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7k Infinium SNP genotyping

The improved second generation 7k chip (referred to commercially as the Cornell-IR RiceLD Array) has all of the benefits of the 6K chip (, but with a larger number of high quality SNP markers, including trait-specific markers.

The improved 7k chip provides continuity with the 6k chip, running on the same Illumina Infinium technology, while increasing the number of high quality SNP loci that can be interrogated. The 7,098 SNPs on the final production array include 4,007 SNPs from the 6K array, 2,056 SNPs from the high density rice array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets (OPA2.1, 3.1, 4.0, 5.0, 6.2 and 7.0), 189 SNPs from the 44K array, and 21 gene-based SNPs. Trait-specific markers for grain parameters (GS3, ALK, WAXY), for resistance to bacterial leaf blight (Xa4, xa5, Xa21, Xa23), blast (Pita) , brown plant hopper (BPH17, BPH3) and tungro (RTSV1) as well as tolerance of submergence (Sub1).

The 7k chip is informative for detecting genome-wide polymorphism between individuals within the indica, aus, and tropical japonica subpopulations, between any pairwise combination of accessions from the indica, aus, tropical japonica, temperate japonica, or aromatic subpopulations, and between O. sativa and O. rufipogon. The array is expected to be moderately informative for detecting polymorphism within the aromatic subpopulation, and least informative for detecting polymorphism within the temperate japonica subpopulation.