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Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

Author

Listed:
  • Xinkai Tong

    (Jiangxi Agricultural University
    Jiangxi Normal University)

  • Dong Chen

    (Jiangxi Agricultural University)

  • Jianchao Hu

    (Jiangxi Agricultural University)

  • Shiyao Lin

    (Jiangxi Agricultural University)

  • Ziqi Ling

    (Jiangxi Agricultural University)

  • Huashui Ai

    (Jiangxi Agricultural University)

  • Zhiyan Zhang

    (Jiangxi Agricultural University)

  • Lusheng Huang

    (Jiangxi Agricultural University)

Abstract

High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

Suggested Citation

  • Xinkai Tong & Dong Chen & Jianchao Hu & Shiyao Lin & Ziqi Ling & Huashui Ai & Zhiyan Zhang & Lusheng Huang, 2023. "Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40434-3
    DOI: 10.1038/s41467-023-40434-3
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    References listed on IDEAS

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    1. Heng Du & Lei Zhou & Zhen Liu & Yue Zhuo & Meilin Zhang & Qianqian Huang & Shiyu Lu & Kai Xing & Li Jiang & Jian-Feng Liu, 2024. "The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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