Kim Jae-Yoon, Jeong Seongmun, Kim Kyoung Hyoun, Lim Won-Jun, Lee Ho-Yeon, Kim Namshin
Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.
Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea.
Front Genet. 2019 Aug 8;10:699. doi: 10.3389/fgene.2019.00699. eCollection 2019.
Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; = 16, 11, 5, 5, 2, 13), and their ancestral species (; = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes ( infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of .
本土品种通过长期适应当地环境或文化而形成自身的基因组特征。它们中的大多数在商业层面上产量并不特别高，但具有在恶劣环境中生存或耐受特定疾病的能力。它们的适应性特征作为改良商业品种的遗传材料发挥着重要作用。作为朝着这一目标迈出的一步，我们分析了10个山羊品种中的韩国本土山羊的基因组。我们通过对46只新山羊进行测序并采用90只公开可用的山羊，收集了136只山羊个体。我们的全基因组数据由三个本土品种（韩国本土山羊、伊朗本土山羊和摩洛哥本土山羊；分别为29只、18只、20只）、六个商业品种（萨能山羊、波尔山羊、英努山羊、英国阿尔卑斯山羊、阿尔卑斯山羊和韩国杂交山羊；分别为16只、11只、5只、5只、2只、13只）以及它们的祖先物种（17只）组成。我们发现伊朗本土山羊和摩洛哥本土山羊在一大类基因组多样性中具有相对相似的基因组特征，但发现韩国本土山羊具有与其他九个品种不同的独特基因组特征。通过群体分析，我们证实这些特征是由具有强烈遗传漂变的近乎隔离的环境导致的。韩国本土山羊在大约2000年前进入朝鲜半岛时经历了严重的遗传瓶颈，随后很少与其他山羊品种发生遗传相互作用。通过选择分析和基因集富集分析，我们在韩国本土山羊的基因组中揭示了针对感染和心肌病的选择信号。这些适应性特征通过基于基因组的证据得到了进一步确认。在几个候选基因中，我们发现了脂多糖结合蛋白（LBP）和杀菌/通透性增加蛋白（BPI）基因（感染相关）以及肌联蛋白（TTN）和整合素β6（ITGB6）基因（心肌病相关）的选择性清除的基因组区域。基于广泛的比较，我们的研究呈现了韩国本土山羊独特的基因组特征和独特的选择信号。尽管这些适应性性状需要通过生物学实验进一步验证，但我们的发现有望为未来的生物多样性保护策略提供方向，并为基于基因组的育种计划贡献另一种选择，以提高……的生存能力。
