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

Nature Genetics volume 47, pages 217–225 (2015)Cite this article

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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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Figure 1: Genomic variation in Chinese pigs.
Figure 2: Identification of candidate genes for local adaptation on the autosomes.
Figure 3: The selective sweep region around the VPS13A gene.
Figure 4: Characterization of the X-linked selective sweep region.
Figure 5: The X-linked selective sweep in northern Chinese pigs was possibly introgressed from an extinct Sus species.

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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).

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Author notes

  1. Huashui Ai, Xiaodong Fang and Bin Yang: These authors contributed equally to this work.

  2. Jun Ren and Lusheng Huang: These authors jointly directed this work.

Authors and 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.

Corresponding authors

Correspondence to Jun Ren or Lusheng Huang.

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The authors declare no competing financial interests.

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Ai, H., Fang, X., Yang, B. et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47, 217–225 (2015). https://doi.org/10.1038/ng.3199

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