FIGURE LEGENDS
Figure 1. Overview of the time series samples of embryo and endosperms. Dotted line indicates the manual dissection of endosperm, cutting it into upper and bottom endosperms. DAF, days after fertilization; E, embryo; En, endosperm; EnB, bottom part of endosperm; EnU, upper part of endosperm; NB, notched-belly rice mutant; WT, wild type of Wuyujing-3. Bar = 1 mm
Figure 2. Global transcriptome relationships among tissues and developmental stages. (a) Venn diagram of the 20820 genes expressed in the embryo and endosperm. (b) Number of genes detected in each tissue. (c) Comparison of gene activity between embryo and endosperm. (d) PCA of the seed tissue mRNA populations. PCA plot shows two distinct groups of embryo and endosperm mRNA populations: group I for embryo and group II for endosperm. (e) and (f) Clustered dendrogram showing global transcriptome relationships of time series samples from the embryo of WT and NB, respectively. (g) to (h) Clustered dendrogram showing global transcriptome relationships of the upper and bottom endosperms of WT, respectively. (i) to (j) Clustered dendrogram showing global transcriptome relationships of the upper and bottom endosperms of NB, respectively. The bottom row indicates the developmental phases according to the cluster dendrogram of the time series data. Except in (a), data of 5, 10, 15…, and 60 represent sampling timepoints (days after fertilization).
Figure 3. Expression patterns of genes in different co-expression modules for embryo and endosperm of WT (a, b) and NB (c, d). Co-expression modules are ordered according to the sample time points of their peak expression. For each gene, the FPKM value normalized by the maximum value of all FPKM values of the gene over all time points is shown. The numbers of genes and TFs in each module are shown on the right.
Figure 4. Carbohydrates, proteins, SnRK1, and hormones, and their regulating genes in the embryo and endosperm of WTthroughout development. Each value represents the mean ± SE of three replicates. Black, orange, and blue indicate non-tissue, embryo, and endosperm specific genes, respectively.
Figure 5. Minerals in the embryo and endosperm of WT and NB across the developmental stages. Each value represents the mean ± SE of three replicates.
Figure 6. Diagrammatic representation of the new comparison method for quantifying the embryo effect on endosperm development. This method assembles three key components: (a) Quantification of the position effect (PE) by comparison between the upper (WT_EnU) and bottom (WT_EnB) endosperms of WT. This reflects the difference in position between upper and bottom endosperms within the WT grain, where nutrients and signals move freely without being blocked by the notched line as in NB. (b) Quantification of the compound effect (CE) of position and embryo by comparison between the upper (NB_EnU) and bottom (NB_EnB) endosperms of NB. Due to the notched line, movement of nutrients and signals are severely constrained between the two endosperms. Therefore, the influence of the embryo is trapped and thus mainly expressed in the bottom endosperm. Note that 2/3 interface between the upper and bottom is cut down by the notched line. (c) Evaluation of the embryo effect (EE) by secondary comparison of CE/PE to exclude the position effect. Three metabolites are used to exemplify the working principle of this method. For example, Asn content is up-regulated in the bottom endosperm of both WT and NB. By contrast, comparison of NB and WT reveals that the embryo effect is down-regulating it in the endosperm. Red and navy blue squares indicate up and down-regulation in the bottom endosperm, respectively.
Figure 7. Putative role of T6P-SnRK1 signaling in developmental transition of the endosperm as revealed by the proposed new comparison method. Effects of position, compound, and embryo are all shown. (a) Schematic diagram showing the putative T6P-SnRK1 signaling pathway. (b) Heatmap of differentially expressed genes associated with position, compound, and embryo effects. ADP-G, ADP-glucose; AGPase, ADP-glucose pyrophosphorylase; DBE, debranching enzyme; Fru, fructose; G6P/PT, glucose-6-phosphate/phosphate translocator; G1P, glucose 1-phosphate; GA, gibberellin; GBSS, granule-bound starch synthase; Glc, glucose; IAA, indoleacetic acid; INV, invertase; ISA, isoamylase; MST, monosaccharide transporter; PM, plasm membrane; SBE, starch branching enzyme; SnRK1, sucrose non-fermenting-1 related protein kinase 1; SSP, seed storage protein; SSS, soluble starch synthase; SuSy, sucrose synthase; SUT, sucrose transporter; T6P, trehalose 6-phosphate; TAR2, tryptophan aminotransferase 2; TPP, trehalose 6-phosphate phosphatase; TPS, trehalose 6-phosphate synthase; Trp, tryptophan; UDP-G, UDP-glucose; UGPase, UDP-glucose pyrophosphorylase; α-AMY, α-amylase; β-AMY, β-Amylase. Red and navy rectangles indicate up- and down-regulation, respectively.
Figure 8. Holistic and dynamic picture of seed development. (a) Schematic illustration of the morphological changes in embryo (longitudinal section) and endosperm (transversal). Varying colors of the pericarp and testa show the progression of degradation in maternal tissues, while those of the starch endosperm show the grain-filling process. (b) Dynamic accumulation of storage materials (sucrose, starch, FAAs, storage proteins, and minerals) and the increase in grain weight, length, width, and thickness. (c) Molecular signatures of the embryo and endosperm at different developmental stages.