Recently, the Bioinformatics Group from HZAU’s College of Informatics has published a paper entitled “Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation” on Nucleic Acids Research. Based on genetic variation data of 12 plant species like rice and maize, researchers established the first high-quality reference panel database, which can serve as an important resource for genetic breeding and population evolution research.
Multiple plant database for genotype imputation
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), and thus is widely adopted in cheaper and low-density SNP-chips sequencing to facilitate the wide application of genome-wide association analysis (GWAS). However, lacking high-quality reference panels of most plants greatly limits genotype imputation.
To overcome the limitation, the group developed Plant-ImputeDB, a comprehensive database with reference panels of 12 plant species like cotton and soybean. They integrated genotype data and whole-genome resequencing data of these species, including about 69.9 million SNPs from 34,244 samples. Researchers can browse, search or download reference panels and relevant information in the database, which accepts submissions of different types of genomic variations and provides free and open access to all publicly available data to support related research worldwide.
Graduate student Gao Yingjie, doctoral students Yang Zhiquan and Yang Wenqian from College of Informatics of HZAU, are the co-first authors of the paper; associate Prof. Niu Xiaohui, Yang Qingyong and Prof. Gong Jing are the co-corresponding authors；doctoral student Yang Yanbo also participates in the research. The research was funded by Fundamental Research Funds for the Subordinate Universities of MOE (Huazhong Agricultural University) [2662018PY068 to Q.Y.Y.], China’s National Key Research and Development Plan [2017YFE0104800 to Q.Y.Y.], Huazhong Agricultural University Scientific & Technological Self-innovation Foundation [11041810351 to J.G.] and other projects.
Source: http://news.hzau.edu.cn/2020/1110/58715.shtml
Database：http://gong_lab.hzau.edu.cn/Plant_imputeDB/
Article：https://doi.org/10.1093/nar/gkaa953
Translated by: Yan Xiruo
Supervised by: Wang Xiaoyan
