sorghum grains
Sorghum grains at 12 DAP were collected and ground into powder in liquid nitrogen, and incubated with lysis buffer at 4C for 10 min. The ATAC-seq libraries was constructed according to Bajic et al. (2018). To perform tagmentation, 50,000 nuclides were added to the transposition reaction solution. Tn5 transposed DNA was purified by AMPure DNA magnetic beads and PCR amplification, and the final qualified library was sequenced on the Illumina Nova-seq platform (San Diego, CA, U.S.A.) with PE150 mode. Bowtie2 (v2.3.5) was used to align Clean Data with the reference genome sequence, and Samtools (v1.9) was used to extract the alignment results . When MACS3 was used to detect the candidate peaks, nomodel was selected, and the sift and extsize were set as 75 and 150, respectively. The annotations of detected peaks, visualizing of IGV, and detection of differential Peaks were correspondingly performed through the modules of ChIPseeker, Gviz, and Diffbind that implemented in R (v3.20) with default settings. For example, the default setting for differential Peak detecting were Log2FoldChange > 0.58 or FDR < 0.05.GO and KEGG were used for gene annotation and enrichment of the peak associated genes. MEME Suite was used for motif scanning and enrichment analysis of peak sequences in the JASPAR database (http://jaspar.genereg.net/). In addition, Venn analysis was performed between the gene set that selected from RNAseq data profile with FPKM  1 (Xiao et al., 2022a) and that set with detected Peaks within 5URT and promoter regions (3 Kb) from ATAC-seq data profile through the online Venn diagrams (https://bioinformatics.psb.ugent.be/webtools/Venn/).