Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds

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.

Figure 1. PCA results obtained with the whole data set (1,121 individuals, 44,706 SNPs).

Individuals are plotted according to their coordinates on the first two principal components. Ellipses characterize the dispersion of each breed around its center of gravity (assuming the cloud is a random sample distributed according to a bivariate gaussian distribution, the probability for an individual to be within the ellipse is 0.9).

Figure 2. Neighbor-Joining tree relating the 1,125 individuals (1,121 cattle and 4 american bisons).

The tree was constructed using allele sharing distances averaged over 44,706 SNPs. Edges are colored according to the individual breed of origin.

Figure 3. Unsupervised hierarchical clustering of the 1,121 individuals genotyped for 44,706 SNPs.

Results for an inferred number of clusters K varying from 2 to 6, K = 10 and K = 47 (i.e. the number of breeds) are shown.

Figure 4. Neighbor-Joining tree relating the 47 cattle populations and American bison (OBB) outgroup based on Reynolds genetic distances computed using allele frequencies at 44,706 SNPs.

Reliability of the nodes (percentage over 100 bootstrap samples) are indicated for each node.

Figure 5. Projection on a map of Europe of the colorplots synthesizing the breed coordinates on the three first sPCA principal components.

These plots can show up to three coordinates at the same time by translating each coordinate into a channel of color (Red, Green, and Blue). The obtained values are used to compose a color under the RGB system. The Danubian (solid line) and Mediterranean (dashed line) migration routes are also reproduced on the map .