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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #418336
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

Author
item LIU, LEI - Collaborator
item YI, GUOQIANG - Chinese Academy Of Agricultural Sciences
item YAO, YILONG - Chinese Academy Of Agricultural Sciences
item LIU, YUWEN - Chinese Academy Of Agricultural Sciences
item LI, JIANG - Collaborator
item YANG, YALAN - Chinese Academy Of Agricultural Sciences
item LIU, MEI - Hunan Agricultural University
item FANG, LINGZHAO - Aarhus University
item MO, DELIN - Sun Yat-Sen University
item ZHANG, LONGCHAO - Chinese Academy Of Agricultural Sciences
item LIU, YONGGANG - Yunnan Agricultural University
item NIU, YONGCHAO - Collaborator
item WANG, LIYUAN - Chinese Academy Of Agricultural Sciences
item QU, XIAOLU - Chinese Academy Of Agricultural Sciences
item PAN, ZHANGYUAN - Chinese Academy Of Agricultural Sciences
item WANG, LEI - Chinese Academy Of Agricultural Sciences
item CHEN, MUYA - Chinese Academy Of Agricultural Sciences
item FAN, XINHAO - Chinese Academy Of Agricultural Sciences
item CHEN, YUN - Chinese Academy Of Agricultural Sciences
item ZHANG, YONGSHENG - Chinese Academy Of Agricultural Sciences
item LI, XINGZHENG - Chinese Academy Of Agricultural Sciences
item WANG, ZHEN - Chinese Academy Of Agricultural Sciences
item TANG, YIJIE - Chinese Academy Of Agricultural Sciences
item HUANG, HETIAN - Henan Agricultural University
item YUAN, PENGXIANG - Chinese Academy Of Agricultural Sciences
item LIAO, YUYING - Guangxi University
item LI, XINJIAN - Henan Agricultural University
item YIN, ZONGJUN - Anhui Agricultural University
item LIU, DI - Heilongjiang Academy Of Agricultural Sciences
item ZHANG, DONGJIE - Heilongjiang Academy Of Agricultural Sciences
item ZHOU, QUANYONG - Jiangxi Academy Of Agricultural Sciences
item WU, WANGJUN - Nanjing Agricultural University
item JIANG, JICAI - North Carolina State University
item GAO, YAHUI - University Of Maryland
item Liu, Ge
item WANG, LIXIAN - Chinese Academy Of Agricultural Sciences
item CHEN, YAOSHENG - Sun Yat-Sen University
item LI, KUI - Chinese Academy Of Agricultural Sciences
item GROENEN, MARTIEN - Wageningen University
item TANG, ZHONGLIN - Chinese Academy Of Agricultural Sciences

Submitted to: iMeta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2024
Publication Date: 12/15/2024
Citation: Liu, L., Yi, G., Yao, Y., Liu, Y., Li, J., Yang, Y., Liu, M., Fang, L., Mo, D., Zhang, L., Liu, Y., Niu, Y., Wang, L., Qu, X., Pan, Z., Wang, L., Chen, M., Fan, X., Chen, Y., Zhang, Y., Li, X., Wang, Z., Tang, Y., Huang, H., Yuan, P., Liao, Y., Li, X., Yin, Z., Liu, D., Zhang, D., Zhou, Q., Wu, W., Jiang, J., Gao, Y., Liu, G., Wang, L., Chen, Y., Li, K., Groenen, M.A., Tang, Z. 2024. Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs. iMeta. https://doi.org/10.1002/imt2.250.
DOI: https://doi.org/10.1002/imt2.250

Interpretive Summary: The genetic basis of complex traits and phenotypic differences in livestock like pigs is not yet fully understood. We built a pig pan-genome and showed how genetic changes from artificial selection influence traits like fat deposition and immune response, offering insights for improving pig genetics. These results fill our knowledge gaps and provide the foundation for the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Based on seven newly generated high-quality de novo assembled genomes and 1,081 resequencing genomes, we built a pan-genome and identified 134.24 Mb non-redundant non-reference sequence, 1,099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 SNPs. Analysis of selective domestication revealed BRCA1 associated with enhancing adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptome and 162 methylome of skeletal muscle across 27 developmental stages revealed regulation mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection could have resulted in reshaping local DNA methylation status and impart regulatory effects in progression patterns of heterochronic genes like GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement program in pigs.