Análisis externo

induced DEGs were displayed in blue, while the significantly suppressed DEGs were displayed in red. The statistically significant changes in gene expression between SCN- infected versus uninfected roots were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

33

Figure 2.3 Bar graphs and heatmaps showing the gene frequency and expression profiles of pattern-triggered immunity (PTI)/effector-triggered immunity (ETI) receptor and calcium- mediated signaling genes (A and B) and pathogenesis-related genes (C and D). The bar graphs on the top of heatmaps represent the number of differentially expressed genes (DEGs) in each genotype which were uniquely identified or overlapped either susceptible or other resistant genotypes. The heatmaps display the expression patterns of each DEG in each of four genotypes (Fayette, Peking, Glycine soja PI 468916, and Williams 82). The colors in heatmaps represent the up-regulation (blue) and down-regulation (red) of DEGs with different magnitudes (brightness) of log2 fold change values, comparing between inoculated and uninoculated roots. The statistically significant changes in gene expression were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

34

Figure 2.4 Bar graph and heatmap showing the gene frequency and expression profiles of transcription factor genes that were differentially expressed in response to nematode invasion at 8 hours post inoculation (hpi). (A) The bar graph represents the number of transcription factor genes which were uniquely identified or overlapped either susceptible or other resistant genotypes. (B) The heatmap displays the expression patterns of each transcription factor genes in four genotypes (Fayette, Peking, Glycine soja PI 468916, and Williams 82). The colors in the heatmap show the up-regulation (blue) and down-regulation (red) of genes with different magnitudes (brightness) of log2 fold change values, comparing between inoculated and uninoculated roots. The statistically significant changes in gene expression were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

35

Figure 2.5 Bar graph (A) and heatmap (B) showing the gene frequency and expression profiles of differentially expressed genes (DEGs) related to hormone biosynthesis and signaling. The bar graph on the top of heatmap represents the number of DEGs in each genotype which were uniquely identified or overlapped either susceptible or other resistant genotypes. The heatmap displays the expression patterns of each DEG in each of four genotypes (Fayette, Peking, Glycine soja PI 468916, and Williams 82). The colors in heatmaps represent the up-regulation (blue) and down- regulation (red) of DEGs with different magnitudes (brightness) of log2 fold change values, comparing between inoculated and uninoculated roots. The statistically significant changes in gene expression were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

36

Figure 2.6 Bar graphs and heatmaps showing the gene frequency and expression profiles of differentially expressed genes (DEGs) involved in phenylpropanoid pathway (A and B) and oxidation-reduction process (C and D). The bar graphs on the top of heatmaps represent the number of DEGs in each genotype which were uniquely identified or overlapped either susceptible or other resistant genotypes. The heatmaps display the expression patterns of each DEG in each of four genotypes (Fayette, Peking, Glycine soja PI 468916, and Williams 82). The colors in heatmaps represent the up-regulation (blue) and down-regulation (red) of DEGs with different magnitudes (brightness) of log2 fold change values, comparing between inoculated and uninoculated roots. The statistically significant changes in gene expression were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

37

Figure 2.7 Bar graphs and heatmaps showing the gene frequency and expression profiles of differentially expressed genes (DEGs) classified in transport protein family (A and B) or involved in carbohydrate metabolism (C and D). The bar graphs on the top of heatmaps represent the number of DEGs in each genotype which were uniquely identified or overlapped either susceptible or other resistant genotypes. The heatmaps display the expression patterns of each DEG in each of four genotypes (Fayette, Peking, Glycine soja PI 468916, and Williams 82). The colors in heatmaps represent the up-regulation (blue) and down-regulation (red) of DEGs with different magnitudes (brightness) of log2 fold change values, comparing between inoculated and uninoculated roots. The statistically significant changes in gene expression were identified using a false-discovery rate (FDR) cut-off set at 0.05. “.” FDR < 0.1, “*” FDR < 0.05, “**” FDR < 0.01, “***” FDR < 0.001.

38

Table 2.1 The over-represented GO terms identified in differentially expressed genes (DEGs) of each genotype across the experiment, using the AgriGO web-server.

GO biological processes

GO term GO biological processes description False discovery rate (FDR)

†

Fayette Peking G. soja Williams 82

GO:0055114 oxidation reduction 7.20E-06 3.30E-09 2.20E-16 0.00018 GO:0006979 response to oxidative stress 0.006 5.70E-07 4.80E-11 0.00021 GO:0009607 response to biotic stimulus 0.014 - 2.70E-05 - GO:0006950 response to stress 0.027 0.0049 1.70E-05 0.82

GO:0042221 response to chemical stimulus 0.038 0.00015 1.70E-07 0.00021

GO:0006952 defense response 0.04 - 0.0014 -

GO:0050896 response to stimulus 0.047 0.024 0.00013 0.046 GO:0008152 metabolic process 0.19 0.0042 4.80E-06 1

GO:0051704 multi-organism process - - 0.0062 -

GO molecular function

GO term GO molecular function description False discovery rate (FDR)

†

Fayette Peking G. soja Williams 82

GO:0005506 iron ion binding 2.40E-10 2.40E-11 4.70E-12 1.50E-05 GO:0020037 heme binding 3.40E-10 2.40E-11 7.20E-13 1.10E-05 GO:0046906 tetrapyrrole binding 3.40E-10 2.40E-11 7.20E-13 1.10E-05 GO:0016705

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

1.50E-06 8.30E-07 3.70E-06 0.022 GO:0016491 oxidoreductase activity 2.40E-06 1.30E-09 3.10E-16 0.00016 GO:0046914 transition metal ion binding 1.00E-05 8.60E-08 0.00015 0.0012 GO:0009055 electron carrier activity 2.00E-05 0.00066 0.004 6.60E-02

GO:0003824 catalytic activity 0.00013 0.012 2.50E-06 0.6

GO:0043167 ion binding 0.0013 1.10E-07 4.70E-05 0.00016 GO:0046872 metal ion binding 0.0013 1.10E-07 4.70E-05 0.00016 GO:0043169 cation binding 0.0013 1.10E-07 4.70E-05 0.00016 GO:0016684 oxidoreductase activity, acting on

peroxide as acceptor 0.0017 2.70E-07 1.00E-12 0.00016 GO:0004601 peroxidase activity 0.0017 2.70E-07 1.00E-12 0.00016 GO:0016209 antioxidant activity 0.0033 1.10E-06 7.20E-13 0.00031

GO:0016829 lyase activity 0.041 - 1 -

GO:0015075 ion transmembrane transporter activity 0.044 1 1 - GO:0045735 nutrient reservoir activity - 0.0013 0.83 0.002 GO:0004312 fatty-acid synthase activity - 0.0037 0.00024 -

39 Table 2.1 Continued

GO molecular function (Continued)

GO term GO molecular function description False discovery rate (FDR)

†

Fayette Peking G. soja Williams 82

GO:0004315 3-oxoacyl-[acyl-carrier-protein]

synthase activity - 0.0037 0.00024 -

GO:0016706

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2- oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors

- 0.078 0.035 -

GO cellular component

GO term GO cellular component description False discovery rate (FDR)

†

Fayette Peking G. soja Williams 82

GO:0044421 extracellular region part - 0.029 - -

GO:0031012 extracellular matrix - 0.029 - -

†

The analysis of GO term enrichment was performed on DEGs of each genotype, compared to genes in whole genome as a background, using the hypergeometric tests with FDR cut-off set at 0.05.

40

Table 2.2 The over-represented KEGG pathway in biological process category identified in differentially expressed genes (DEGs) of each genotype across the experiment, using the KOBAS.

KEGG ID KEGG pathway False discovery rate (FDR)

†

Fayette Peking G. soja Williams 82

gmx00940 Phenylpropanoid biosynthesis 1.10E-08 7.04E-12 1.09E-20 1.79E-08 gmx01110 Biosynthesis of secondary

metabolites 8.33E-07 7.04E-12 4.78E-20 1.67E-05 gmx00460 Cyanoamino acid metabolism 0.000 0.014 2.65E-06 0.105

gmx01100 Metabolic pathways 0.001 2.37E-07 6.16E-12 1.67E-05 gmx04626 Plant-pathogen interaction 0.012 1.03E-05 0.076 - gmx00500 Starch and sucrose metabolism 0.032 0.150 0.009 0.359

gmx00941 Flavonoid biosynthesis 0.035 0.001 2.65E-06 0.105

gmx00130 Ubiquinone and other terpenoid-

quinone biosynthesis 0.164 0.014 0.023 - gmx00270 Cysteine and methionine

metabolism 0.287 0.014 0.046 0.057

gmx04712 Circadian rhythm - plant 0.164 0.014 0.006 - gmx00900 Terpenoid backbone biosynthesis 0.164 0.356 0.023 - gmx00591 Linoleic acid metabolism - - 0.024 0.005 gmx00902 Monoterpenoid biosynthesis - - 0.024 -

gmx00910 Nitrogen metabolism 0.159 - 0.045 -

†

The analysis of GO term enrichment was performed on DEGs of each genotype, compared to genes in whole genome as a background, using the hypergeometric tests with FDR cut-off set at 0.05.

41 CHAPTER 3

IDENTIFICATION OF DEFENSE MECHANISMS INVOLVED IN RHG1-MEDIATED