Selection Signatures in Worldwide Sheep Populations

Abstract

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions

“…Correspondingly, we detected several genes located in the selection regions or containing unique function-altering mutations with potential relationship with adaption such as the genes in Table 1. In the precious research, the selection near the TRPM8 gene was reported to be related to adaptation to cold climate [26] and this gene also showed selection evidence in this study. The adaption process is complex and the potential role of many selection signatures in the adaptation of sheep breeds remains unclear.…”

“…In the former group one conspicuous cluster related to reproduction; 59 genes belonged to this category (13 genes were related to single fertilization and 24 genes were related to spermatogenesis). Another conspicuous cluster with 284 genes was related to response to stimulus (Table 1 and Additional file 6: Table S5); one of these genes TRPM8 has been shown to be a major determinant of cold perception in the mouse [25] and was reported to be related to adaptation to cold climate on sheep [26]; 12 of the 284 genes were related to response to light stimulus and we suggested these genes might had potential relationship with seasonal estrous. In the latter group one conspicuous cluster related to reproduction as well; 15 genes belonged to this category (12 genes were related to spermatogenesis).…”

“…This remarkable genetic diversity indicated that TSHR showed strong evidence of selective pressure. In selection signal analysis of sheep breeds from all over the world, positive selection was also detected surrounding TSHR [2, 26].

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“…In the recent large scale selection signature studies on sheep, reproduction has been identified as one of the selected targets and candidate genes associated with reproduction are detected in selection regions [2, 26, 36]. Kijas (2012) reported 31 genome regions with extreme differentiation among 74 world-wide sheep breeds by computing the globe F ST at all SNP in the genome, which included candidate genes related to coat pigmentation, skeletal morphology, body size, growth, and reproduction [2].…”

“…Kijas (2012) reported 31 genome regions with extreme differentiation among 74 world-wide sheep breeds by computing the globe F ST at all SNP in the genome, which included candidate genes related to coat pigmentation, skeletal morphology, body size, growth, and reproduction [2]. Fariello (2014) used a new approach FLK/hapFLK to re-scan the sheep genome for selection based on the Sheep HapMap dataset among 7 broad geographical groups and also identified 71 new selection signatures, with candidate genes related to coloration, morphology or production traits [26]. The candidate gene related to reproduction TSHR were both detected in the above two studies and identified as ancestral signatures of selection in the latter one.…”