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Fig. 3 | BMC Biology

Fig. 3

From: Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size

Fig. 3

Expression pattern of cell cycle genes in SN and LGR and genes preferential to LGR S3 stage. A Venn diagram showing the number of upregulated cell cycle transcripts common and specific to the seed tissues of SN and LGR. B The distribution of the LGR-specific genes (denoted by black box in a) was plotted (as represented in the color legend). S3 stage of LGR had the maximum number of cell cycle-related upregulated genes (marked by asterisk in the graph). C Heat map by hierarchical clustering was prepared to study the expression pattern (log2FPKM) of the cell cycle genes commonly upregulated in the seed tissues in SN and LGR (denoted by red box in a; S1–S5 represent seed developmental stages, Leaf represents flag leaf). LGR S1–S3 grouped with SN S1–S2, as marked with blue boxes. Genes that promote endoreduplication and have different expression patterns in SN and LGR have been marked with red boxes. D Percent similarity between DEGs of consecutive stages of LGR (bars above and below the axis represent up- and downregulated genes, respectively). Least similarity was observed between the transcriptomes of LGR S2 and S3 stages as marked by asterisk in the graph. E Pathway analysis of DEGs (using MapMan) that are preferential to LGR S3, i.e., upregulated in LGR S3 but not in LGR S2 and SN S3. Pathways related to cell enlargement and enhanced cellular activity, such as cell cycle, DNA synthesis and repair, degradation of starch, mitochondrial ETC, protein synthesis, nucleotide metabolism, and TCA cycle, were distinctly upregulated (≥ 50% genes upregulated out of total DE genes; demarcated with pink asterisks in the figure). Size of circle represents log2 gene number present in a category as indicated in the legend

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