Fig. 3: A comparison of hQTL for grain yield heterosis detected by hQTL-ODS and hQTL-MSS using experimental series I data.

Manhattan plots showing the results of (a) hQTL-MSS using 90k SNP chip data (17,372 SNPs), which were adopted from Jiang et al. ¹⁹, b hQTL-ODS using the same 90k SNP chip, and (c) hQTL-ODS using whole-genome sequencing data (about 1.2 million SNPs). In (a–c), significance was assessed by the likelihood ratio test, and the thresholds (P < 0.05 after Bonferroni-Holm correction for multiple testing) were indicated as red dashed horizontal lines. d Venn diagram showing the number of hQTL detected in (a), (b), and (c), (indicated in blue, purple, and black, respectively) as well as the overlapping. Note that it is possible that different numbers of hQTL detected in two or three data sets colocalized, since significant SNPs were merged into hQTL in each of the three data sets separately. To be consistent with the results from Jiang et al. ¹⁹, we only considered hQTL located on known chromosomes.