**5. Conclusions**

We performed GWAS using a set of 771,914 SNPs, identifying seven and four QTL for MC and HC, respectively. Above all, chromosome 3 encompassed three QTL harboring promising candidate genes for MC. Three of the QTL associated with HC contained plausible candidate genes related to seed coat and anthocyanin biosynthesis. These favorable QTL alleles will assist the design of market specific flaxseed cultivars with reduced HC while maintaining high MC for food and low MC for feed. The application of the identified SNP markers in molecular-assisted breeding for MC and HC, two complex traits whose phenotyping is labor-intensive and time-consuming, might enable a rapid transfer of favorable alleles into well adapted elite flaxseed cultivars, thus shortening the

breeding cycle. Based on our results and previous gene expression studies, we hypothesize that the genetic control of mucilage and hull content in flax might share conserved pathways with Arabidopsis. Further validation of candidate genes, like *LuTT8*, *LuSBT1.7*, *LuMUM4*, and *LuAGL62*, through gene expression analysis or gene editing, will be necessary to validate the hypothesis mentioned above. Characterization of genes underlying the QTL will expand knowledge of the high complexity of cell wall dynamics involved in seed mucilage and seed coat biosynthesis in flaxseed.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/10/ 2870/s1.

**Author Contributions:** B.J.S.-C. designed the research experiments, performed the GWAS, interpreted the results and wrote the manuscript. S.C. performed the resequencing of the association panel, co-wrote and edited the manuscript. R.Q. planted the association panel and performed the phenotyping. H.A.G. planted the association panel and performed statistical analysis of the phenotypic data. M.O. wrote scripts and generated the figures. F.M.Y. generated the genome-wide SNP data.

**Acknowledgments:** This work was supported by the Agriaquaculture Nutritional Genomic Center (CGNA), the Programa Regional de Investigación Científica y Tecnológica and the Gobierno Regional de La Araucania, Chile. CGNA acknowledges the collaboration of Agriculture and Agri-Food Canada (AAFC) and the Total Utilization Flax GENomics (TUFGEN) project formerly funded by Genome Canada and other stakeholders of the Canadian flax industry.

**Conflicts of Interest:** The authors declare no conflict of interests.
