Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Aug;21(6):2077-2092.
doi: 10.1111/1755-0998.13396. Epub 2021 Apr 26.

The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication

Rong Zhou  1 , Shang-Tong Li  2 , Wen-Ye Yao  1 , Chun-Di Xie  1 , Zhiqiang Chen  3 , Zhi-Jie Zeng  1   4 , Di Wang  3 , Kui Xu  1 , Zhao-Ji Shen  5   6 , Yulian Mu  1 , Wenbin Bao  7 , Wenkai Jiang  3 , Ruiqiang Li  3 , Qiqi Liang  3 , Kui Li  1
Affiliations

The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication

Rong Zhou et al. Mol Ecol Resour. 2021 Aug.

Abstract

There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

Keywords: Meishan pig; genome assembly; genome evolution; structural variation.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

REFERENCES

    1. Adey, A., Kitzman, J. O., Burton, J. N., Daza, R., Kumar, A., Christiansen, L., Ronaghi, M., Amini, S., L. Gunderson, K., Steemers, F. J., & Shendure, J. (2014). In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research, 24(12), 2041-2049.
    1. Ai, H., Fang, X., Yang, B., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L. U., Cui, L., He, W., Yang, J., Yao, X., Zhou, L., Han, L., Li, J., Sun, S., Xie, X., Lai, B., Su, Y., … Huang, L. (2015). Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nature Genetics, 47(3), 217.
    1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410.
    1. Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31(2), 166-169.
    1. Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289-300.

LinkOut - more resources