背景:云南的中国土猪表现出相当大的表型多样性,但是它们的种群结构和人工选择特征的生物学解释需要进一步研究。为了揭示种群遗传多样性,迁移事件,和中国家猪的人工选择签名,我们从云南的四个品种中抽取了111只云南猪,这被认为是中国牲畜驯化中心之一,并使用Illumina猪SNP60KBeadChip对其进行基因分型。然后,我们利用多个生物信息学数据库工具来进一步研究签名和相关的复杂特征。
结果:种群结构和迁移分析显示,滇南小儿猪与其他云南猪具有不同的遗传背景,高黎贡山可能经历了从宝山和沙巴猪的迁徙事件。有趣的是,我们确定了云南本地猪在5号染色体265.09kb区域共享人工选择的可能共同目标,该区域的基因与心血管和免疫系统有关。我们还检测到几个与饮食适应相关的候选基因,体型(例如,PASCIN1,GRM4,ITPR2),和生殖性能。此外,品种共享基因MMP16被鉴定为人类介导的基因。哺乳动物基因组的多种证据,转录组,和表型水平进一步支持了MMP16变异与代谢性疾病之间因果关系的证据,大脑发育,和中国猪的软骨组织。我们的结果表明,抑制MMP16会直接导致中国本土猪的神经元活动和骨骼发育不活跃和不敏感。
结论:在这项研究中,对云南土猪进行群体遗传分析和人工选择特征的鉴定有助于了解人类介导的选择机制对中国土猪表型性状的影响。需要进一步的研究来充分表征人类介导的基因和生物学机制的过程。
BACKGROUND: Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation. To uncover population genetic diversity, migration events, and artificial selection signatures in Chinese domestic pigs, we sampled 111 Yunnan pigs from four breeds in Yunnan which is considered to be one of the centres of livestock domestication in
China, and genotyped them using Illumina Porcine SNP60K BeadChip. We then leveraged multiple bioinformatics database tools to further investigate the signatures and associated complex traits.
RESULTS: Population structure and migration analyses showed that Diannanxiaoer pigs had different genetic backgrounds from other Yunnan pigs, and Gaoligongshan may undergone the migration events from Baoshan and Saba pigs. Intriguingly, we identified a possible common target of sharing artificial selection on a 265.09 kb region on chromosome 5 in Yunnan indigenous pigs, and the genes on this region were associated with cardiovascular and immune systems. We also detected several candidate genes correlated with dietary adaptation, body size (e.g., PASCIN1, GRM4, ITPR2), and reproductive performance. In addition, the breed-sharing gene MMP16 was identified to be a human-mediated gene. Multiple lines of evidence at the mammalian genome, transcriptome, and phenome levels further supported the evidence for the causality between MMP16 variants and the metabolic diseases, brain development, and cartilage tissues in Chinese pigs. Our results suggested that the suppression of MMP16 would directly lead to inactivity and insensitivity of neuronal activity and skeletal development in Chinese indigenous pigs.
CONCLUSIONS: In this study, the population genetic analyses and identification of artificial selection signatures of Yunnan indigenous pigs help to build an understanding of the effect of human-mediated selection mechanisms on phenotypic traits in Chinese indigenous pigs. Further studies are needed to fully characterize the process of human-mediated genes and biological mechanisms.