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

摘要

class="head no_bottom_margin" id="sec1title">IntroductionPig (Sus scrofa) has served not only as one of the most economically important livestock but also as an important model organism used in many areas of medical research, including obesity, cardiovascular disease, endocrinology, diabetes, alcoholism, nephropathy, and organ transplantation, owing to parallels with humans in anatomy and physiology (, , , , ). There are over 730 distinct pig breeds worldwide, whose diverse phenotypes are shaped by the combined effects of local adaptation and artificial selection (). However, the vast majority of pig breeds have been developed with a focus on economic benefits, rather than breeding an ideal laboratory animal, which directly resulted in almost non-existence of excellent inbred pig strains as model organisms used in biomedical research.After several hundred years of intense artificial selection, current commercial pig breeds, represented by Duroc, have undergone drastic phenotypic changes and genetic adaptations that are economically important to the pig industry (e.g., reduction in feeding costs) and the consumer (e.g., higher production of lean meats) (, , ). In this context, a series of absolutely visible traits of current commercial pigs, such as large body size (adult individuals can reach 300–400 kg in weight), long life cycle, and weak inbreeding level (), have become obstacles in using pigs as biomedical animal models, especially in the studies of obesity and diabetes mellitus, because they result in high maintenance costs, specialized facility requirements, long experimental periods, and poor repeatability (). Moreover, the different biomedical responses and performance of commercial pig breeds from those of wild boars, including severe resistance to “diabetogenic” (high-calorie and low-activity) environment (), also go against the construction of some pig models for human diseases. These defects mean the urgent need for a professionally experimental pig strain, which drove us to develop a laboratory Asian miniature pig inbred line— Bama miniature pig (BM) based on Bama xiang pig (BX), a primitive breed without artificial imprinting for commercial characters, whose many characteristics, such as small volume, early maturity, and long-term adaptation to inbreeding, are valuable in the construction of an ideal inbred laboratory pig line (), more than 30 years ago.It is known that reference genome sequence is quite important to biomedical studies using pig model (, ). Although the genomes of some pig breeds had been published (href="#bib24" rid="bib24" class=" bibr popnode">Groenen et al., 2012, href="#bib43" rid="bib43" class=" bibr popnode">Li et al., 2017), the chromosome-level genomes with comprehensive annotation are still scarce resources to date. Moreover, most of the currently reported pig genomes are from commercial pig breeds, except, to our knowledge, only one highly fragmented draft genome sequence from an experimental inbreeding line, Wuzhishan miniature pig (href="#bib18" rid="bib18" class=" bibr popnode">Fang et al., 2012). Therefore, there is an inevitable quandary in most of the health studies involved in pig genome, that the Duroc reference genome (Sscrofa11.1, GenBank assembly accession: GCA_000003025.6) nearly becomes the only choice, no matter which kind of pig breed is selected. The presentation of BM high-quality reference genome can enrich the Sus scrofa genome database to effectively improve this dilemma, and likewise provide essential information needed to shed light on the genetic components of the BM phenotypes advantages to diabetic study, especially the relatively lower resistance to diabetic pressure, by comparative genomic analyses.In this study, we have successfully inbred BMs to generation 19 (inbred line F19), which is, to our knowledge, the pig line with the highest inbreeding coefficient to date. Using combined technologies, we presented a chromosome-level genome sequence and the available annotation of highly inbred BM. Comparative analyses of BM and Duroc genomes revealed substantial genomic differences between them, as well as identified genetic basis underlying the BM's superior traits to study diabetic diseases. Resequencing analyses between BX and BM populations confirmed the leading inbreeding degree of BMs at the genome-wide level. Besides the positively selected genes (PSGs), selective sweep and transcriptome analyses also found some changes of energy metabolism systems, like phosphatidylinositol 3-kinase (PI3K)-Akt signaling pathway, related to diabetic resistance. This study provided not only an inbred miniature pig line to overcome these preexisting obstacles of using pig in diabetic researches but also a comprehensive molecular basis as reference to further optimize breeding of the experimental animal's phenotypes advantageous to diabetic diseases researches. Meanwhile, it systematically boosted the understanding of the mechanism of resistance to diabetogenic pressure from the genome level to the transcriptome level.