**5. Conclusions**

Using a diverse worldwide flax core collection of 370 accessions as a training and test population with 500 QTL identified by GWAS, the 5-year average PS data and the RR-BLUP statistical model, we developed a highly effective GP model with a prediction accuracy as high as 0.92 for pasmo, a low heritability and high inheritance complexity trait. This is the highest reported accuracy value of all GP models for plant disease resistance traits and comparable with previously published results. As an alternative, we developed a linear regression prediction model based on NPQTL that also produced a high prediction accuracy of 0.86. The GP model and the NPQTL-based regression equation were validated and deemed to be applicable to the evaluation of flax germplasm including parent selection for PR. The use of all potential QTL associated with a target trait would be beneficial because the exclusion of a large proportion of unrelated markers would facilitate the construction of highly accurate GP models.

**Supplementary Materials:** Supplementary Materials can be found at http://www.mdpi.com/1422-0067/20/2/359/s1.

**Author Contributions:** Conceptualization, F.M.Y. and S.C.; Methodology, F.M.Y.; Software, F.M.Y.; Formal Analysis, F.M.Y., G.J., P.L. and L.H.; Resources, K.Y.R. (field phenotypic data), S.C. and F.M.Y.; Data Curation, F.M.Y., K.Y.R. and Z.Y.; Writing-Original Draft Preparation, F.M.Y., L.H. and J.X.; Writing-Review & Editing, F.M.Y., S.C. and X.W.; Visualization, Z.Y.; Supervision, F.M.Y., S.C. and X.W.; Funding Acquisition, S.C., K.R. and F.M.Y.

**Funding:** This work was part of the Total Utilization Flax GENomics (TUFGEN) project funded by Genome Canada and other stakeholders, the A-base project (J-001004) funded by Agriculture and Agri-Food Canada and the flax cluster project funded by the Western Grains Research Foundation (WGRF) and the Canada-China science and technology and innovation action plan (2017ZJGH0106002).

**Acknowledgments:** We thank the China Scholarship Council for their financial support of L.H. for his research at Agriculture and Agri-Food Canada (AAFC).

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analysis or interpretation of the data; in the writing of the manuscript; and in the decision to publish the results.
