Fig. 4

Manhattan plots of -Log10 (P) vs. chromosomal position of SNP markers associated with soybean simulated trait that had 60% heritability and 10 QTLs from three randomly selected repetitions (R4, R7, and R9) using the real SNP markers dataset, and quantile-quantile (QQ) plots in soybean from the Fixed and random model Circulating Probability Unification (FarmCPU). Estimated marker-based heritability of this simulated trait was 48.6% in R4, 43.2% in R7, and 39.1% in R9, which was used in the formula to select significant thresholds -Log10 (P) values, such 3.54 in R4, 3.38 in R7, and 3.26 in R9. A red line represents the significant threshold values in these different repetitions. For all three repetitions, 10 markers were identified above the threshold value but in some cases these may be hidden behind other markers