Figure 1.

Patterns of decay in linkage disequilibrium (LD), represented by the squared correlation between expected gametic phases (r²) in (A) WS4U-C2 and (B) Liberty-C2; the blue curve corresponds to the mean value from a cubic-regression spline model assuming a Gamma distribution for r². (C) Concordance, from WS4U-C2 to Liberty-C2, in LD as represented by the correlation between expected gametic phases (r); the blue curve corresponds to the mean value (and its 95%-confidence interval) from a cubic-regression spline model assuming a Normal distribution for r in Liberty-C2. Values of r were inferred as described in Weir (1979) using the R package SNPRelate (Zheng et al. 2012). Cubic-regression spline models were fitted using the R package mgcv (Wood 2006). The values of r and r² shown here are based on random pairs of markers polymorphic in both WS4U-C2 and Liberty-C2, with each marker represented only once across all pairs.