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.
Highlights
Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments
Single-nucleotide polymorphism (SNP) annotations The numbers of SNPs and indels in the coding sequences (CDS) of the 3 breeds are shown in Additional file 5: Table S4
We identified 803 genes that contained missense SNPs or stop gained/loss variants in both Small-tailed Han sheep and Duolang sheep, but not in Mongolian sheep
Summary
Throughout 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. With the development of animal husbandry and the application of directed mating technology, phenotypic radiation under selection has resulted in the spectrum of modern sheep breeds, adapted to a diverse range of environments and specialized for the production of meat, milk, and wool [1, 2]. China has a long history of sheep domestication and rich resources of sheep breeds [3, 4]. According to archaeological and genetic research, Mongolian sheep is the common ancestor of Chinese short fat-tailed sheep breeds. From the Mongolian plateau to various ecoregions around almost the entire country, Mongolian sheep have experienced changes in climate, environment and feeding conditions
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