Sequence-based high-throughput genotyping. Rice RILs were developed from a cross between indica and japonica cultivars. Genome sequences of the parents were aligned and SNPs were identified. Genomes of the RILs were resequenced on the Illumina Genome Analyzer using the multiplexed sequencing strategy. Three-base indexed DNAs of 16 RILs were combined and sequenced in one lane. Sequences were sorted and aligned with the pseudomolecules of parental genome sequences for SNP detection. Detected SNPs were arranged along chromosomes according to their physical locations with genotypes indicated. A sliding window approach was used for genotype calling, recombination breakpoint determination, and map construction.
