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1. Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs

Author

Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), Colli L. (ORCID:0000-0002-7221-2905), Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), and Colli L. (ORCID:0000-0002-7221-2905)

Abstract

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might ac

Published
2019

2. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, European Cattle Genetic Diversity Consortium, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, and European Cattle Genetic Diversity Consortium

Abstract

This corrects the article DOI: 10.1038/hdy.2016.79.

Published
2017

3. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, Kantanen, J, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, and Kantanen, J

Abstract

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.Heredity advance online publication, 28 September 2016; doi:10.1038/hdy.2016.79.

Published
2017

4. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, Kantanen, J, Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, and Kantanen, J

Published
2017

5. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, European Cattle Genetic Diversity Consortium, Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, and European Cattle Genetic Diversity Consortium

Published
2017

6. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, European Cattle Genetic Diversity Consortium, Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, and European Cattle Genetic Diversity Consortium

Published
2017

7. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, Kantanen, J, Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, and Kantanen, J

Published
2017

8. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, European Cattle Genetic Diversity Consortium, Afd Pharmaceutics, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D.E., Park, S D E, Magee, David A., Matassino, Donato, Ciani, F, Megens, H.J., van Arendonk, J A M, Groenen, M A M, and European Cattle Genetic Diversity Consortium

Published
2017

9. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, Kantanen, J, Sub Physical Oceanography, LS IRAS Tox Algemeen, Sub Veterinary Genetics, LS Ges. van de bouwkunst, dIRAS RA-1, Upadhyay, M R, Chen, W, Lenstra, J A, Goderie, C R J, MacHugh, D E, Park, S D E, Magee, D A, Matassino, D, Ciani, F, Megens, H-J, van Arendonk, J A M, Groenen, M A M, Marsan, P A, Balteanu, V, Dunner, S, Garcia, J F, Ginja, C, and Kantanen, J

Published
2017

10. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Author

Upadhyay, M. R., Chen, W., Lenstra, J. A., Goderie, C. R. J., Machugh, D. E., Park, S. D. E., Magee, D. A., Matassino, D., Ciani, F., Megens, H. J., Van Arendonk, J. A. M., Groenen, M. A. M., Ajmone Marsan, Paolo, Balteanu, V., Dunner, S., Garcia, J. F., Ginja, C., Kantanen, J., Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Upadhyay, M. R., Chen, W., Lenstra, J. A., Goderie, C. R. J., Machugh, D. E., Park, S. D. E., Magee, D. A., Matassino, D., Ciani, F., Megens, H. J., Van Arendonk, J. A. M., Groenen, M. A. M., Ajmone Marsan, Paolo, Balteanu, V., Dunner, S., Garcia, J. F., Ginja, C., Kantanen, J., and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)

Abstract

The domestication of taurine cattle initiated ∼10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Published
2017

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