title: Rice genomic DNA was extracted from young green leaf
design: Map-to-reference short-read high-throughput sequencing using paired-end reads ranging 60bp to 129bp on Illumina GAII, GAIIx, and HiSeq instruments (Illumina Inc, San Diego CA). Sequences were aligned to the Michigan State University Assembly of Oryza sativa cv. Nipponbare (temperate japonica) version 7 of this assembly which is the same as IRGSP version 1.0. Alignment and SNP calling were performed by custom software (PANATI) and polymorphisms submitted were confirmed to segregate using a custom-designed Affymetrix Hybridization GeneChip Array. "