Rice Galaxy: an open resource for plant science

Area of Science:

• Plant genetics
• Genomics
• Bioinformatics

Background:

• Modern rice research utilizes sequencing and high-density genotyping for genome variation analysis and gene discovery.
• Rice gene banks offer diverse germplasm with available genome sequences and genotype data.
• Integrating phenotypic and genotypic data enables genome-wide association studies for trait discovery.

Purpose of the Study:

• To present Rice Galaxy, a web resource for analyzing large-scale rice genomic datasets.
• To provide tools for researchers, including those less experienced with computation, to perform advanced analyses.
• To support fundamental and applied rice science through accessible big data.

Main Methods:

• The Rice Galaxy resource shares high-density genotypes from the 3,000 Rice Genomes project and annotated sequences.
• It includes a web server and installer with tools for SNP assay design, GWAS, population diversity, and genomic prediction.
• A prototype compliant with Open Access, Open Data, and FAIR principles is also presented.

Main Results:

• Rice Galaxy provides access to extensive genotypic and sequence data for rice research.
• The platform offers a suite of bioinformatics tools tailored for plant genomics.
• A functional prototype adhering to open science principles has been developed.

Conclusions:

• Rice Galaxy is a freely available resource empowering the plant research community.
• It enables state-of-the-art analyses using publicly available big datasets.
• The resource supports both fundamental and applied rice science.