Ultra High Density Genetic Map of Carthamus tinctorius (Safflower)

Accurate assembly of complete genomes is facilitated by very high density genetic maps. We performed whole genome sequencing on 96 F6 Recombinant Inbred lines (RILs) to ≈2x genome coverage and the parents to ≈21x genome coverage on a single Illumina HiSeq run. A draft genome assembly of the parental line was made with SOAPdenovo and a single size short insert library, corresponding to roughly 2/3 of the expected 1.3 GB genome size, but in ≈2 million contigs.  Reads from the RILs were mapped to the assembly with bowtie2 and SNPs were called using samtools. A genetic map was then assembled with 2,485,340 genetically located SNPs in 1,238 different genetic bins, ordering contigs totaling ≈45% the expected genome size.