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1k RiCA (v.1.0) SNP genotyping
The 1k Rice Custom Amplicon (RiCA) SNP set features more than 950 evenly spaced SNPs, including 27 tag-SNP for 13 rice key trait genes: GS3, wx, ALK, Xa7, Xa21, Xa23, Xa4, Xa13, Xa5, RTSV1, and Sub1.
The panel was optimized to identify SNPs evenly distributed across the genome, with high quality score and validation status, maximizing minor allele frequency values within indica accessions.
Quality tests on the 1k-RiCA SNP set showed high consistency between technical replicates, high reproducibility between biological replicates, and high levels of accuracy when compared with overlapped SNPs from the Infinium 6K SNP chip, and 3,000 Rice Genomes Project data set (http://snp-seek.irri.org/).
This new platform presents faster turn around time and a better per sample cost effective solution for interrogating genetic variation in rice varieties, offering sufficient SNP density for typical fingerprinting and classification of rice germplasm, QTL analysis for small size biparental populations, marker assisted backcrossing applications for selecting genetic backgrounds, and assessment of allele frequencies for 13 key traits in different rice accessions sets.
The 1k-RiCA SNP set is run using Illumina’s TruSeq Custom Amplicon chemistry (see video below), compatible with the MiSeq system (https://www.illumina.com/systems/sequencing-platforms/miseq.html).
Distribution of SNPs in the 1k-RiCA panel
1k-RiCA SNPs physical positions. Genome-wide physical position distribution of 995 SNPs from the 1k-RiCA-assay across all rice chromosomes. SNPs designed from the C6AIR (Thomson et al. 2017) are represented in blue color, SNPs from the ‘3000 rice genomes’ are in yellow (Mansueto et al. 2017, and Wang et al. 2018), and trait-markers are in green