An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

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.

Keywords: breeds; candidate genes; cattle; diversity; domestication; selection signals; selective sweep.

Figure 1

Graphical representation of the Core Selection Sweep (CSS) regions defined in the present work across the 29 bovine autosomes, based on the selection sweeps reported by the 21 genome-wide selection-mapping scans reviewed in the present study. Note that the proximal end of each chromosome (centromere) is represented at the bottom of the plot. ANG, Angus; AUS-ANG, Australian Angus; AUSHOL-vs.-AUSANG, Australian Holstein vs. Australian Angus; BB, Belgian Blue; BLO, Blonde d'Aquitaine; BRA, Braunvieh; BRSW, Brown Swiss; CHA, Charolais; CHA-vs.-HOL, Charolais vs. Holstein; CHI-HOL, Chinese Holstein; DBB, Dual-purpose Belgian blue; FINA, Finnish Ayrshire; FLE, Fleckvieh; FRGE, Franken Gelbvieh; GAL, Galloway; GUE, Guernsey; HER, Hereford; HOL, Holstein; ISR-HOL, Israeli Holstein; IT-BR, Italian Brown; IT-HOL, Italian Holstein; JAPBL-vs.-JAHOL, Japanese Black vs. Japanese Holstein; JER, Jersey; HAN, Korean Hanwoo; LIM, Limousin; MAR, Marchigiana; MONT, Montbéliarde; MUR, Murnau-Werdenfelser; MUG, Murray Gray; NORM, Normande; NORW, Norwegian Red; OBRA, Original Braunvieh; PIE, Piedmontese; PIE-vs.-ITBR, Piedmontese vs. Italian Brown; REDA, Red Angus; RED-HOL, Red Holstein; ROM, Romagnola; SAL, Salers; SHOR, Shorthorn; SIM, Simmental; WAG, Wagyu.