*4.7. Candidate Gene Mining*

Genome-wide gene scan along chromosomes for significant QTL was performed to characterize the underlying genomic regions and identify candidate genes. First, all orthologous genes of the model species *Arabidopsis thaliana* were mapped to the flax genome using BLASTP of flax protein sequences against *A. thaliana* protein sequences at an E-value of 1.0 <sup>×</sup> <sup>10</sup>−10. A total of 15,323 unique *A. thaliana* genes were mapped. A list of known flax or *A. thaliana* genes associated with our studied traits and their associations was drawn based on literature and database searches [49,51,84]. We investigated candidate genes within QTL regions or within a 500 kb window upstream and downstream of the peaks depending on the LD decay estimates. In addition, previously identified QTL (SSR markers) in flax [7,8,53] were mapped to the flax pseudomolecules to validate the QTL results from this study.
