HapRice, an SNP haplotype database and a web tool for rice.

Area of Science:

• Genetics
• Bioinformatics
• Agricultural Science

Background:

• Genome-wide single nucleotide polymorphism (SNP) analysis is crucial for understanding rice genetic diversity and traits.
• Next-generation sequencing facilitates rapid discovery of numerous SNPs across diverse rice varieties.
• Validation of SNPs using high-throughput genotyping systems is essential for creating accurate SNP sets.

Purpose of the Study:

• To develop analysis tools and a database for enhancing the utility of genome-wide SNPs in rice genetics and breeding.
• To construct an SNP haplotype database for visualizing SNP allele frequencies within a genome browser.
• To create web tools for identifying polymorphic SNPs and designing markers.

Main Methods:

• Construction of the 'HapRice' SNP haplotype database.
• Calculation of allele frequencies for validated SNPs in world and Japanese rice accessions.
• Development of web tools for SNP comparison and primer design for cleaved amplified polymorphic sequence (CAPS) markers.

Main Results:

• The HapRice database visualizes allele frequencies for 3,334 SNPs in world rice and 3,252 SNPs in Japanese rice accessions.
• SNP haplotypes were defined based on allele frequencies within cultivar groups (world rice) and irrigation types (Japanese rice).
• A core SNP set of 768 uniformly distributed SNPs was established for practical rice genetic analysis.

Conclusions:

• The HapRice database and associated web tools provide valuable resources for rice geneticists and breeders.
• These tools facilitate the analysis of genetic diversity and the identification of important genetic traits in rice.
• The established core SNP set offers a manageable and effective resource for rice genetic studies.