Selection Signatures in the Cattle Genome: Lessons from Largescale Resequencing of Four International Breeds

In this study, we exploit individual resequencing data in four cattle breeds, gathered by the 1000 bull genomes project (Daetwyler et al. 2014), to identify genomic footprints of selection. To this aim, we applied two different approaches: a within-population approach (Boitard et al. 2009) on each breed to detect directional selection events (hard sweeps) through the identification of regions of reduced heterozygosity, and a differentiation based approach looking for regions where breeds show excessive haplotype divergence (Fariello et al. 2013). We found that exploiting full sequence data allows to increase power to detect selection events compared to high density genotyping. While known causal variants for morphological traits can be detected using such selection signatures approach, most selection signatures lie outside coding regions and further annotation of the cattle genome will be required to elucidate the underlying selected phenotypes. Although we observed some overlap between the two methods used here, we found them to be complementary in that they tend to detect different selection events.

Boitard et al. (2009) Genetics 181:1567
Daetwyler et al., (2014) Nat. Genet.  46:858
Fariello et al. (2013) Genetics 193:929