There are several genotyping platforms developed for rice, the majority of them have not been optimized for breeding, and all other important parameters for their utility are cost, turnaround time, throughput, density, and informativeness. With this in mind, a 1K-Rice Custom Amplicon, or 1k-RiCA v4, was developed by Agriplex Genomics, Cleveland, OH 44106 (www.agriplexgenomics.com) a robust custom sequencing-based amplicon panel of more than 1000-SNPs that are uniformly distributed across the rice genome, and which is designed to be highly informative within indica rice breeding pools, and has been tailored for genomic prediction in elite indica rice breeding programs. The International Rice Research Institute (IRRI) designed the first version of the 1K-Rice Custom Amplicon (1k-RiCA) panel. The 955 SNP markers were multiplexed in-to a PlexSeq™ panel as the 1k-RiCA v2.
In a study conducted in 2019 by Jan David Arbelaez et.al., they validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.
Version 4 of the IRRI Rice Custom Amplicon SNP panel is made of 1,040 markers and maintains the basic structure of the original panel. In addition, the panel was augmented with more trait-associated markers. Altogether 133 new SNPs were added to the revised panel, which now targets over 90 genes and QTLs of interest.
A list of traits and genes targeted are given below. from https://www.agriplexgenomics.com/irri-v4