*3.4. Selection Signatures Associated with Seed Yield and Seed Quality Traits*

GW3S has been used for screening putative genomic regions under selection pressure caused by domestication or artificial selection [36,38]. Usually, contrasting genetic populations are compared (such as wild accessions vs. cultivated accessions, landraces vs. breeding lines) to identify the allele frequency differentiation between different populations. In this study, we alternatively used two contrasting bi-parental mapping populations and identified 114 selection signatures with an average size of 226.3 kb. Some of these selection signatures support nearly 50% of the 23 GWAS-detected genomic regions associated with 33 QTL. Some of the QTL identified by GWAS have no overlapping selection signatures, partially because the regions of QTL had XP-CLR (Cross Population Composite Likelihood Ratio) scores less than the predetermined cut-off values. On the other hand, many selection signatures have high XP-CLR scores but no associated QTL (Figure 7). These significant selection signatures may be associated with QTL for traits not included in this study. This is suggested by the

fact that five previously identified genomic regions related to seven QTL overlapped with the selection signatures identified in our current study comparing BM and EV (Table S10). These putative selection signatures provide useful candidates for further QTL-trait association study. Our results combined with previous studies demonstrate that GW3S combined with GWAS is a powerful approach for dissecting genetic structure of breeding populations and for the identification of underlying genomic regions for breeding improvement. Using GWAS with bi-parental populations and selection signatures allowed the cross validation of QTL previously identified by other mapping methods and established the foundation for genomic assisted breeding in flax.
