## 2 Results and Discussion
### MapMan Analysis of Koshihikari Rice Seed Differentially Expressed Genes in Grades 2 and 3
(**B**) Map for HRDE genes related to Koshihikari rice grade Y3. Numbering for each data point on the figure was given in left to right order to identify relevant gene information from supplementary Table S3. These numbers represent serial numbers for the genes in the supplementary table accordingly. Expression of specific genes of interest like PME, cellulose synthases, pectin lysates, XET, raffinose synthase, TAG lipases, DGK, Omega-6-desaturases, SPT2, amylase and Susy family genes can be observed in Y2(1, 3), Y3(6), Y3(7, 8), Y3(4), Y3(2), Y2(2), Y3(9), Y3(12, 13, 14), Y3 (10), respectively. For each of the above pathway maps, a total of 15, 151 and 46 HRDE genes of Y2 and 53, 457 and 152 HRDE genes of Y3, were mapped as data points. All these genes are listed in supplementary Tables S2-S4, along with their bin-numbers and functions. For the cell function, metabolism-overview and biotic-abiotic stress pathway maps (Figures 4-6), the numbering for each data point was given in left to right order to identify relevant gene information from supplementary Tables S2-S4. Serial numbers for the genes in the supplementary tables were numbered accordingly. Overall mapping results indicate that around 650 genes related to various cellular functions were differentially regulated in both Y2 and Y3, respectively (Figure 4, supplementary Table S2). Y2 appears to respond specifically to the genes in the supplementary tables. Figure 6: An abiotic-biotic map of differentially expressed genes that are categorized into abiotic and biotic stress-responsive pathways generated using Mapman. (**A**) Map for HRDE genes related to Koshihikari rice grade Y2. (**B**) Map for HRDE genes related to Koshihikari rice grade Y3. Numbering for each data point on the figure was given in left to right order to identify relevant gene information from supplementary Table S4. These numbers represent serial numbers for the genes in the supplementary table accordingly. Expression of specific genes of interest like sHsp, MYB4, DREB1/CBF, ERF, OsWRKY, GGPS, anthocyanins, and flavonoid biosynthesis, COMT, lacasses, OsSAUR, FIP1, lipoxygenase2 and OPR family genes can be observed in Y3(115/138), Y2/Y3(35/114), Y3(101, 102), Y3(98), Y3(110-112), Y2(41),Y3(133-135), Y3(178,179), Y2/Y3(47/186), Y2/Y3(1), Y2/Y3(2,3/2,3,4,5), Y2/Y3 (4/10) and Y2/Y2 (5/11,12) grid boxes, respectively. Y2/Y3 represents similar genes detected in both Y2 and Y3. by down regulation of genes in biotic-abiotic stress, transcription, RNA processing, protein degradation, hormones and regulation. While Y3 exhibited quite opposite response by upregulation of genes in respective mechanisms, with few downregulated genes. Genes related to protein modification are downregulated in both Y2 and Y3. Specifically, from the metabolic-overview map (Figure 5), results indicate that highly up-, or downregulated genes are mainly related to cell wall, lipid, starch, and secondary metabolic pathways. In Y2, very few genes were differentially regulated (7 downregulated and 8 upregulated). Among these, genes related to cell wall remodeling proteins (pectin methyl esterase's- PMEs), sucrose synthase, triacylglycerglycerol (TAG) lipase, phosphatase synthase and a few secondary metabolism-related genes (tyrosine decarboxylase, terpene cyclase, isoflavrooid reductase) were highly downregulated. On the other hand, Y3 data showed upregulation of cell wall modification proteins like transglucosylases (XET), diacylglycerol kinases, omega-6 fatty acid desaturases, male sterility proteins, \(\alpha\)-amylase isozymes, rubisco interacting proteins, mitochondrial electron-transport proteins (transposons) and many proteins related to secondary metabolites (terpenes, flavonoids, and phenolics) (Supplementary Table S3). Out of both Y2 and Y3, commonly upregulated metabolic pathways were related to starch, chitinase, phenylpropanoids and phenolics, and aromatic amino acid synthases. While the commonly downregulated genes are related to PME and sucrose synthase.