Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development

Abstract

Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions, and the proportion of distal ACRs was increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed light on the improvement of wheat yields and qualities.

Supplementary information: The online version contains supplementary material available at 10.1007/s42994-023-00095-8.

Keywords: Chromatin accessibility; Grain development; Regulatory network; Subgenome-divergence; Wheat.

Fig. 1

Chromatin accessibilities are relative to the differential gene expression during wheat grain development. A UpSet Plot showing the ACR distribution across five tissues (DAP, days after pollination). B Density plot showing the distribution between ACR centers and their nearest genes. Black dot line indicates 10 Kb away from genes. C Distribution of ACRs on different genomic features. Genic, ACRs with their centers in gene bodies; Proximal, ACRs with their centers <  = 2 Kb upstream of TSS or <  = 2 Kb downstream of TES; Distal, ACR with their centers > 2 Kb away from genes. D Distribution of sequence variations around ACR centers. SNPs from Zhou et al. were used. E The expression of genes with ACRs in their 2 Kb nearby regions (ACR present) and without ACRs in their 2 Kb nearby regions (ACR absent) across the five tissues. F Distribution of eight differential ACR (diffACR) clusters on different genomic features. The definition of each group is same with C. G The overlapping information of eight diffACR clusters related genes and eight DEG clusters. H Chromatin accessibilities of regions from 2 Kb upstream to 100 bp downstream of TSS and associated genes’ expression levels. Chromatin accessibilities were represented by Tn5 transposome integration sites (TISs) and expression levels by transcripts per million (TPM). I Gene ontology (GO) enrichment analysis for the overlapped gene groups in G

Fig. 2

Subgenome-divergent regulation during wheat grain development A Motif density of 40 clustered motifs from JASPAR database (Castro-Mondragon et al. 2022) in eight diffACR clusters. B Ternary plot showing expression bias of the syntenic genes from three subgenomes. The balanced category: balanced expression of the triad genes. A dominant, B dominant and D dominant: higher expression from A, B or D than the other two orthologs. A suppressed, B suppressed and D suppressed: lower expression from A, B or D than the other two orthologs. C Sankey diagram showing expression dynamic of the syntenic genes during grain development. D Sankey diagram showing the chromatin accessibility dynamics of the promoter regions (from 2 Kb upstream to 100 bp downstream of TSS) of the syntenic genes during grain development. E The subgenome diversified expressions of key transcription factors. F Motif density of eight diffACR clusters in each subgenome (* indicate motif density > 1)

Fig. 3

Construction of regulatory networks for starch and gluten biosynthesis by integration the chromatin accessibility and expression data. A and B Promoter chromatin accessibility dynamics (A) and expression dynamics (B) of genes involved in glutenin and starch accumulation in leaf and grain samples. Regions from 2 Kb upstream to 100 bp downstream of transcriptional start sites were considered as promoters. C Genome browser tracks showing the expression and promoter chromatin accessibility patterns of starch synthesis genes (TaSBEIIa, TaSuSy2, TaSBEIb and TaGBSSI) and key TF genes (TaZIP28 and TaNAC019). D Regulatory networks involving the starch and gluten biosynthesis genes and key TFs. TF families are shown as circles with different colors. Starch biosynthesis genes are shown as grey square; Gliadin genes as orange triangle; Glutenin genes as blue diamond. TF-to-gene edges are shown with three colors represent three grain phases. DAP9, green; DAP15 blue; DAP20, pink

Fig. 4

Dual-luciferase transcriptional activity assay to assess the capability of key TFs to transactivate predicted target gene expression. A The distribution of key TF-binding motifs in the promoters of starch and protein synthesis genes. B Schematic diagrams of the effector and reporter constructs for the dual-luciferase transcriptional activity assay. C Reporter assay showed that NAC100-A or NAC100-D regulates both starch and protein synthesis pathways. D NAC100 and MYB-B coordinately regulate TaISA2 and TaAGPL1 genes. LUC/REN indicates the signal ratio of LUC (firefly luciferase) to REN (Renilla reniformis luciferase) activity. Data are represented as means ± SD from three replicates. (Student’s t-test; *P < 0.05, **P < 0.01)