Mapping and functional characterization of structural variation in 1060 pig genomes

Liu Yang, Hongwei Yin, Lijing Bai, Wenye Yao, Tan Tao, Qianyi Zhao, Yahui Gao, Jinyan Teng, Zhiting Xu, Qing Lin, Shuqi Diao, Zhangyuan Pan, Dailu Guan, Bingjie Li, Huaijun Zhou, Zhongyin Zhou, Fuping Zhao, Qishan Wang, Yuchun Pan, Zhe ZhangKui Li*, Lingzhao Fang*, George E Liu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

BACKGROUND: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.

RESULTS: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies.

CONCLUSIONS: This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Original languageEnglish
Article number116
JournalGenome Biology
Volume25
Issue number1
DOIs
Publication statusPrint publication - 7 May 2024

Bibliographical note

© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.

Keywords

  • Animals
  • Genome
  • Genomic Structural Variation
  • Sus scrofa/genetics
  • Polymorphism, Single Nucleotide
  • Swine/genetics
  • Chromosome Mapping
  • Structure variation
  • Functional genome
  • Gene expression
  • Population diversity
  • Pig

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