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Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

Nature Genetics volume 47, pages 217225 (2015) | Download Citation

Abstract

Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

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Acknowledgements

We thank L. Andersson for critical discussions and reading of the manuscript. This study is supported by the National Key Research Project of China (2013ZX08006-5), the Natural Science Foundation of China (31230069) and the Changjiang Scholars and Innovative Research Team in University (IRT1136).

Author information

Author notes

    • Huashui Ai
    • , Xiaodong Fang
    •  & Bin Yang

    These authors contributed equally to this work.

    • Jun Ren
    •  & Lusheng Huang

    These authors jointly directed this work.

Affiliations

  1. Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.

    • Huashui Ai
    • , Bin Yang
    • , Hao Chen
    • , Feng Zhang
    • , Leilei Cui
    • , Jie Yang
    • , Lisheng Zhou
    • , Jing Li
    • , Xianhua Xie
    • , Ying Su
    • , Hui Yang
    • , Tao Huang
    • , Wenjiang Deng
    • , Jun Ren
    •  & Lusheng Huang
  2. BGI-Tech, BGI-Shenzhen, Shenzhen, China.

    • Xiaodong Fang
    • , Zhiyong Huang
    • , Likai Mao
    • , Lu Zhang
    • , Weiming He
    • , Xiaoming Yao
    • , Lijuan Han
    • , Silong Sun
    • , Boxian Lai
    • , Yao Lu
    •  & Rasmus Nielsen
  3. Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.

    • Rasmus Nielsen

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Contributions

L. Huang and J.R. designed the study and analyzed the data. J.R., B.Y., H.A., X.F., R.N. and L. Huang wrote the manuscript. H.A., X.F., B.Y., Z.H., H.C., L.M., F.Z., L. Zhang, L.C., W.H., T.H., W.D. and R.N. performed bioinformatics analyses. J.Y., X.Y., L. Zhou, L. Han, J.L., S.S., X.X., B.L., Y.S., Y.L. and H.Y. collected data and performed sequencing and genotyping experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jun Ren or Lusheng Huang.

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DOI

https://doi.org/10.1038/ng.3199