Abstract
The gene SFB encodes an F-box protein that has appropriate S-haplotype-specific variation to be the pollen determinant in the S-RNase-based gametophytic self-incompatibility (GSI) reaction in Prunus (Rosaceae). To further characterize Prunus SFB, we cloned and sequenced four additional alleles from sweet cherry (P. avium), SFB 1, SFB 2, SFB 4, and SFB 5. These four alleles showed haplotype-specific sequence diversity similar to the other nine SFB alleles that have been cloned. In an amino acid alignment of Prunus SFBs, including the four newly cloned alleles, 121 out of the 384 sites were conserved and an additional 65 sites had only conservative replacements. Amino acid identity among the SFBs ranged from 66.0% to 82.5%. Based on normed variability indices (NVI), 34 of the non-conserved sites were considered to be highly variable. Most of the variable sites were located at the C-terminal region. A window-averaged plot of NVI indicated that there were two variable and two hypervariable regions. These variable and hypervariable regions appeared to be hydrophilic or at least not strongly hydrophobic, which suggests that these regions may be exposed on the surface and function in the allele specificity of the GSI reaction. Evidence of positive selection was detected using maximum likelihood methods with sites under positive selection concentrated in the variable and hypervariable regions.
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Acknowledgements
The authors gratefully acknowledge the gifts of plant material from the National Institute of Fruit Tree Science (Morioka, Japan). This work was supported by the Japan-US Cooperative Science Program, a Grant-in-Aid (no. 13460014) for Scientific Research (B) to R.T., and a Grant-in-Aid (no. 15004783) from the Japan Society for the Promotion of Science (JSPS) Research Fellows to K.U., who is a Research Fellow of JSPS.
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K. Ikeda and B. Igic contributed equally to this paper
Nucleotide sequence data reported will appear in the EMBL, GenBank and DDBJ nucleotide sequence databases under the accession numbers AB111518, AB111519, AB111520, and AB111521, for SFB 1, SFB 2, SFB 5, and SFB 4, respectively
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Ikeda, K., Igic, B., Ushijima, K. et al. Primary structural features of the S haplotype-specific F-box protein, SFB, in Prunus . Sex Plant Reprod 16, 235–243 (2004). https://doi.org/10.1007/s00497-003-0200-x
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DOI: https://doi.org/10.1007/s00497-003-0200-x