SoyOD

SoyOD integrates extensive multi-omics datasets with analytical toolkits to mine candidate genes and support soybean molecular breeding and biological research.

Key Features:

• Genomic Data Integration: SoyOD incorporates 59 assembled genomes and genetic variation data from 3904 soybean accessions.
• Transcriptomic Data: The database includes 162 novel transcriptomic datasets from seeds at different developmental stages and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions.
• Phenotypic Data: SoyOD contains 53 phenotypic datasets, more than 2500 phenotypic images, and 225 sets of existing phenotypic data.
• Deep-Sequencing Data: Novel data derived from deep-sequencing of 984 germplasms are included in the database.
• Gene Mining Capability: SoyOD enables mining of candidate genes for important agronomic traits, as demonstrated in a case study on plant height.
• Data Search Functionality: The toolkit supports rapid search of genotypic and phenotypic data in particular germplasms.

Scientific Applications:

• Candidate Gene Mining: Researchers can identify genes associated with important agronomic traits such as plant height.
• Molecular Breeding: SoyOD supports soybean molecular breeding by integrating genotype-to-phenotype datasets.
• Multi-omics Data Analysis: The database facilitates basic and applied research through comprehensive data analysis tools applied to genomic, transcriptomic, and phenomic data.

Methodology:

SoyOD integrates new datasets generated from deep-sequencing of 984 germplasms with existing public datasets including assembled genomes, genetic variation data, transcriptomic sequences, and phenotypic data.