Mapping and functional characterization of structural variation in 1060 pig genomes

Authors: YANG, LIU - Chinese Academy Of Agricultural Sciences; YIN, HONGWEI - Chinese Academy Of Agricultural Sciences; BAI, LIJING - Chinese Academy Of Agricultural Sciences; YAO, WENYE - Chinese Academy Of Agricultural Sciences; TAO, TAN - Chinese Academy Of Agricultural Sciences; ZHAO, QIANYI - Chinese Academy Of Agricultural Sciences; GAO, YAHUI - University Of Maryland; TENG, JINYAN - South China Agricultural Univerisity; XU, ZHITING - South China Agricultural Univerisity; LIN, QING - South China Agricultural Univerisity; DIAO, SHUQI - South China Agricultural Univerisity; PAN, ZHANGYUAN - University Of California, Davis; GUAN, DAILU - University Of California, Davis; LI, BINGJIE - Sruc-Scotland'S Rural College; ZHOU, HUAIJUN - University Of California, Davis; ZHOU, ZHONGYIN - Chinese Academy Of Sciences; ZHAO, FUPING - Chinese Academy Of Agricultural Sciences; WANG, QISHAN - Zhejiang University; PAN, YUCHUN - Zhejiang University; ZHANG, ZHE - South China Agricultural Univerisity; LI, KUI - Chinese Academy Of Agricultural Sciences; FANG, LINGZHAO - Aarhus University; Liu, Ge - George

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2024
Publication Date: 5/7/2024
Citation: Yang, L., Yin, H., Bai, L., Yao, W., Tao, T., Zhao, Q., Gao, Y., Teng, J., Xu, Z., Lin, Q., Diao, S., Pan, Z., Guan, D., Li, B., Zhou, H., Zhou, Z., Zhao, F., Wang, Q., Pan, Y., Zhang, Z., Li, K., Fang, L., Liu, G. 2024. Mapping and functional characterization of structural variation in 1060 pig genomes. Genome Biology. 25. Article e116. https://doi.org/10.1186/s13059-024-03253-3.
DOI: https://doi.org/10.1186/s13059-024-03253-3

Interpretive Summary: Structural variation are importrant variations in livestock genome. We reported a comprehensive structural variation catalog and provided new knowledge of the diversity and evolution of pigs. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, breeders, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Structural variations (SVs) have profound consequences on complex phenotypes through rearranging large regions of DNA sequence. Here, we report a comprehensive SV catalog based on the whole genome sequence of 1,060 pigs representing 101 breeds. It covers 9.6% of the pig genome nonredundantly, including 42,487 deletions, 37,913 mobile element insertions, 3,308 duplications, 1,664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization between pig breeds using genotyped SVs generated similar results to those using single nucleotide polymorphisms. For example, we observed hundreds of deletions that have been stratified across geographic groups and breeds. We confirmed that the known duplications of KIT gene were underlying the dominant white coat color in European pigs. We also explored the impacts of SVs on gene expression, functional elements, and complex traits of economic importance by systematically integrating them with expression quantitative trait loci (eQTLs) from 34 major tissues, chromatin states from 14 tissues, and sequence-based genome-wide association study (GWAS) signals of 14 complex traits from the Pig Genotype-Tissue Expression (PigGTEx) project, as part of FarmGTEx project. We further found a recent SINE element (Pre_SS01) insertion in the 3’-UTR of MYO5A gene mainly in European pigs, distributing according to the geographic distributions. We hypothesized that this insertion, overlapping an intron of MYO5A, could affect the alternative splicing pattern of this gene, facilitating coat color changes. A Yorkshire-specific copy number gain within ABCG2 could potentially downregulate its host gene, and increase the expression of its long distance downstream (~79.5 kb) gene SPP1 overleaping its nearby gene PKD2 (~ 7.0 kb) in multiple tissues by reorganizing chromatin interactions. In summary, this SV catalog is a valuable resource for studying diversity and evolutionary history in pigs and how domestication, trait-based breeding, and adaptive evolution have functionally shaped the pig genome.