Plant-ImputeDB


33137192	Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation. [PMID: 33137192] Gao Y, Yang Z, Yang W, Yang Y, Gong J, Yang QY, Niu X. Abstract 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. Nucleic Acids Res. 2021:49(D1) \| 12 Citations (from Europe PMC, 2025-03-15)

Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation. [PMID: 33137192]

Gao Y, Yang Z, Yang W, Yang Y, Gong J, Yang QY, Niu X.

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.

Nucleic Acids Res. 2021:49(D1) | 12 Citations (from Europe PMC, 2025-03-15)

URL:	http://gong_lab.hzau.edu.cn/Plant_imputeDB
Full name:	an integrated multiple plant reference panel database for genotype imputation
Description:	The Plant Imputation database (Plant-ImputeDB) strives to collect the publicly available genomic sequencing data to construct high-quality reference panels
Year founded:	2021
Last update:
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA
Data object:	Plant
Database category:	Genotype phenotype and variation
Major species:	Arabidopsis thaliana Brassica napus Phaseolus vulgaris Gossypium hirsutum Cucumis sativus Cucurbita pepo Zea mays Cucumis melo Oryza sativa Glycine max Citrullus lanatus Triticum aestivum
Keywords:	SNPs genotype imputation

University/Institution:	Huazhong Agricultural University
Address:	Gong Lab, Huazhong Agricultural University, Wuhan 430070, P.R. China
City:	Wuhan
Province/State:	Hubei
Country/Region:	China
Contact name (PI/Team):	Jing Gong
Contact email (PI/Helpdesk):	gong.jing@mail.hzau.edu.cn

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases