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

Zhipeng Wang; Jing Guo; Yuanyuan Guo; Yonglin Yang; Teng Teng; Qian Yu; Tao Wang; Meng Zhou; Qiusi Zhu; Wenwen Wang; Qin Zhang; Hua Yang

doi:10.3389/fgene.2020.00558

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

Front Genet. 2020 Jun 9:11:558. doi: 10.3389/fgene.2020.00558. eCollection 2020.

Authors

Zhipeng Wang^{1

2}, Jing Guo^{1

2}, Yuanyuan Guo^{1

2}, Yonglin Yang³, Teng Teng⁴, Qian Yu³, Tao Wang^{1

2}, Meng Zhou^{1

2}, Qiusi Zhu^{1

2}, Wenwen Wang⁵, Qin Zhang⁵, Hua Yang³

Affiliations

¹ College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.
² Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.
³ State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
⁴ Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China.
⁵ Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.

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 OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.

Keywords: SNP; body weight; breed-specific; copy number variation; sheep.