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Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

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  • Mathieu Gautier
  • Denis Laloë
  • Katayoun Moazami-Goudarzi

Abstract

Background: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. Methodology/Principal Findings: This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. Conclusions/Significance: Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations—the African taurine, the European taurine and zebus—may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence.

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  • Mathieu Gautier & Denis Laloë & Katayoun Moazami-Goudarzi, 2010. "Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-11, September.
    • Handle: RePEc:plo:pone00:0013038
    DOI: 10.1371/journal.pone.0013038
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    References listed on IDEAS

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    1. Jared Diamond, 2002. "Evolution, consequences and future of plant and animal domestication," Nature, Nature, vol. 418(6898), pages 700-707, August.
    2. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    3. Christopher S. Troy & David E. MacHugh & Jillian F. Bailey & David A. Magee & Ronan T. Loftus & Patrick Cunningham & Andrew T. Chamberlain & Bryan C. Sykes & Daniel G. Bradley, 2001. "Genetic evidence for Near-Eastern origins of European cattle," Nature, Nature, vol. 410(6832), pages 1088-1091, April.
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    1. David Berthier & Moana Peylhard & Guiguigbaza-Kossigan Dayo & Laurence Flori & Souleymane Sylla & Seydou Bolly & Hassane Sakande & Isabelle Chantal & Sophie Thevenon, 2015. "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-21, May.
    2. Markus Neuditschko & Mehar S Khatkar & Herman W Raadsma, 2012. "NetView: A High-Definition Network-Visualization Approach to Detect Fine-Scale Population Structures from Genome-Wide Patterns of Variation," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-13, October.
    3. Liesbeth François & Katrien Wijnrocx & Frédéric G Colinet & Nicolas Gengler & Bettine Hulsegge & Jack J Windig & Nadine Buys & Steven Janssens, 2017. "Genomics of a revived breed: Case study of the Belgian campine cattle," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-14, April.

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