College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Research Division of Food Functionality, Research Group of Healthcare, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
Genes Genomics. 2020 Mar;42(3):263-272. doi: 10.1007/s13258-019-00891-x. Epub 2019 Dec 12.
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.
In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics.
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.
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.
小型猪在代谢特征和器官比例方面与人非常相似，因此越来越多地被用作生物医学研究的哺乳动物模型动物。然而，尽管它们很重要，但对小型猪的全基因组研究却严重缺乏。
本研究对 Medi Kinetics 公司提供的 20 头微型猪进行全基因组测序分析，以阐明其基因组特征。
共产生约 595 吉字节（Gb）的序列读段，用于映射到猪参考基因组组装（Sus scrofa 10.2）；平均而言，序列读段以 9.6 倍的平均覆盖率覆盖参考基因组的 99.15%。我们共检测到 19518548 个 SNP，其中 8.7%为新发现的 SNP。对所有 SNP 进行进一步注释后，我们共检索到 144507 个非同义 SNP（nsSNP）；其中，在本研究中使用的 20 个个体中均发现了 5968 个 SNP。对这些 SNP 进行 SIFT 预测，发现 402 个基因中的 812 个 nsSNP 为有害 SNP。在这 402 个基因中，我们发现了一些可能影响微型猪感兴趣性状的基因，如 RHEB 和 FRAS1。此外，我们进行了纯合子运行分析，以定位基因组中的潜在选择特征，检测到几个可能与微型猪表型特征相关的基因座，如 MSTN、GDF5 和 GDF11。
在本研究中，我们发现了许多可能作为候选遗传标记的 nsSNP，这些 SNP 可能与感兴趣的性状有关。此外，我们还检测到了可能与最近对小型猪进行的选择有关的潜在选择足迹。
