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

Maulik Upadhyay*, Chiara Bortoluzzi, Mario Barbato, Paolo Ajmone-Marsan, Licia Colli, Catarina Ginja, Tad S. Sonstegard, Mirte Bosse, Johannes A. Lenstra, Martien A.M. Groenen, Richard P.M.A. Crooijmans

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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 account for the presence of non-European cattle ancestry in these cattle breeds.

Original languageEnglish
Pages (from-to)951-963
JournalEvolutionary Applications
Volume12
Issue number5
DOIs
Publication statusPublished - Jun 2019

Fingerprint

Single Nucleotide Polymorphism
cattle
genome
Genome
ancestry
taurine
cattle breeds
Taurine
single nucleotide polymorphism
zebu
homozygosity
polymorphism
nucleotides
breeds
divergence
Balkans
Nucleotides
founder effect
linkage disequilibrium
Balkan Peninsula

Keywords

  • admixture
  • African taurine
  • cattle
  • genetic diversity
  • haplotype
  • indicine ancestry
  • SNPs
  • southern European

Cite this

Upadhyay, Maulik ; Bortoluzzi, Chiara ; Barbato, Mario ; Ajmone-Marsan, Paolo ; Colli, Licia ; Ginja, Catarina ; Sonstegard, Tad S. ; Bosse, Mirte ; Lenstra, Johannes A. ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. / Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs. In: Evolutionary Applications. 2019 ; Vol. 12, No. 5. pp. 951-963.
@article{911e419c5e6946708f4e344e1fdf8caf,
title = "Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs",
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 account for the presence of non-European cattle ancestry in these cattle breeds.",
keywords = "admixture, African taurine, cattle, genetic diversity, haplotype, indicine ancestry, SNPs, southern European",
author = "Maulik Upadhyay and Chiara Bortoluzzi and Mario Barbato and Paolo Ajmone-Marsan and Licia Colli and Catarina Ginja and Sonstegard, {Tad S.} and Mirte Bosse and Lenstra, {Johannes A.} and Groenen, {Martien A.M.} and Crooijmans, {Richard P.M.A.}",
year = "2019",
month = "6",
doi = "10.1111/eva.12770",
language = "English",
volume = "12",
pages = "951--963",
journal = "Evolutionary Applications",
issn = "1752-4563",
publisher = "Wiley",
number = "5",

}

Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs. / Upadhyay, Maulik; Bortoluzzi, Chiara; Barbato, Mario; Ajmone-Marsan, Paolo; Colli, Licia; Ginja, Catarina; Sonstegard, Tad S.; Bosse, Mirte; Lenstra, Johannes A.; Groenen, Martien A.M.; Crooijmans, Richard P.M.A.

In: Evolutionary Applications, Vol. 12, No. 5, 06.2019, p. 951-963.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs

AU - Upadhyay, Maulik

AU - Bortoluzzi, Chiara

AU - Barbato, Mario

AU - Ajmone-Marsan, Paolo

AU - Colli, Licia

AU - Ginja, Catarina

AU - Sonstegard, Tad S.

AU - Bosse, Mirte

AU - Lenstra, Johannes A.

AU - Groenen, Martien A.M.

AU - Crooijmans, Richard P.M.A.

PY - 2019/6

Y1 - 2019/6

N2 - 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 account for the presence of non-European cattle ancestry in these cattle breeds.

AB - 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 account for the presence of non-European cattle ancestry in these cattle breeds.

KW - admixture

KW - African taurine

KW - cattle

KW - genetic diversity

KW - haplotype

KW - indicine ancestry

KW - SNPs

KW - southern European

U2 - 10.1111/eva.12770

DO - 10.1111/eva.12770

M3 - Article

VL - 12

SP - 951

EP - 963

JO - Evolutionary Applications

JF - Evolutionary Applications

SN - 1752-4563

IS - 5

ER -