CropGS-Hub


38000385	CropGS-Hub: a comprehensive database of genotype and phenotype resources for genomic prediction in major crops. [PMID: 38000385] Jiaxin Chen, Cong Tan, Min Zhu, Chenyang Zhang, Zhihan Wang, Xuemei Ni, Yanlin Liu, Tong Wei, XiaoFeng Wei, Xiaodong Fang, Yang Xu, Xuehui Huang, Jie Qiu, Huan Liu Abstract The explosive amount of multi-omics data has brought a paradigm shift both in academic research and further application in life science. However, managing and reusing the growing resources of genomic and phenotype data points presents considerable challenges for the research community. There is an urgent need for an integrated database that combines genome-wide association studies (GWAS) with genomic selection (GS). Here, we present CropGS-Hub, a comprehensive database comprising genotype, phenotype, and GWAS signals, as well as a one-stop platform with built-in algorithms for genomic prediction and crossing design. This database encompasses a comprehensive collection of over 224 billion genotype data and 434 thousand phenotype data generated from >30 000 individuals in 14 representative populations belonging to 7 major crop species. Moreover, the platform implemented three complete functional genomic selection related modules including phenotype prediction, user model training and crossing design, as well as a fast SNP genotyper plugin-in called SNPGT specifically built for CropGS-Hub, aiming to assist crop scientists and breeders without necessitating coding skills. CropGS-Hub can be accessed at https://iagr.genomics.cn/CropGS/. Nucleic Acids Res. 2024:52(D1) \| 6 Citations (from Europe PMC, 2025-03-15)

CropGS-Hub: a comprehensive database of genotype and phenotype resources for genomic prediction in major crops. [PMID: 38000385]

Jiaxin Chen, Cong Tan, Min Zhu, Chenyang Zhang, Zhihan Wang, Xuemei Ni, Yanlin Liu, Tong Wei, XiaoFeng Wei, Xiaodong Fang, Yang Xu, Xuehui Huang, Jie Qiu, Huan Liu

Abstract

The explosive amount of multi-omics data has brought a paradigm shift both in academic research and further application in life science. However, managing and reusing the growing resources of genomic and phenotype data points presents considerable challenges for the research community. There is an urgent need for an integrated database that combines genome-wide association studies (GWAS) with genomic selection (GS). Here, we present CropGS-Hub, a comprehensive database comprising genotype, phenotype, and GWAS signals, as well as a one-stop platform with built-in algorithms for genomic prediction and crossing design. This database encompasses a comprehensive collection of over 224 billion genotype data and 434 thousand phenotype data generated from >30 000 individuals in 14 representative populations belonging to 7 major crop species. Moreover, the platform implemented three complete functional genomic selection related modules including phenotype prediction, user model training and crossing design, as well as a fast SNP genotyper plugin-in called SNPGT specifically built for CropGS-Hub, aiming to assist crop scientists and breeders without necessitating coding skills. CropGS-Hub can be accessed at https://iagr.genomics.cn/CropGS/.

Nucleic Acids Res. 2024:52(D1) | 6 Citations (from Europe PMC, 2025-03-15)

URL:	https://iagr.genomics.cn/CropGS/
Full name:	A comprehensive database of genotype and phenotype resources for genomic prediction in major crops
Description:	CropGS-Hub, a comprehensive database of genotype and phenotype resources for genomic prediction and crossing design in major crops. It is dedicated to accelerating genome-designed breeding driving by multi-omics data and advancing modern breeding towards precision and efficiency.
Year founded:	2022
Last update:	2023-08-20
Version:	v1.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA
Data object:	Plant
Database category:	Gene genome and annotation Genotype phenotype and variation Interaction
Major species:	Oryza sativa Zea mays Cicer arietinum Setaria italica Gossypium hirsutum Brassica napus Glycine max
Keywords:	GWAS genomic selection genotype phenotype crop breeding

University/Institution:	BGI Research
Address:	BGI Bioverse, Shenzhen 518083, China
City:	Shenzhen
Province/State:	Guangdong
Country/Region:	China
Contact name (PI/Team):	Huan Liu
Contact email (PI/Helpdesk):	liuhuan@genomics.cn

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