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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.
Highlights
Modern domestic species are a result of selective breeding for many traits of economic and adaptive importance since domestication [1,2,3,4]
In total 16,158 (European = 13,640, Zebu = 1,246, African = 1,112 and Composite = 160) individual selection signature scores contributed to the meta-assembly
Overall peaks with extreme MSS in a meta-assembly map identify the hotspots of positive selection within cattle groups (Fig 2)
Summary
Modern domestic species are a result of selective breeding for many traits of economic and adaptive importance since domestication [1,2,3,4]. The footprints of selective breeding on genomic architecture can be characterized with the development of molecular genomic and advanced computational biology tools [5,6,7]. Differentiate, the rapid expansion of genomic data generated from global sequencing and genotyping projects are providing greater insights of selection on genomes of domestic species [8]. Long-term selection pressures have operated on the genomic regions that control traits for adaptive fitness. Selection for various unique morphological traits during the development of specialized breeds (for example; coat colors, presence of horns, etc.) have left their selective signatures in the genome
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