Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.
College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P.R. China.
Nucleic Acids Res. 2021 Jan 8;49(D1):D1480-D1488. doi: 10.1093/nar/gkaa953.
Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.
基因型推断是一种根据参考面板中的单倍型和基因型来估计缺失基因型的方法。它可以有效地增加单核苷酸多态性（SNP）的密度，提高识别遗传关联的能力，并促进遗传研究的结合。然而，对于大多数植物来说，缺乏高质量的参考面板，这极大地阻碍了基因型推断的应用。在这里，我们开发了 Plant-ImputeDB（http://gong_lab.hzau.edu.cn/Plant_imputeDB/），这是一个综合数据库，包含 12 个植物物种的参考面板，可用于在线基因型推断、SNP 和块搜索，并提供免费下载。通过整合来自不同研究和数据库的植物基因型数据和全基因组重测序数据，当前的 Plant-ImputeDB 为 12 个植物物种提供了高质量的参考面板，其中包含来自 34244 个样本的约 6990 万个 SNP。它还提供了一个易于使用的在线工具，其中包含两个专门为基因型推断设计的流行工具的选项。此外，Plant-ImputeDB 接受不同类型基因组变异的提交，并免费提供所有公开可用数据的开放访问，以支持全球相关研究。总的来说，Plant-ImputeDB 可以作为植物基因型推断的重要资源，极大地方便了植物遗传研究。
