Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease

Li Zhang; Yuemeng Huang; Meng Wang; Yafen Guo; Jing Liang; Xiurong Yang; Wenjing Qi; Yanjun Wu; Jinglei Si; Siran Zhu; Zhe Li; Ruiqiang Li; Chao Shi; Shuo Wang; Qunjie Zhang; Zhonglin Tang; Lixian Wang; Kui Li; Ji-Feng Fei; Ganqiu Lan

doi:10.1016/j.isci.2019.07.025

Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease

iScience. 2019 Sep 27:19:162-176. doi: 10.1016/j.isci.2019.07.025. Epub 2019 Jul 20.

Authors

Li Zhang¹, Yuemeng Huang², Meng Wang³, Yafen Guo¹, Jing Liang⁴, Xiurong Yang¹, Wenjing Qi¹, Yanjun Wu¹, Jinglei Si¹, Siran Zhu¹, Zhe Li³, Ruiqiang Li³, Chao Shi⁵, Shuo Wang⁶, Qunjie Zhang⁷, Zhonglin Tang⁸, Lixian Wang⁹, Kui Li⁹, Ji-Feng Fei¹⁰, Ganqiu Lan¹¹

Affiliations

¹ College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
² College of Animal Science and Technology, Guangxi University, Nanning 530004, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
³ Novogene Bioinformatics Institute, Beijing 100083, China.
⁴ College of Animal Science and Technology, Guangxi University, Nanning 530004, China. Electronic address: liangjing@gxu.edu.cn.
⁵ Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China. Electronic address: chaoshi@qust.edu.cn.
⁶ Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
⁷ Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
⁸ Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
⁹ Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
¹⁰ Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China.
¹¹ College of Animal Science and Technology, Guangxi University, Nanning 530004, China. Electronic address: gqlan@gxu.edu.cn.

Abstract

Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.

Keywords: Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics.