Supplemental Material for Hartanto et al., 2020

Figure S1. Density distribution of the absolute eQTL effect, -log(p), and explained phenotypic variance (R2) for local and distant eQTLs. Figure S2. The histogram of the number of distant eQTLs per marker location for the PD2 (A) and RP4 (B) hotspot. Supplementary Table 1. Gene ontology enrichment for genes with distinctive expression patterns during seed germination. Supplementary Table 2. Distant eQTL hotspots of the four seed germination stages Supplementary Table 3. The mean rank and standard deviation of candidate genes as the most likely causal genes for the RP4 hotspot across different thresholds Supplementary Table 4. The mean rank and standard deviation of candidate genes as the most likely causal genes for the PD2 hotspot across different thresholds. Supplementary Table 5. The location and type of SNPs on candidate genes for the RP4 eQTL hotspot and MUM2. Supplementary Table 6. The location and type of SNPs on candidate genes for the PD2 eQTL hotspot. Supplementary Table 7. The list of genetic markers used for QTL mapping. Supplementary Table 8. The genetic map of Bay-0 x Sha parents and the RIL population. Supplementary Table 9. Gene expression levels of Bay-0 x Sha parents and the RIL population. Supplementary Table 10. Phenotype measurements of Bay-0 x Sha parents and the RIL population. Supplementary Table 11. Metabolite measurements of Bay-0 x Sha parents and the RIL population. Supplementary Table 12. Differentially expressed genes between any of two consecutive stages. Supplementary Table 13. The list of expression QTL. Supplementary Table 14. The list of phenotype QTL. Supplementary Table 15. The list of metabolite QTL.