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Functional and expression analyses of kiwifruit SOC1-like genes suggest that they may not have a role in the transition to flowering but may affect the duration of dormancy.

Voogd C, Wang T, Varkonyi-Gasic E - J. Exp. Bot. (2015)

Bottom Line: Largely overlapping spatial domains but distinct expression profiles in buds were identified between the SOC1-like gene family members.Ectopic expression of AcSOC1e, AcSOC1i, and AcSOC1f in Actinidia chinensis had no impact on establishment of winter dormancy and failed to induce precocious flowering, but AcSOC1i reduced the duration of dormancy in the absence of winter chilling.These findings add to our understanding of the SOC1-like gene family and the potential diversification of SOC1 function in woody perennials.

View Article: PubMed Central - PubMed

Affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland 1142, New Zealand.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis of kiwifruit SOC1-like protein sequences. (A) Alignment of the C-terminal region of SOC1-like amino acid sequences. The amino acid residues in the alignment are shaded according to their similarity scores: white on black, 100% similar; white on grey, 80–100% similar; black on grey, 60–80% similar; grey on white, <60% similar. The conserved SOC1 motif is underlined. The observed deviation of this motif in AcSOC1h appears to be due to a putative 1bp deletion within the motif leading to a frameshift from EVETELFFGLA to EVETELSLALL. (B) Phylogenetic tree based on the amino acid alignment of kiwifruit SOC1-like predicted proteins and SOC1-like proteins from other plant species. The tree was generated using the Geneious Tree Builder plug-in (Geneious 5.5.6) using the Neighbor–Joining method with Arabidopsis AGL6 as an outgroup. Numbers below the branches represent bootstrap support values from 1000 replicates (values ≥50% are indicated). Origins of the genes, with the exception of Arabidopsis, are indicated by a prefix as follows: Ac, Actinidia chinensis; Vv, Vitis vinifera; Pt, Populus tremuloides; Ps, Pisum sativum; Ph, Petunia hybrida; Fv, Fragaria vesca; Pa, Prunus armeniaca; Md, Malus×domestica; their GenBank accession numbers are indicated to the right. Arabidopsis genes SOC1, AGL14, AGL19, AGL42, AGL71, and AGL72 are associated with their unique IDs. Kiwifruit SOC1-like genes in different clades are indicated by arrows. (This figure is available in colour at JXB online.)
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Figure 1: Phylogenetic analysis of kiwifruit SOC1-like protein sequences. (A) Alignment of the C-terminal region of SOC1-like amino acid sequences. The amino acid residues in the alignment are shaded according to their similarity scores: white on black, 100% similar; white on grey, 80–100% similar; black on grey, 60–80% similar; grey on white, <60% similar. The conserved SOC1 motif is underlined. The observed deviation of this motif in AcSOC1h appears to be due to a putative 1bp deletion within the motif leading to a frameshift from EVETELFFGLA to EVETELSLALL. (B) Phylogenetic tree based on the amino acid alignment of kiwifruit SOC1-like predicted proteins and SOC1-like proteins from other plant species. The tree was generated using the Geneious Tree Builder plug-in (Geneious 5.5.6) using the Neighbor–Joining method with Arabidopsis AGL6 as an outgroup. Numbers below the branches represent bootstrap support values from 1000 replicates (values ≥50% are indicated). Origins of the genes, with the exception of Arabidopsis, are indicated by a prefix as follows: Ac, Actinidia chinensis; Vv, Vitis vinifera; Pt, Populus tremuloides; Ps, Pisum sativum; Ph, Petunia hybrida; Fv, Fragaria vesca; Pa, Prunus armeniaca; Md, Malus×domestica; their GenBank accession numbers are indicated to the right. Arabidopsis genes SOC1, AGL14, AGL19, AGL42, AGL71, and AGL72 are associated with their unique IDs. Kiwifruit SOC1-like genes in different clades are indicated by arrows. (This figure is available in colour at JXB online.)

Mentions: Nine transcripts with sequence homology to Arabidopsis SOC1 were identified in the Plant & Food Research EST database (Crowhurst et al., 2008), and designated AcSOC1a through AcSOC1i. 5ʹ RACE was used where necessary before PCR amplification and cloning of the complete coding sequence from A. chinensis bud tissue (GenBank accession nos KP407147–KP407155). Analysis of the deduced amino acid sequence revealed that the open reading frames encode a predicted protein of between 200 and 220 amino acids and each included the conserved MADS-box, I-region, K-box, and C-terminal SOC1 motif (Fig. 1A; Supplementary Fig. S1 at JXB online). Each coding sequence mapped to a different pseudo-chromosome (Huang et al., 2013) and is encoded by seven exons. With the exception of AcSOC1h, all proteins are associated in pairs, with members sharing >80% identity. AcSOC1e, AcSOC1i, AcSOC1f, and AcSOC1g are most similar to Arabidopsis SOC1, sharing between 64% and 66% identity (Supplementary Table S2). Phylogenetic analysis using the full-length deduced amino acid sequences confirmed that of the nine proteins, AcSOC1e, AcSOC1i, AcSOC1f, and AcSOC1g are most closely related to SOC1. AcSOC1a, AcSOC1b, AcSOC1c, and AcSOC1d are more closely related to AGL14 and AGL19, and AcSOC1h is most closely related to AGL42, AGL71, and AGL72 (Fig. 1B). Analysis of flanking gene models in the draft genome of A. chinensis (Huang et al., 2013) revealed homology to genes on Arabidopsis chromosome numbers 2, 4, and 5 in close proximity to Arabidopsis SOC1-like genes and confirmed the above groupings (Supplementary Table S3).


Functional and expression analyses of kiwifruit SOC1-like genes suggest that they may not have a role in the transition to flowering but may affect the duration of dormancy.

Voogd C, Wang T, Varkonyi-Gasic E - J. Exp. Bot. (2015)

Phylogenetic analysis of kiwifruit SOC1-like protein sequences. (A) Alignment of the C-terminal region of SOC1-like amino acid sequences. The amino acid residues in the alignment are shaded according to their similarity scores: white on black, 100% similar; white on grey, 80–100% similar; black on grey, 60–80% similar; grey on white, <60% similar. The conserved SOC1 motif is underlined. The observed deviation of this motif in AcSOC1h appears to be due to a putative 1bp deletion within the motif leading to a frameshift from EVETELFFGLA to EVETELSLALL. (B) Phylogenetic tree based on the amino acid alignment of kiwifruit SOC1-like predicted proteins and SOC1-like proteins from other plant species. The tree was generated using the Geneious Tree Builder plug-in (Geneious 5.5.6) using the Neighbor–Joining method with Arabidopsis AGL6 as an outgroup. Numbers below the branches represent bootstrap support values from 1000 replicates (values ≥50% are indicated). Origins of the genes, with the exception of Arabidopsis, are indicated by a prefix as follows: Ac, Actinidia chinensis; Vv, Vitis vinifera; Pt, Populus tremuloides; Ps, Pisum sativum; Ph, Petunia hybrida; Fv, Fragaria vesca; Pa, Prunus armeniaca; Md, Malus×domestica; their GenBank accession numbers are indicated to the right. Arabidopsis genes SOC1, AGL14, AGL19, AGL42, AGL71, and AGL72 are associated with their unique IDs. Kiwifruit SOC1-like genes in different clades are indicated by arrows. (This figure is available in colour at JXB online.)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 1: Phylogenetic analysis of kiwifruit SOC1-like protein sequences. (A) Alignment of the C-terminal region of SOC1-like amino acid sequences. The amino acid residues in the alignment are shaded according to their similarity scores: white on black, 100% similar; white on grey, 80–100% similar; black on grey, 60–80% similar; grey on white, <60% similar. The conserved SOC1 motif is underlined. The observed deviation of this motif in AcSOC1h appears to be due to a putative 1bp deletion within the motif leading to a frameshift from EVETELFFGLA to EVETELSLALL. (B) Phylogenetic tree based on the amino acid alignment of kiwifruit SOC1-like predicted proteins and SOC1-like proteins from other plant species. The tree was generated using the Geneious Tree Builder plug-in (Geneious 5.5.6) using the Neighbor–Joining method with Arabidopsis AGL6 as an outgroup. Numbers below the branches represent bootstrap support values from 1000 replicates (values ≥50% are indicated). Origins of the genes, with the exception of Arabidopsis, are indicated by a prefix as follows: Ac, Actinidia chinensis; Vv, Vitis vinifera; Pt, Populus tremuloides; Ps, Pisum sativum; Ph, Petunia hybrida; Fv, Fragaria vesca; Pa, Prunus armeniaca; Md, Malus×domestica; their GenBank accession numbers are indicated to the right. Arabidopsis genes SOC1, AGL14, AGL19, AGL42, AGL71, and AGL72 are associated with their unique IDs. Kiwifruit SOC1-like genes in different clades are indicated by arrows. (This figure is available in colour at JXB online.)
Mentions: Nine transcripts with sequence homology to Arabidopsis SOC1 were identified in the Plant & Food Research EST database (Crowhurst et al., 2008), and designated AcSOC1a through AcSOC1i. 5ʹ RACE was used where necessary before PCR amplification and cloning of the complete coding sequence from A. chinensis bud tissue (GenBank accession nos KP407147–KP407155). Analysis of the deduced amino acid sequence revealed that the open reading frames encode a predicted protein of between 200 and 220 amino acids and each included the conserved MADS-box, I-region, K-box, and C-terminal SOC1 motif (Fig. 1A; Supplementary Fig. S1 at JXB online). Each coding sequence mapped to a different pseudo-chromosome (Huang et al., 2013) and is encoded by seven exons. With the exception of AcSOC1h, all proteins are associated in pairs, with members sharing >80% identity. AcSOC1e, AcSOC1i, AcSOC1f, and AcSOC1g are most similar to Arabidopsis SOC1, sharing between 64% and 66% identity (Supplementary Table S2). Phylogenetic analysis using the full-length deduced amino acid sequences confirmed that of the nine proteins, AcSOC1e, AcSOC1i, AcSOC1f, and AcSOC1g are most closely related to SOC1. AcSOC1a, AcSOC1b, AcSOC1c, and AcSOC1d are more closely related to AGL14 and AGL19, and AcSOC1h is most closely related to AGL42, AGL71, and AGL72 (Fig. 1B). Analysis of flanking gene models in the draft genome of A. chinensis (Huang et al., 2013) revealed homology to genes on Arabidopsis chromosome numbers 2, 4, and 5 in close proximity to Arabidopsis SOC1-like genes and confirmed the above groupings (Supplementary Table S3).

Bottom Line: Largely overlapping spatial domains but distinct expression profiles in buds were identified between the SOC1-like gene family members.Ectopic expression of AcSOC1e, AcSOC1i, and AcSOC1f in Actinidia chinensis had no impact on establishment of winter dormancy and failed to induce precocious flowering, but AcSOC1i reduced the duration of dormancy in the absence of winter chilling.These findings add to our understanding of the SOC1-like gene family and the potential diversification of SOC1 function in woody perennials.

View Article: PubMed Central - PubMed

Affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland 1142, New Zealand.

No MeSH data available.


Related in: MedlinePlus