Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)

Abstract

Grain development, as a vital process in the crop's life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts' activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in "essential" genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a 'regulator' to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.

Keywords: Barley; Grain development; RNA editing; RNA-seq; Transcriptional dynamics.

Figure 1

Global characterization of gene expression patterns during the four stages of barley grain development. (A) Correlation coefficients between gene expression data sets from two biological duplicates and stages. (B) Cluster dendrogram showing global relationships of gene expression in different stages. The branch length indicates the degree of variance. (C) Venn diagram analyses of stage-specific genes in barley. (D) Overview of genes with different activity degree among the four stages. The different number suggests different activity ranking at each stage and the activity degree decreases as the number increases. For example, ‘1′ indicates gene showed the most activity at this stage and ‘4′ suggests the most inactive stage. (E) to (F) Functional categories of genes showing peak expression at the prestorage phase (stage01 and stage02) (E) and storage phase (stage03 and stage04). (F) Padj-adjusted p values, * p < 0.05 and ** p < 0.01. Observed, numbers of genes observed in this study; Expected, numbers of genes in this same category of annotated barley gene models.

Figure 2

Differential expression genes during barley grain development. (A) Number of genes showing up- or downregulated expression during barley grain development (Padj < 0.05 and |log2Ratio| ≥1). (B) Venn diagram analyses of genes that were differentially expressed between any two consecutive stages in barley. (C) KEGG enrichment analysis of DEGs in cluster V during barley grain development. (D) KEGG enrichment analysis of DEGs in cluster VII.

Figure 3

Characterization of transcription factors (TFs) differentially expressed during barley grain development. (A) Number of transcription factors (TFs) differentially expressed between any two stages of barley grain development. (B) Characterization of TF in each expression pattern.

Figure 4

Identification of the RNA editing events during barley grain development. (A) The frequency of different types of nucleotide editing at four stages of barley grain development. (B) Venn diagram analysis of the abundance of RNA editing events among four stages of barley grain development. (C) The localization of RNA editing events in genic regions.

Figure 5

Frequency and functional enrichment of RNA-edited differentially expressed genes (DEGs). (A) The abundance of genes harbored the edit sites ranging from 1 to 15. (B) The regulatory network of the identified DEGs with RNA editing sites involved in embryonic defects. (C) Frequency of RNA-edited DEGs in nine expression clusters. (D) KEGG enrichment analysis of the RNA-edited DEGs identified in this study.