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The 1k-RiCA mid-density genotyping panel for rice


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, but currently is offered at Agriplex1,2 and DArT1,3. 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 are commonly used in purity and F1 hybridity testing at Intertek1,4, providing linkage between datasets, and up to 200 trait markers distinguishing 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.


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References

Arbelaez J.D., Dwiyanti M.S., Tandayu E., Llantada K., Jarana A., Ignacio J.C., Platten J.D., Cobb J., Rutkoski J.E., Thomson M.J., Kretzschmar T. (2019) 1k-RiCA (1k-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. Rice 12:55