High Density Rice Array (HDRA6.4) developed by the McCouch-Rice Lab at Cornell University

A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site. Using the HDRA, SNP variation was assayed in a collection of 1,568 diverse O. stiva accessions and the resulting genotypic dataset was analyzed for population structure and used for Genome Wide Association Studies (GWAS).