| Mapping and functional characterization of structural variation in 1060 pig genomes |
| Yang, L; Yin, HW; Bai, LJ; Yao, WY; Tao, T; Zhao, QY; Gao, YH; Teng, JY; Xu, ZT; Lin, Q; Diao, SQ; Pan, ZY; Guan, DL; Li, BJ; Zhou, HJ; Zhou, ZY; Zhao, FP; Wang, QS; Pan, YC; Zhang, Z; Li, K; Fang, LZ; Liu, GE
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| 2024
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| 发表期刊 | GENOME BIOLOGY
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| ISSN | 1474-760X
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| 卷号 | 25期号:1 |
| 摘要 | 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 similar to 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. |
| 收录类别 | sci
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| 语种 | 英语
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| 文献类型 | 期刊论文
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| 条目标识符 | http://ir.kiz.ac.cn/handle/152453/14276
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| 专题 | 科研部门_分子进化与基因组多样性（张亚平）
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推荐引用方式
GB/T 7714 |
Yang, L,Yin, HW,Bai, LJ,et al. Mapping and functional characterization of structural variation in 1060 pig genomes[J]. GENOME BIOLOGY,2024,25(1).
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| APA |
Yang, L.,Yin, HW.,Bai, LJ.,Yao, WY.,Tao, T.,...&Liu, GE.(2024).Mapping and functional characterization of structural variation in 1060 pig genomes.GENOME BIOLOGY,25(1).
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| MLA |
Yang, L,et al."Mapping and functional characterization of structural variation in 1060 pig genomes".GENOME BIOLOGY 25.1(2024).
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