A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Qimeng Yang, Yuan Xu, Mengsi Xu, Huanhuan Zhang, Yunfeng Zhang, Xuelei Dai, Yuanpeng Gao, Zhuangbiao Zhang, Wenwen Fang, Yuta Yang, Weiwei Fu, Chunna Cao, Peng Yang, Zeinab Amiri GhanatsamanNiloufar Jafarpour Negari, Hojjat Asadollahpour Nanaei, Xiangpeng Yue, Yuxuan Song, Xianyong Lan, Weidong Deng, Xihong Wang, Chuanying Pan, Ruidong Xiang, Eveline M Ibeagha-Awemu, Pat J S Heslop-Harrison, Benjamin D Rosen, Johannes A Lenstra, Shangquan Gan*, Yu Jiang*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Original languageEnglish
Pages (from-to)463-477
Number of pages15
JournalGenome Research
Volume33
Issue number3
DOIs
Publication statusPublished - Mar 2023

Keywords

  • Animals
  • Sheep/genetics
  • Genome-Wide Association Study
  • Tail
  • 5' Untranslated Regions
  • Alleles
  • Phenotype

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