title: Genetic Mapping of Millions of SNPs in Safflower (Carthamus tinctorius L.) via Whole-Genome Resequencing.
abstract: 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 bp (∼two-thirds) of the expected 1.35 Gbp genome after sequencing a single, short insert library to ∼21 × 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 1178 unique positions. A total of 57,270 scaffolds, each containing five 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 rearrangements, 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 a low-cost draft genome of safflower, and the same general approach is expected to work for other species.
authors.affiliation: Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602.
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.affiliation: Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602.
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Pearl
authors.affiliation: Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 jmburke@uga.edu.
authors.forename: John M
authors.initials: JM
authors.lastname: Burke
mesh_terms: D031187:Carthamus tinctorius / Q000235:genetics*; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D015723:Gene Library; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: WGS map; genetic map; safflower