Genome analysis of Yucatan miniature pigs to assess their potential as biomedical model animals

• Published in: Animal bioscience Vol. 32; no. 2; pp. 290 - 296
• Main Authors: Kwon, Dae-Jin, Lee, Yeong-Sup, Shin, Donghyun, Won, Kyeong-Hye, Song, Ki-Duk
• Format: Journal Article
• Language: English
• Published: Korea (South) Asian - Australasian Association of Animal Production Societies 01.02.2019; Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST); Asian-Australasian Association of Animal Production Societies; 아세아·태평양축산학회
• Subjects: Analysis; Animal experimentation; Functional Annotation; Genetic aspects; Genetic Association Database; Medical research; Next Generation Sequencing; Non-synonymous Single Nucleotide Polymorphisms; Single nucleotide polymorphisms; Swine breeds; Yucatan Miniature Pigs; 축산학; Non-synonymous Single Nucleotide Polymorphisms; Functional Annotation; Yucatan Miniature Pigs; Next Generation Sequencing; Genetic Association Database
• ISSN: 1011-2367; 2765-0189; 1976-5517; 2765-0235
• DOI: 10.5713/ajas.18.0170

Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.