Volume 5, Issue 2, Pages 442-451 (March 2012) Deciphering Starch Quality of Rice Kernels Using Metabolite Profiling and Pedigree Network Analysis  Miyako Kusano, Atsushi Fukushima, Naoko Fujita, Yozo Okazaki, Makoto Kobayashi, Naoko Fujita Oitome, Kaworu Ebana, Kazuki Saito  Molecular Plant  Volume 5, Issue 2, Pages 442-451 (March 2012) DOI: 10.1093/mp/ssr101 Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 1 Visual Phenotypes of Rice Seeds and Brown Rice of the Five Cultivars and the Two Knockout Mutants. (A) Nipponbare, (B) Kinmaze, (C) Soft158, (D) Yumetoiro, (E) Hoshiyutaka, (F) e1, and (G) 4019. Scale bar (white) = 5 mm. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 2 Scanning Electron Microscopy (SEM) of the Starch Granules. SEM images are magnified 1000× for starch granules of (A) Nipponbare, (B) Kinmaze, (C) Soft158, (D) Yumetoiro, (E) Hoshiyutaka, (F) e1, and (G) 4019. SEM images are magnified 4000× for (H) e1 and (I) 4019. Scale bar (white) = 10 μm at a magnification of 1000× and 5 μm at a magnification of 4000×. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 3 Cross-Sections of Endosperm in Rice Kernels. SEM images are magnified 3000× for (A) and (C) Nipponbare, (B) e1, and (D) 4019. The mutant kernels of e1 and those of Nipponbare were harvested on 2005, while 4019 and the corresponding Nipponbare were on 2008. Scale bar (white) = 5 μm at a magnification of 4000×. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 4 Heatmap with Cluster Dendrogram of the Differentially Changed Metabolites by Hierarchical Cluster Analysis (HCA). Annotated or identified metabolites using gas chromatography–mass spectrometry (GC–MS) (99 metabolites) and ion trap–mass spectrometry (IT–MS) (10 metabolites) appear in the rows and the samples appear in the columns. HCA was performed using the matrix (log2-fold change; cultivars or mutants versus control NB). The complete list of differentially changed metabolites is available in Supplemental Data 1 and 2. Abbreviations: HCA, hierarchical cluster analysis; NB, Nipponbare; Kin, Kinmaze; Hoshi, Hoshiyutaka; Yume, Yumetoiro. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 5 Venn Diagram of Significantly Changed Metabolites in Common or Those that Differ in (A) Hoshiyutaka and Yumetoiro and (B) e1 and 4019. The Venn diagram in (A) shows the number of commonly decreased metabolites in Hoshiyutaka and Yumetoiro compared to Nipponbare (NB), while the Venn diagram in (B) represents the number of commonly increased metabolites in e1 and 4019. Significant levels were set at false discovery rate (FDR) < 0.05 discovery rate and log2-fold change (FC) > |1|. See also Table 2 for more detail. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 6 Rice Pedigree Network Analysis Based on Information of Rice Relationships in Japan. Each node represents a cultivar. The orange node shows the cultivars used for the study, while the blue node displays single (e1 and be) or double (4019) knockout mutants. The green nodes are the common ancestors of Hoshiyutaka and Yumetoiro. Two Indica cultivars, Mudgo and O. nivara, are shown as pink nodes. Edges represent pedigrees in rice breeding history. The green edge shows a parent–child relation (pcr), while the pink double line shows a pair relationship. The blue line and purple broken edges show mutations and selections, respectively. TN1, Taichungnative1. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 7 The Coordinate Plot of Multidimensional Scaling (MDS) Analysis Using Normalized Metabolite Profiles of Four Cultivars and the Eight Representative Cultivars Chosen from the Rice Diversity Research Set (RDRS). Euclidean distance and log2 ratio values compared to the metabolite profiles of Nipponbare were used (see ‘Methods’). I, Indica; J, Japonica. Molecular Plant 2012 5, 442-451DOI: (10.1093/mp/ssr101) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions