Genetic Mapping of Millions of SNPs in Safflower (Carthamus tinctorius L.) via Whole Genome Re-sequencing

Accurate assembly of complete genomes is facilitated by very high density genetic maps. We performed low-coverage, whole-genome shotgun sequencing on 96 F₆ recombinant inbred lines (RILs) of a cross between safflower (Carthamus tinctorius L.) and its wild progenitor (C. palaestinus Eig). We also produced a draft genome assembly of C. tinctorius covering 866 million basepairs (ca. two-thirds) of the expected 1.35 Gbp genome after sequencing a single, short insert library to ca. 21x depth. Sequence reads from the RILs were mapped to this genome assembly to facilitate SNP identification, and the resulting polymorphisms were used to construct a genetic map. The resulting map included 2,008,196 genetically located SNPs in 1,178 unique positions. A total of 57,270 scaffolds, each containing 5 or more mapped SNPs, were anchored to the map. This resulted in the assignment of sequence covering 14% of the expected genome length to a genetic position. Comparison of this safflower map to genetic maps of sunflower and lettuce revealed numerous chromosomal re-arrangements, and the resulting patterns were consistent with a whole genome duplication event in the lineage leading to sunflower. This sequence-based genetic map provides a powerful tool for the assembly of low-cost draft genome of safflower, and the same general approach is expected to work for other species.

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