1K1RG-Documentations

🌾 Feature Review: SNP-Seek Genotype Search

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🌾 Overview

The SNP-Seek Genotype Search is a core genomics tool supporting the 1K Rice Genome Project – Philippines, which focuses on sequencing, analyzing, and utilizing the genomes of 1,001 traditional Philippine rice varieties. It facilitates the rapid identification of genetic markers associated with:

• Yield
• Stress tolerance
• Disease resistance
• Nutritional quality

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🔬 Purpose

SNP-Seek enables researchers and breeders to query, analyze, and visualize SNPs and genotype data across thousands of rice accessions. Its primary applications include:

• Genomic characterization
• Varietal comparison
• Marker-assisted selection (MAS)
• Haplotype mapping
• Interactive genome browsing via JBrowse

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🚀 Key Features

🔍 Search by Genomic Position or Gene

• Input chromosome coordinates or gene IDs
• Retrieve SNPs located within the selected region
• View associated genotypes across all accessions

🎯 Filter by Alleles

• Specify reference and/or alternate alleles
• Track specific variants across different rice lines

🧬 Genotype Matrix

• Results displayed as a matrix:
  • Rows: SNPs
  • Columns: Rice accessions
• Genotype formats: AA, TT, CC, GG, or missing (.)
• Interactive sorting and filtering supported

📁 Export Options

• Download results in multiple formats:
  • VCF
  • Tab-delimited text
  • FASTA sequences

🧩 Haplotype View

• Visualize haplotypes in selected genomic regions
• Compare variation across subpopulations or groups

🧬 Allele Frequency Viewer

• View allele frequency across subpopulations
• Helps identify rare or major alleles in the dataset
• Useful for trait association and diversity studies

🌐 JBrowse Integration

• Interactive genome browser for detailed visualization
• View SNPs, gene structures, QTLs, and annotations
• Zoom in to see SNP positions in relation to coding regions

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📌 Notes

• Integration with JBrowse allows users to view SNPs in their genomic context
• SNP-Seek is especially valuable in MAS workflows, population genetics, and rice breeding

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📚 References

1. Alexandrov, N. et al. (2015). SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research, 43(D1), D1023–D1027. https://doi.org/10.1093/nar/gku1039
2. 3K RGP (3,000 Rice Genomes Project Consortium). (2014). The 3,000 rice genomes project. GigaScience, 3(1), 7. https://doi.org/10.1186/2047-217X-3-7
3. IRRI SNP-Seek Database. International Rice Research Institute. https://snp-seek.irri.org
4. JBrowse Genome Browser. Buels, R. et al. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biology, 17(1), 66. https://doi.org/10.1186/s13059-016-0924-1
5. IRRI Tools and Data Portals. https://www.irri.org/tools