Genome-Wide Specific Selection in Three Domestic Sheep Breeds

<div><p>Background</p><p>Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.</p><p>Results</p><p>We first combined locus-specific branch lengths and <i>d_i</i> statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, <i>APOBR</i> and <i>FTO</i> are associated with body mass index. For meat traits, <i>ALDOA</i>, <i>STK32B</i> and <i>FAM190A</i> are related to marbling. For reproduction traits, <i>CCNB2</i> and <i>SLC8A3</i> affect oocyte development. We also found two well-known genes, <i>GHR</i> (which affects meat production and quality) and <i>EDAR</i> (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (<i>POL</i>, <i>RPL7</i>, <i>MSL1</i> and <i>SHISA9</i>) were associated with pre-weaning gain in our previous genome-wide association study.</p><p>Conclusions</p><p>Our results indicated that combine locus-specific branch lengths and <i>d_i</i> statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.</p></div

The annotation details in specific selected and overlapping selected region.

<p>The annotation details in specific selected and overlapping selected region.</p

The information of main candidate gene of three breeds.

<p>Underlined fonts indicate candidate gene in our former GWAS study.</p><p>The information of main candidate gene of three breeds.</p

Histogram of the LSBL and <i>d</i>_<i>i</i> statistics distribution for each breed.

<p>Histogram of the LSBL and <i>d</i>_<i>i</i> statistics distribution for each breed.</p

Three-branch phylogeny constructed from pairwise F_ST.

<p>Three-branch phylogeny constructed from pairwise F_ST.</p

Genome-Wide Specific Selection in Three Domestic Sheep Breeds - Fig 1

<p>A. Animals clustered on the basis of principal component (PC) analysis using individual genotypes B. Scree-plot of proportion of variance.</p

Myostatin-Pax7 pathways in muscle in Texel and Ujumqin sheep.

<p>The shortest Myostatin-Pax7 pathways in Texel and Ujumqin were generated using the tools in IPA. The gray ones indicate the DE genes in muscle for both breeds during the five fetal stages. The pink ones indicate the genes differentially expressed in Texel, and the pale green in Ujumqin. The physically direct or indirect interaction between genes is indicated as the solid line or dotted line in the figure.</p

Correlation between LSBL and <i>d</i>_<i>i</i> statistics.

<p>Correlation between LSBL and <i>d</i>_<i>i</i> statistics.</p

The descried of LSBL and <i>d</i>_<i>i</i> values for each breed

<p>The descried of LSBL and <i>d</i>_<i>i</i> values for each breed</p

The diversity of OAR13_67857725.1 SNP in 3 sheep breeds.

<p>The diversity of OAR13_67857725.1 SNP in 3 sheep breeds.</p