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 Agriplex^1,2 and DArT^1,3. 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 Intertek^1,4, 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