Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays

Abstract

Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as <i>OR6C76</i>, <i>OR4Q2</i>, and <i>OR4K14</i>. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including <i>FOXF2</i>, <i>MAPK12</i>, <i>MAP3K11</i>, <i>STRBP</i>, and <i>C14orf132</i>. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.