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The 1k-RiCA mid-density genotyping panel for rice
Overview
Overview
The 1k-Rice Custom Amplicon (RiCA) panel is the mid-density genotyping panel developed at IRRI to enable affordable, efficient genomic selection. It has been implemented at several service providers and platforms, and is currently offered in two versions (Table 1) at two service providers. Both platforms use custom amplicon workflows that reliably deliver almost all markers from all samples. The panel consists of roughly 800 genome-wide markers designed to give a fingerprint of breeding material that can be used as the basis for calculating genomics-estimated breeding values in standard GS workflows. The genome-wide panel is supplemented with 22 quality-control markers that IRRI commonly uses in purity and F1 hybridity testing, providing linkage between datasets, and over 200 trait markers distinguishing up to 87 high-value genes and QTLs. Together these capabilities enable genomic selection (including integration of major genes as fixed effects), variety typing, QTL mapping and QTL profiling (fingerprinting) of elite material.
1TruSeq Custom Amplicon genotyping is a targeted sequencing method that uses custom-designed probes and multiplex PCR to amplify specific genomic regions for high-throughput variant detection using Illumina platforms.2PlexSeq genotyping is a high-throughput, amplicon-based sequencing method that uses multiplex PCR and NGS to accurately genotype custom-selected SNPs across thousands of plant samples.3DArTag genotyping is a targeted sequencing method where custom probes enrich specific DNA regions for SNP or indel detection using next-generation sequencing
Table 1. Versions and availability of the 1k-RiCA mid-density SNP genotyping (MDSG) platform
Click here for more details. Prices may have changed. Please contact irri-gsl@cgiar.org
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