A Meta-Assembly of Selection Signatures in Cattle

Abstract

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed "selection signatures". This article reviews 64 recent (2009-2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.

Fig 1. Plot of relationship matrix and DNA score (d_i) weighting computed from 46 studies that published selection signature using European cattle.

n_i shows total number of DNA samples from European breed(s) from a particular study. The relationship score was computed as proportion of common samples between each pair of studies and it range between 0 and 1.

Fig 2. Meta-assembly of selection signatures in four groups within European, Zebu, African and Composite breeds of cattle.

Fig 3. Meta-assembly of selection signatures of Holstein, Brown Swiss, Jersey, Simmental (Fleckvieh), Angus, Charolais, Hanwoo, Hereford, Limousin, Piedmontese, Brahman, Gir and Nellore cattle.

Fig 4. Meta-assembly of selection signatures of Belgian Blue, Braunvieh, Guernsey, Italian Brown, Marchigiana, Murray Grey, Norwegian Red, Romagnola, Shorthorn, Santa Gertrudis, NDama and Sheko.

Fig 5. Map of selection signature hotspots captured in the meta-assembly of cattle breeds and groups.

Middle Panels labelled as “Cattle Breeds” and “Cattle Groups”, show the location of prominent regions in the cattle breeds and groups, respectively represented with the unique colours as shown in the legends. The clustered dots, within a locus, located on top of each other represent shared selection signatures across the breeds and groups, each of which has been validated in multiple investigations. Lower Panel labelled as “Gene density” shows distribution of bovine genes on each chromosome that ranges 0–80 genes/Mb (S7 Fig shows high-resolution comparison of MSS and genes per Mb in European). Top Panel labelled as "Candidate Genes" shows genomic locations of a few major genes underlying the outstanding peaks representing classic selective sweep regions in the meta-assemblies. Complete list of prominent regions, localized top MSS and underlying genes within the groups and breeds of cattle are respectively shown in S4 and S5 Tables.