Fig. 4

Distant eQTL hotspot identification. a The genomic distribution of distant eQTL hotspots and the enrichment of TWAS significant genes of SOC, SGC, and SCC in the hotspots. Dot plots represent the distribution of eQTL (outer: 20 DAF, inner: 40 DAF). And the red and light green dots indicate eQTLs in hotspots at 20 DAF and 40 DAF, respectively. Heatmaps represent the enrichment of TWAS significant genes of SOC, SGC, or SCC (outer: SOC, mid: SGC, inner: SCC) in hotspots at 20 DAF and 40 DAF (outer: 20 DAF, inner: 40 DAF). The pentagram indicates the location of Hotspot87-88. The bars indicate the number of hotspots. “Special” indicates the specific hotspot, “Partial” indicates the partially overlapping hotspot, and “Overlap” indicates the fully overlapping hotspot at two stages. b XGBoost predicts the importance of TFs. The horizontal coordinate indicates the statistics of the number of TFs ranked first in each TWAS significant gene of SOC prediction. The vertical coordinate indicates the ranking of the top 10 TFs predicted by XGBoost. c TWAS significant genes of SOC and reported SOC-related gene expression correlation analysis with BnaA09.SCL31 and SOC. The horizontal coordinates indicate the correlation between gene expression and SOC at 20 DAF, and the vertical coordinates indicate the correlation between gene expression and BnaA09.SCL31. Green dots indicate significantly correlated genes and yellow dots indicate uncorrelated genes. d Manhattan plot on A09 chromosome. Points represent the log-transformed P values for variations from GWAS of SOC BLUP value. The bottom plot indicates the BnaA09.SCL31 position. e Box plots for SOC, based on the haplotypes of variations in gene region and upstream 2-kb region of BnaA09.SCL31. f SOC phenotype of SCL31 T-DNA mutant lines (scl31-1, scl31-2) in Arabidopsis thaliana. Values are means (SD; n = 5 biological repeats). ***P < 0.001 compared with WT in Student’s t test. g Silique length phenotype of SCL31 T-DNA mutant lines (scl31-1, scl31-2) in Arabidopsis thaliana. Values are means (SD; n = 5 biological repeats). ***P < 0.001 compared with WT in Student’s t test