The experimental and bioinformatic pipeline for MSG. (1) Genomic DNA is fragmented with a restriction enzyme (RE) that leaves “sticky ends.” (2) Individual bar-coded adaptors are ligated to these restriction fragments. (3) Samples are pooled and, (4) the ligation products are size selected, PCR-amplified, and (5) sequenced on an Illumina Genome Analyzer. (6) Reads from the sequencing run are parsed based by barcode. (7) Each read is mapped to each of two parental genomes (indicated as red and blue, respectively). (8) Ancestry of chromosomal segments (blue: homozygous for parent 1; red: homozygous for parent 2; no color: heterozygous) is estimated using a Hidden Markov Model (HMM). (9) Genotypes and recombination breakpoints are used in downstream analyses, such as QTL mapping.
