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.
Highlights
Modern cattle originated from at least two different species of wild aurochs: Bos primigenius primigenius (European aurochs) and Bos pri‐ migenius namadicus (Indian aurochs)
Recent studies based on ge‐ nome‐wide single nucleotide polymorphisms (SNPs) refuted this hypothesis of a third domestication centre and, instead, proposed the gene flow from African aurochs resulting in high divergence of African taurine (Decker et al, 2014; Pitt et al, 2018)
These results could indicate that British cat‐ tle are the most suitable surrogates for the European taurine that contributed to Busha, Pajuna and Marchigiana cattle ancestry or it could indicate an artefact of the ascertainment bias of BovineHD SNP array
Summary
Modern cattle originated from at least two different species of wild aurochs: Bos primigenius primigenius (European aurochs) and Bos pri‐ migenius namadicus (Indian aurochs). Recent studies based on ge‐ nome‐wide single nucleotide polymorphisms (SNPs) refuted this hypothesis of a third domestication centre and, instead, proposed the gene flow from African aurochs resulting in high divergence of African taurine (Decker et al, 2014; Pitt et al, 2018) This hypoth‐ esis of African aurochs introgression, is yet to be tested because DNA from an ancient specimen of African cattle is not available. Based on the archaeological evidences (Martins et al, 2015; Zilhao, 1993) and genomic analysis of DNA sequences of ancient farmers (Hofmanová et al, 2016), at least two migration routes have been suggested to explain the expansion of Neolithic farmers along with their domesticated animals after early domestication of European aurochs in the Near East Following these early mi‐ grations, various instances of gene flow involving non‐European cattle into the gene pool of southern European cattle have been suggested. We used the geno‐ types obtained from WGS of European cattle to assess genetic heterozygosity and change in recent demography, followed by identification and assessment of non‐European ancestry in south‐ ern European cattle (Iberian, and BAI cattle) using BovineHD SNP array data
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