler
- School of Agricultural, Forest and Food Sciences HAFL Bern University of Applied Sciences 3052 Zollikofen Switzerland
| | - S. Joller
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - G. Hirsbrunner
- Clinic for Ruminants Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - G. Mészáros
- Division of Livestock Sciences University of Natural Resources and Life Sciences Vienna 1180Vienna Austria
| | - J. Sölkner
- Division of Livestock Sciences University of Natural Resources and Life Sciences Vienna 1180Vienna Austria
| | - C. Flury
- School of Agricultural, Forest and Food Sciences HAFL Bern University of Applied Sciences 3052 Zollikofen Switzerland
| | - T. Leeb
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| | - C. Drögemüller
- Institute of Genetics, Vetsuisse Faculty University of Bern 3001 Bern Switzerland
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Švara T, Cociancich V, Šest K, Gombač M, Paller T, Starič J, Drögemüller C. Pulmonary hypoplasia and anasarca syndrome in Cika cattle. Acta Vet Scand 2016; 58:36. [PMID: 27267454 PMCID: PMC4896035 DOI: 10.1186/s13028-016-0220-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 11/26/2022] Open
Abstract
Background Hydrops foetalis is defined as excessive fluid accumulation within the foetal extravascular compartments and body cavities. It has been described in human and veterinary medicine, but despite several descriptive studies its aetiology is still not fully clarified. Pulmonary hypoplasia and anasarca (PHA) syndrome is a rare congenital abnormality in cattle that is characterised by hydrops foetalis including extreme subcutaneous oedema (anasarca) and undeveloped or poorly formed lungs (pulmonary hypoplasia). Until now, sporadic cases of PHA were reported in cattle breeds like Australian Dexter, Belted Galloway, Maine-Anjou, and Shorthorn. This report describes the first known cases of PHA syndrome in Slovenian Cika cattle. Case presentation A 13-year-old cow aborted a male calf in the seventh month of pregnancy, while a male calf was delivered by caesarean section on the due date from a 14-year-old cow. The pedigree analysis showed that the calves were sired by the same bull, the dams were paternal half-sisters and the second calf was the product of a dam-son mating. Gross lesions were similar in both cases and characterized by severe anasarca, hydrothorax, hydropericardium, ascites, hypoplastic lungs, absence of lymph nodes, and an enlarged heart. The first calf was also athymic. Histopathology of the second affected calf confirmed severe oedema of the subcutis and interstitium of the organs, and pulmonary hypoplasia. The lymph vessels in the subcutis and other organs were severely dilated. Histopathology of the second calf revealed also lack of bronchus associated lymphoid tissue and adrenal gland hypoplasia. Conclusions The findings were consistent with known forms of the bovine PHA syndrome. This is the first report of the PHA syndrome occurring in the local endangered breed of Cika cattle. Observed inbreeding practice supports that this lethal defect most likely follows an autosomal recessive mode of inheritance. In the light of the disease phenotype it is assumed that a mutation causing an impaired development of lymph vessels is responsible for the hydrops foetalis associated malformations in bovine PHA.
Collapse
|
7
|
Maretto F, Cassandro M. Temporal Variation in Genetic Diversity and Population Structure of Burlina Cattle Breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Simčič M, Smetko A, Sölkner J, Seichter D, Gorjanc G, Kompan D, Medugorac I. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed. PLoS One 2015; 10:e0123253. [PMID: 25923207 PMCID: PMC4414476 DOI: 10.1371/journal.pone.0123253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/23/2015] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Collapse
Affiliation(s)
- Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Anamarija Smetko
- Division of Livestock Science, Department Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Science, Department Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | | | - Gregor Gorjanc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Dragomir Kompan
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| |
Collapse
|