Additional file 1 of Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus

Abstract

Additional file 1: Fig. S1. Overview of experimental and research analysis methods. Fig. S2. Venn diagram of the distribution of genes regulated by different types of eQTLs (local eQTL and distant eQTL) at 20 DAF and 40 DAF. (a) Distribution number of genes which were regulated by different types of eQTLs at 20 DAF. (b) Distribution number of genes which were regulated by different types of eQTLs at 40 DAF. Fig. S3. Manhattan plot of BnaA05.FAD7 eGWAS at 40 DAF. Fig. S4. Study design on ATAC-seq of 6 representative accessions of B. napus. Fig. S5. Correlation analysis of 59 ATAC-seq samples. The samples are named according to “(22, 26, 34 or 40) DAF” + “accession_cellular ploidy (2C, 3C or 4C)” + “biological replicate” format naming. Fig. S6. Regional plot of ATAC-seq data and eGWAS results of BnaA08.TGD1. BnaA08.TGD1 is marked by a dashed line. The shaded area indicates the lead SNP of the local eQTL affecting BnaA08.TGD1. Fig. S7. Comparison of the explained variance (r2) of eQTLs for expression variation in or not in OCRs. Fig. S8. Expression correlation analysis of adjacent genes and randomly sampled gene pairs. Violin plot shows that the expression correlation of adjacent genes is significantly higher than that of randomly sampled gene pairs, *** indicates P 0.05, * indicates P < 0.05, ** indicates P < 0.01 and *** indicates P < 0.001 compared with WT in Student’s t test. Fig. S34. Transcriptional regulation of genes are activated by BnaA09.SCL31 or BnaA07.NAC13. a Schematic representation of the constructs used for the dual-luciferase assay. The effector constructs contain BnaA09.SCL31 and BnaA07.NAC13 driven by the CaMV35S promoter, respectively. The reporter construct contains the firefly luciferase driven by BnaA07.NAC13, BnaC07.LPAAT, BnaC03.SLP1 and BnaA07.SRO3 promoter, and the Renilla luciferase (REN) driven by the CaMV35S promoter. And the black square is the terminator. b Bar graph showing the relative LUC/REN ratio in the dual-luciferase assay. Values are means(SD) (n = 3 biological repeats). BnaA07.SRO3 (SIMILAR TO RCD ONE 3)