Improved reference assembly and core collection re-sequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius L.

We report an improved de novo genome assembly of safflower (Safflower_A2). A chromosome-level assembly with telomeres and centromeric repeats, was constructed using PacBio HiFi reads, optical maps, Illumina short reads, and Hi-C sequencing. Safflower_A2 shows better contiguity, completeness, and high-quality annotation than previous assemblies. The assembly was further validated with the help of a single nucleotide polymorphism (SNP)-based linkage map. A genome-wide survey identified genes for comprehensive exploration of disease resistance in the safflower. Employing the de novo genome assembly as a reference, we used resequencing data of a global core-collection of 123 accessions to carry out a SNP-based genome-wide association study, which identified significant associations for several traits, their haplotypes of agronomic value, including seed oil content. Resequencing data was also applied for a pan-genome analysis which provided critical insights into genome diversity identifying an additional ~11000 genes and their functional enrichment that will be useful for region-specific breeding lines.