Figure S1. Validation of gene expression levels in Ler and dyt1 anthers using RT-PCR and real-time PCR. (a) RT-PCR of DYT1-regulated genes. UBQ1 was used as an internal control. (b) Real-time PCR of 7 genes coding for enzyme and 9 genes encoding transcription factors down-regulated in dyt1. Normalized expression levels in Ler were set to 1 when compared with those in dyt1.

Figure S2. DYT1 binds to gene promoter sequences containing the consensus binding site. (a) Probes (oMC6808-oMC6819) representing promoter regions containing TCACGTGA sites. Putative binding sites are underlined. (b) Gel shift assay demonstrating that DYT1 could bind to pMS1 (positive control) and probes listed in (a).

Figure S3. MYB35-RNAi abnormal anthers and MYB35-SRDX normal male meiosis. (a–e) Wild-type (WT) anthers. (f–j) Anthers from the MYB35-RNAi transgenic plant. (a) WT anther showing stained mature pollen grains. (f) MYB35-RNAi anther lacking stained pollen grains. (b–e) WT anthers of stage 6–9. (g–j) MYB35-RNAi anthers of stage 6-9. (k–o) WT and (p–t) MYB35-SRDX male meiosis. Prophase I (k, p), metaphase I (l, q), anaphase I (m, r), anaphase II (n, s), and telophase II (o, t). MYB35-SRDX shows no obvious abnormal phenotype in meiosis. Scale bars, 50 μm in (a) and (f); 10 μm in (b–e) and (g)-(j); 10 μm in (k–t).

Table S1. 435 genes downregulated in dyt1 anthers.

Table S2. 220 genes upregulated in dyt1 anthers.

Table S3. Real-time PCR of 9 transcription factor genes and 7 enzyme genes to validate microarray data.

Table S4. 22 transcription factors genes downregulated in dyt1 anthers.

Table S5. Lipid metabolism-related genes downregulated in dyt1 anthers.

Table S6. Pollen coat-related genes downregulated in dyt1 anthers.

Table S7. Cell wall modification-related genes downregulated in dyt1 anthers.

Table S8. Lignin and flavonoid biosynthetic pathway genes with reduced expression in dyt1 anthers.

Table S9. Transporter genes showed lower expression in dyt1 anthers.

Table S10. Genes differentially expressed in dyt1 and contain the consensus DYT1 binding site in promoters.

Table S11. Down- or up-regulated genes in ams anthers.

Table S12. Comparing 22 transcription factors downregulated in dyt1 vs. 17 transcription factors downregulated in ams anthers.

Table S13. 1796 genes with fold change >2 in dyt1 or ams grouped into 8 sets representing different patterns of regulation by DYT1 and AMS (Figure 8).

Table S14. Oligonucleotides used in this study.

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