Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

Linyong Hu; Liangzhi Zhang; Qi Li; Hongjin Liu; Tianwei Xu; Na Zhao; Xueping Han; Shixiao Xu; Xinquan Zhao; Cunfang Zhang

doi:10.3389/fgene.2022.971464

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

Front Genet. 2022 Sep 7:13:971464. doi: 10.3389/fgene.2022.971464. eCollection 2022.

Authors

Linyong Hu¹, Liangzhi Zhang¹, Qi Li¹, Hongjin Liu¹, Tianwei Xu¹, Na Zhao¹, Xueping Han^{1

2}, Shixiao Xu¹, Xinquan Zhao¹, Cunfang Zhang³

Affiliations

¹ Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
² Technology Extension Service of Animal Husbandry of Qinghai, Xining, China.
³ State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.

Abstract

Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Keywords: Tibetan sheep; adaptation; copy number variations; domestication; whole genome resequencing.