TY - JOUR
T1 - Mapping and functional characterization of structural variation in 1060 pig genomes
AU - Yang, Liu
AU - Yin, Hongwei
AU - Bai, Lijing
AU - Yao, Wenye
AU - Tao, Tan
AU - Zhao, Qianyi
AU - Gao, Yahui
AU - Teng, Jinyan
AU - Xu, Zhiting
AU - Lin, Qing
AU - Diao, Shuqi
AU - Pan, Zhangyuan
AU - Guan, Dailu
AU - Li, Bingjie
AU - Zhou, Huaijun
AU - Zhou, Zhongyin
AU - Zhao, Fuping
AU - Wang, Qishan
AU - Pan, Yuchun
AU - Zhang, Zhe
AU - Li, Kui
AU - Fang, Lingzhao
AU - Liu, George E
PY - 2024/5
Y1 - 2024/5
N2 - 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.
AB - 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.
KW - Functional genome
KW - Gene expression
KW - Pig
KW - Population diversity
KW - Structure variation
KW - Genomic Structural Variation
KW - Animals
KW - Sus scrofa/genetics
KW - Swine/genetics
KW - Chromosome Mapping
KW - Polymorphism, Single Nucleotide
KW - Genome
UR - http://www.scopus.com/inward/record.url?scp=85192225403&partnerID=8YFLogxK
U2 - 10.1186/s13059-024-03253-3
DO - 10.1186/s13059-024-03253-3
M3 - Journal article
C2 - 38715020
SN - 1474-7596
VL - 25
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 116
ER -