Identification of large selective sweeps associated with major genes in cattle

Abstract

Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits.

Selection Signatures in Worldwide Sheep Populations

“…Another region harbors the HMGA2 gene, involved in selection for stature in dogs [19] and associated to body size in horses [20] and height in humans [21]. The last region includes two interesting candidate genes: ABCG2, which has been associated to a strong QTL for milk production in cattle [22], and NCAPG, which has been associated to fetal growth [23] and calving ease [24] in cattle and which is located in several selection signatures in this species [25]–[28]. In our analysis, populations with a selection signature in this region belong to three European groups (SWE, ITA and CEU) and our results suggest that selection in these different groups might imply distinct genes (Table 2).…”

Selection signatures in worldwide Sheep populations

“…Another region harbors the HMGA2 gene, involved in selection for stature in dogs [19] and associated to body size in horses [20] and height in humans [21]. The last region includes two interesting candidate genes: ABCG2, which has been associated to a strong QTL for milk production in cattle [22], and NCAPG, which has been associated to fetal growth [23] and calving ease [24] in cattle and which is located in several selection signatures in this species [25][26][27][28]. In our analysis, populations with a selection signature in this region belong to three European groups (SWE, ITA and CEU) and our results suggest that selection in these different groups might imply distinct genes ( Table 2).…”

Genomic response to natural selection within alpine cattle breeds

“…The presence of strong selective footprints across the bovine genome was tested in multiple cattle populations using various approaches mainly based on site frequency spectrum, population differentiation represented by F ST statistic and haplotype length (extend of linkage disequilibrium) (Druet et al 2013;Mancini et al 2014;Zhao et al 2015). The number of identified selective sweeps varied across different studies, depending on methodological approach and analysed populations.…”