Abstract
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.
Highlights
The genetic diversity of livestock species is an economical and cultural inheritance from our ancestors, and an indispensable resource to meet the unpredictable needs of our future (Larson et al, 1992)
A larger number of genes was extracted for the Multibreed core selective sweep (CSS) (2440 genes), which spanned a total of 264.05 Mb across 20 out of the 29 bovine autosomes
More than half of the defined CSSs were associated with a single breed, and these were located across all the autosomes, the breed-specific selection sweeps spanned a shorter genomic length (73.01 Mb) and included a smaller number of genes (839)
Summary
The genetic diversity of livestock species is an economical and cultural inheritance from our ancestors, and an indispensable resource to meet the unpredictable needs of our future (Larson et al, 1992). Four identified CSS regions were only detected in the across-breed FST analyses reported by the Bovine HapMap Consortium (2009), and will be referred to as HapMapUnique CSSs. These four groups of CSSs are indicated by different cell color backgrounds in Supplementary Table S2, which includes the genes that were highlighted by the original studies as possible candidate targets of the identified selection sweep.
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