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Whole-genome resequencing analysis of 20 Micro-pigs

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Abstract

Background

Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs.

Objective

In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics.

Results

Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11.

Conclusion

In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.

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Data availability

The raw sequencing data are available from the corresponding authors upon request.

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Acknowledgements

This work was supported by the Industrial Core Technology Development Program (10049112, Development of the Validation System for Efficacy Studies using Mini Pigs) funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea) and 2016 Research Grant from Kangwon National University.

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Authors and Affiliations

  1. College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Da-Hye Son, Nam-Hyun Hwang, Ha-Seung Seong & Jung-Woo Choi

  2. Research Division of Food Functionality, Research Group of Healthcare, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea

    Won-Hyong Chung

  3. Medikinetics Co., Ltd, 4 Hansan-gil, Cheongbuk-eup, Pyeongtaek-si, Gyeonggi-do, 17792, Republic of Korea

    Hyungbum Lim & Kyung-Soo Kang

  4. Division of Swine Science, National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea

    Eun-Seok Cho & Yong-Min Kim

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  1. Da-Hye Son
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Correspondence to Jung-Woo Choi, Kyung-Soo Kang or Yong-Min Kim.

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Ethical approval

All experiments and all its procedures were carried out in accordance with the regulation approved by the Medi Kinetics Company (Medi Kinetics Company’s Institutional Animal Care and Use Committee).

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Son, DH., Hwang, NH., Chung, WH. et al. Whole-genome resequencing analysis of 20 Micro-pigs. Genes Genom 42, 263–272 (2020). https://doi.org/10.1007/s13258-019-00891-x

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