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.补充图S1. 局部与远端表达数量性状位点（eQTL, expression Quantitative Trait Locus）的绝对效应值、-log(p)值以及表型解释方差（R²）的密度分布。 补充图S2. PD2（A）与RP4（B）热点区域各标记位点的远端eQTL数量直方图。 补充表1. 种子萌发过程中具有特异性表达模式的基因的基因本体（GO, Gene Ontology）富集分析结果。 补充表2. 四个种子萌发阶段的远端eQTL热点区域。 补充表3. 不同阈值下，候选基因作为RP4热点区域最可能因果基因的平均排名与标准差。 补充表4. 不同阈值下，候选基因作为PD2热点区域最可能因果基因的平均排名与标准差。 补充表5. RP4 eQTL热点区域与MUM2相关候选基因上的单核苷酸多态性（SNP, Single Nucleotide Polymorphism）的位置与类型。 补充表6. PD2 eQTL热点区域相关候选基因上的单核苷酸多态性（SNP）的位置与类型。 补充表7. 用于数量性状位点（QTL, Quantitative Trait Locus）定位的遗传标记列表。 补充表8. Bay-0 × Sha亲本及重组自交系（RIL, Recombinant Inbred Line）群体的遗传图谱。 补充表9. Bay-0 × Sha亲本及重组自交系（RIL）群体的基因表达水平。 补充表10. Bay-0 × Sha亲本及重组自交系（RIL）群体的表型测量数据。 补充表11. Bay-0 × Sha亲本及重组自交系（RIL）群体的代谢物测量数据。 补充表12. 任意两个连续发育阶段间的差异表达基因列表。 补充表13. 表达数量性状位点（eQTL）列表。 补充表14. 表型数量性状位点（QTL）列表。 补充表15. 代谢物数量性状位点（mQTL, metabolite Quantitative Trait Locus）列表。