Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Genomic sequence comprising Rf1aand the deduced amino acids from the restorer line MH63. The deletions (red) and the resulting stop codon (small rectangle) inrf1a allele of japonica varieties are indicated.
• Supplemental Figure 2 - Nucleotide sequence of an indica rf1a allele and the deduced amino acids. The mutations are indicated by red.
• Supplemental Figure 3 - Genomic sequence comprising Rf1b and the deduced amino acids from the restorer line MH63. The mutation of N412-to-S that results in the functional defect for the fertility restoration in rf1b alleles is indicated by red.
• Supplemental Figure 4 - Multi-alignment of the deduced amino acid sequences of the PPR subfamily members in rice. The chromosomal locations of ORFs 1-9 are as shown in Fig. 3. The sequences of ORFs #1, #3, #4, #6 are from the restorer line MH63, #5 from IR24, and those of ORFs #2 (GI:22165074), #7 (GI:22128708), #8 (GI:22128712), #9 (GI:22128714) and #10 (OSJNBa0049G15 AutoPredgene43 on chromosome 8) are from the japonicavariety Nipponbare. The PPR repeats are highlighted by red or blue, and the second and third repeats are PPR-like L motif. The N-terminal region (1-137) of ORF #7 is not shown.
• Supplemental Figure 5 - Expression of the Rf alleles in rice. (A) RT-PCR amplification of Rf1b and rf1b cDNAs of the restorer line MH63 (lanes 1, 2, and 3) and CMS-BT line KFA (lanes 4, 5, and 6) from RNAs of roots (lanes 1, 4), leaves (lanes 2, 5), and young panicles (lanes 3, 6). Lane 7 is a negative control using mixture of all the 6 RNA samples without transcription as the template. (B) RT-PCR amplification ofRf1a cDNA of MH63 from roots (lane 1), leaves (lanes 2), stem (lane 3) and young panicles (lane 3). (C) RT-PCR amplification of transgenic Rf1b and endogenous rf1b cDNAs from young panicle of Rf1b-transgenic T0 plants (lanes 1-5) of KFA, using the allele-specific primers of the SNP marker O01-45. (D)RNA gel blot analysis ofRf1b. Mixed probes were prepared by combining 100 ng of the Rf1b and 20 ng of Actin1 fragments and labeling with ³²P-dCTP. Lanes 1-3 are the blotted polyA+ mRNA from young panicles, leaves, and roots of MH63, respectively. Only the Actin1mRNA was detected, demonstrating the very low level of expression of the Rfgenes. (E) RNA gel blot hybridization of the same membrane shown in (D) using the Actin1 probe only.
• Supplemental Table 1
• Supplemental Table 2
• Supplemental Table 3
• Supplemental Table 4