LD analysis
Our GWAS mapping population (n=188) contain 68 samples of the eastern cultivar (36 %) and 106 samples of the western cultivar (56.8%). LD analysis was performed for the whole genome and each Linkage group of GWAS population (n=188) and separate for the whole genome of eastern and western cultivars. The pairwise correlation coefficient ( r2 ) for the whole genome of the GWAS population decreased to half of its maximum value at 25.9 kb (Figure 2a), which is close to the LD decay distance (22.9 kb) found by Hazzouri et al. (Khaled M. Hazzouri et al., 2019). The LD decay was slower for LG12 and LG16. The r2 decreased to half of its maximum value at 38.4 kb and 31.9 kb. The LD decay was faster for LG 4, LG 7 and LG 15 . The r2 decreased to half of its maximum value at 18.9 kb, 20.5 kb and 17.2 kb respectively (Table 1, Supplementary Figure 2). The LD decay analysis of the eastern and western cultivars shows that r2 decreased to half of its maximum value at 21.73 kb and 35.85 kb respectively (Supplementary Figure 3).
Table 1. Decay of Linkage Disequilibrium (LD) with physical distance in each linkage group (LG)