Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and...

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Rice research heavily relies on simple sequence repeat (SSR) markers.
• Previous SSR marker development predates the latest rice genome assembly.
• A unified coordinate system is needed to integrate SSR and single nucleotide polymorphism (SNP) data.

Purpose of the Study:

• To develop an integrative genomic database for rice (Oryza sativa).
• To map existing SSR markers to the latest rice pseudomolecule assembly.
• To create a comprehensive resource for rice genetic discovery and breeding.

Main Methods:

• Developed a new pipeline to map SSR primers to the latest rice pseudomolecule assembly.
• Utilized a stepwise relaxation of stringency for accurate mapping.
• Integrated DNA sequence data, gene annotations, variation data, and marker fragment sizes.

Main Results:

• Successfully mapped SSR markers to the current rice pseudomolecule assembly.
• Established a relational database with a web-based front end for SSR data.
• Created a genome browser track with linked database functionality.

Conclusions:

• Ricebase provides a crucial link between genetic markers, genome context, and allele data.
• The database facilitates the interpretation of new SNP data in the context of historical SSR studies.
• Ricebase serves as a valuable community resource for advancing rice genetics and breeding efforts.