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), SFB1, SFB 2, SFB4, and SFB5. 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.
| Original language | English |
|---|---|
| Pages (from-to) | 235-243 |
| Number of pages | 9 |
| Journal | Sexual Plant Reproduction |
| Volume | 16 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - Jan 2004 |
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Keywords
- Pollen-S
- Rosaceae
- S-RNase
- Self-incompatibility
- SFB
ASJC Scopus subject areas
- Plant Science
Cite this
Primary structural features of the S haplotype-specific F-box protein, SFB, in Prunus. / Ikeda, Kazuo; Igic, Boris; Ushijima, Koichiro; Yamane, Hisayo; Hauck, Nathanael R.; Nakano, Ryohei; Sassa, Hidenori; Iezzoni, Amy F.; Kohn, Joshua R.; Tao, Ryutaro.
In: Sexual Plant Reproduction, Vol. 16, No. 5, 01.2004, p. 235-243.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Primary structural features of the S haplotype-specific F-box protein, SFB, in Prunus
AU - Ikeda, Kazuo
AU - Igic, Boris
AU - Ushijima, Koichiro
AU - Yamane, Hisayo
AU - Hauck, Nathanael R.
AU - Nakano, Ryohei
AU - Sassa, Hidenori
AU - Iezzoni, Amy F.
AU - Kohn, Joshua R.
AU - Tao, Ryutaro
PY - 2004/1
Y1 - 2004/1
N2 - 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), SFB1, SFB 2, SFB4, and SFB5. 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.
AB - 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), SFB1, SFB 2, SFB4, and SFB5. 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.
KW - Pollen-S
KW - Rosaceae
KW - S-RNase
KW - Self-incompatibility
KW - SFB
UR - http://www.scopus.com/inward/record.url?scp=0842266363&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0842266363&partnerID=8YFLogxK
U2 - 10.1007/s00497-003-0200-x
DO - 10.1007/s00497-003-0200-x
M3 - Article
VL - 16
SP - 235
EP - 243
JO - Plant Reproduction
JF - Plant Reproduction
SN - 2194-7953
IS - 5
ER -