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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 #336615
Title: Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization

Author
item ZHAO, PENJU - China Agricultural University
item YU, YING - China Agricultural University
item FENG, WEN - China Agricultural University
item DU, HENG - China Agricultural University
item YU, JIAN - China Agricultural University
item KANG, HUIMIN - China Agricultural University
item ZHENG, XIANRUI - China Agricultural University
item WANG, ZHIQUAN - University Of Alberta
item Liu, Ge - George
item Ernst, Catherine
item RAN, XUEQIN - China Agricultural University
item WANG, JIAFU - Guizhou Academy Of Agricultural Sciences
item LIU, JIAN-FENG - China Agricultural University

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2018
Publication Date: 5/15/2018
Citation: Zhao, P., Yu, Y., Feng, W., Du, H., Yu, J., Kang, H., Zheng, X., Wang, Z., Liu, G., Ernst, C.W., Ran, X., Wang, J., Liu, J. 2018. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. Gigascience. 7(5):1-12. https://doi.org/10.1093/gigascience/giy058.
DOI: https://doi.org/10.1093/gigascience/giy058

Interpretive Summary: Genetic mechanisms underlying domestication and high fertility of Meishan pigs are not well understood. This study applied population-scale sequencing to assess Meishan's nuclear genome as compared to other pigs. These results fill gaps in our knowledge about Meishan's domestication bottlenecks and provide a suite of potential reproduction-related pathways and genes. Farmers, scientists, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Meishan is a famous Chinese indigenous pig breed known for its extremely high fecundity. To explore if Meishan has unique evolutionary process and genome characteristics differing from other pig breeds, we systematically analyzed its genetic divergence, and demographic history by large-scale resequencing the genomes of Meishan pigs which were compared with other pig populations. We found evidence that effective population size of Meishan pigs dropped dramatically around 4,300 years ago with a presence of significant domestication bottlenecks. We further screened genome-wide selective signatures using SNPs and InDels,where a suite of crucial reproduction related pathways and genes was enriched. We also constructed the first CNV map in the genome of Meishan and found 4 duplications near exons 3-8 of AR gene were potentially associated with litter size. Findings here provide new insights into the mechanism of porcine prolificacy from the perspective of evolution and domestication in pigs.