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

Abstract

BackgroundThroughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits.ResultsThis research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds.ConclusionsOur results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3212-2) contains supplementary material, which is available to authorized users.

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

“…; Liu et al . ). Signatures have been observed in regions harboring candidate genes associated with pigmentation (Fariello et al .…”

Novel Variants in GDF9 Gene Affect Promoter Activity and Litter Size in Mongolia Sheep

“…According to archaeological and genetic research, the Mongolia sheep is the common ancestor of Chinese short fat-tailed sheep breeds, such as Sonid, Ujimqin, Hulunbuir, Tan, Bayanbulak, Small-tailed Han, Duolang sheep, and Hu sheep [25]. They are fat-tailed; produce quality meat; carpet wool; and have sound body conformation, strong walking ability, and admirable adaptation to very different ecological conditions [25][26][27]. Recently, the mutton of Mongolia sheep was recognized as a natural green food and has become increasingly popular in China.…”

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

“…Searches for genome intervals, genes and polymorphisms which determine performance for economically important traits in sheep have resulted in revealing signatures of selection likely associated with coat colour [5][6][7], tail fat deposition [8], muscle growth [9], milk yield [10], reproductive traits [6,11], wool [12], resistance to parasites [13], presence/absence of horns [6,11], etc. These chromosome regions contain markers (genes or regulatory sequences) which should be the focus of future efforts on the improvement of local and multinational breeds using the rapidly-developing plethora of contemporary genetics tools.…”

“…For instance, TRPM8 (transient receptor potential cation channel subfamily M member 8) plays a role in thermal sensation in mice [19]. The same gene was linked to cold tolerance in sheep [6,7,11]. These examples demonstrate that different genes could be affected by selection to similar environments, suggesting that studies of multiple breeds adapted to a variety of conditions could help revealing a full set of genomic regions affected during the process of adaptation.…”