Figure S1. Phylogenic tree of deduced amino acid sequences of PpSFBB and
MdSFBB. A neighbor-joining tree was constructed from 74 SFBB genes from
Japanese pear and apple. PiS1-SLF1 from Petunia inflata was used as an outgroup.
Numbers on the branches indicate bootstrap values >50% with 1,000 trials.
Synonymous names of SFBBs are in parentheses (Cheng et al., 2006; Minamikawa
et al., 2010).
Figure S2. Linkage analysis of SFBBs and S-RNase. Each SFBB gene-specific
band was detected by using CAPS, dCAPS or specific primer methods (Table S3).
Figure S3. ORF maps of the S4 haplotype. Green, blue and red bars represent
ORFs predicted by GeneMark, FGENESH and GENESCAN, respectively. The A
nucleotide of the putative initiation codon (ATG) of the S4-RNase gene is positioned
as +1. Yellow area represents the deleted region in the S4sm haplotype. The
redundant genes (genes 4A-4F) were blue- or red-boxed.
Figure S4. Amino acid sequence alignment of the redundant genes in Pyrus S4
haplotype.
Figure S5. Schematic representation of three S haplotype.
Figure S6. RT-PCR of SFBB genes of S4sm homozygous plant. To check the
expression of SFBBx-S4 genes of S4sm haplotype, RT-RCR was conducted by using
cDNA from Chukanbohon Nou no.1 (S4smS4sm). All SFBBs were specifically
expressed in anther except for SFBB1-S4. Abbreviation in this figure: Le, Leaf; St,
Style; An, Anther; gDNA, genomic DNA; +RT, RT-PCR was conducted with reverse
transcriptase; -RT, RT-PCR was conducted without reverse transcriptase; ef1-α,
elongation factor 1 alpha gene (used as control, accession no. AY338250).
Table S1. Primers used for isolation of SFBBs.
Table S2. Sequence information on F-box and S-RNase genes used in this study.
Table S3. Primers and restriction enzymes used for genetic analysis of SFBBs.
Table S4. Interhaplotypic amino acid identity of the S-RNases and SFBBs.
Table S5. Intrahaplotypic amino acid identity of SFBBs.
Table S6. Pyrus S4 haplotype ORFs predicted by GeneScan.
Table S7. Pyrus S4 haplotype ORFs predicted by fgenesh.
Table S8. Pyrus S4 haplotype ORFs predicted by GeneMark.
Table S9. Pyrus S2 haplotype ORFs predicted by GeneScan.
Table S10. Pyrus S2 haplotype ORFs predicted by fgenesh.
Table S11. Pyrus S2 haplotype ORFs predicted by GeneMark.
Table S12. Malus S9 haplotype ORFs predicted by GeneScan.
Table S13. Malus S9 haplotype ORFs predicted by fgenesh.
Table S14. Malus S9 haplotype ORFs predicted by GeneMark.
Table S15. Amino acid sequence identities (%) of redundant genes in Pyrus and
Malus S locus.
Appendix S1: Re-examination of ORFs in the S4 haplotype.