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Identification of genes related to the development of bamboo rhizome bud.

Wang K, Peng H, Lin E, Jin Q, Hua X, Yao S, Bian H, Han N, Pan J, Wang J, Deng M, Zhu M - J. Exp. Bot. (2009)

Bottom Line: In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified.The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets.To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China.

ABSTRACT
Bamboo (Phyllostachys praecox) is one of the largest members of the grass family Poaceae, and is one of the most economically important crops in Asia. However, complete knowledge of bamboo development and its molecular mechanisms is still lacking. In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified. The rice cross-species microarray hybridization showed a total of 318 up-regulated and 339 down-regulated genes, including those involved in regulation and signalling, metabolism, and stress, and also cell wall-related genes, in the bamboo rhizome buds versus the leaves. By referring to the functional dissection of the homologous genes from Arabidopsis and rice, the putative functions of the 52 up-regulated genes in the bamboo rhizome bud were described. Six genes related to the development of the bamboo rhizome bud were further cloned and sequenced. These show 66-90% nucleotide identity and 68-98% amino acid identity with the homologous rice genes. The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets. Furthermore, in situ hybridization showed that the PpRLK1 gene is expressed in the procambium and is closely related to meristem development of bamboo shoots. The PpHB1 gene is expressed at the tips of bamboo shoots and procambium, and is closely related to rhizome bud formation and procambial development. To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development.

Show MeSH
Alignment and phylogenetic analysis of the cloned genes PpHB1 and three REVOLUTA homologues. (A) Alignment of four REVOLUTA homologues. Sequence alignment of the deduced amino acids of Phyllostachys praecox PpHB1, rice OsREV (NM_197030), maize ZmREV (RLD1, AY501430), and Arabidopsis thaliana AtREV (REVOLUTA, AF188994) was conducted with AlignX. Regions of identity (white letters on a black background), conservation (white letters on a grey background), similarity (black letters on a grey background), and differences (white) are indicated. The HD-Zip domain (*) and START domain (+) are predicted according to AtREV. (B) The phylogeny reconstruction of REVOLUTA homologues.
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fig3: Alignment and phylogenetic analysis of the cloned genes PpHB1 and three REVOLUTA homologues. (A) Alignment of four REVOLUTA homologues. Sequence alignment of the deduced amino acids of Phyllostachys praecox PpHB1, rice OsREV (NM_197030), maize ZmREV (RLD1, AY501430), and Arabidopsis thaliana AtREV (REVOLUTA, AF188994) was conducted with AlignX. Regions of identity (white letters on a black background), conservation (white letters on a grey background), similarity (black letters on a grey background), and differences (white) are indicated. The HD-Zip domain (*) and START domain (+) are predicted according to AtREV. (B) The phylogeny reconstruction of REVOLUTA homologues.

Mentions: The sequences of these six genes were further analysed by alignment and phylogeny reconstruction. Interestingly, these bamboo genes (PpHB1, PpRLK1, PpSINA, PpARF1, and PpHK1) have closer relationships with their homologous genes from rice (REVOLUTA, CLAVATA1, SINAT5, ARF, and AHK4) than those from other species (Fig. 3, Supplementary Figs S2–S6 available at JXB online).


Identification of genes related to the development of bamboo rhizome bud.

Wang K, Peng H, Lin E, Jin Q, Hua X, Yao S, Bian H, Han N, Pan J, Wang J, Deng M, Zhu M - J. Exp. Bot. (2009)

Alignment and phylogenetic analysis of the cloned genes PpHB1 and three REVOLUTA homologues. (A) Alignment of four REVOLUTA homologues. Sequence alignment of the deduced amino acids of Phyllostachys praecox PpHB1, rice OsREV (NM_197030), maize ZmREV (RLD1, AY501430), and Arabidopsis thaliana AtREV (REVOLUTA, AF188994) was conducted with AlignX. Regions of identity (white letters on a black background), conservation (white letters on a grey background), similarity (black letters on a grey background), and differences (white) are indicated. The HD-Zip domain (*) and START domain (+) are predicted according to AtREV. (B) The phylogeny reconstruction of REVOLUTA homologues.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2803224&req=5

fig3: Alignment and phylogenetic analysis of the cloned genes PpHB1 and three REVOLUTA homologues. (A) Alignment of four REVOLUTA homologues. Sequence alignment of the deduced amino acids of Phyllostachys praecox PpHB1, rice OsREV (NM_197030), maize ZmREV (RLD1, AY501430), and Arabidopsis thaliana AtREV (REVOLUTA, AF188994) was conducted with AlignX. Regions of identity (white letters on a black background), conservation (white letters on a grey background), similarity (black letters on a grey background), and differences (white) are indicated. The HD-Zip domain (*) and START domain (+) are predicted according to AtREV. (B) The phylogeny reconstruction of REVOLUTA homologues.
Mentions: The sequences of these six genes were further analysed by alignment and phylogeny reconstruction. Interestingly, these bamboo genes (PpHB1, PpRLK1, PpSINA, PpARF1, and PpHK1) have closer relationships with their homologous genes from rice (REVOLUTA, CLAVATA1, SINAT5, ARF, and AHK4) than those from other species (Fig. 3, Supplementary Figs S2–S6 available at JXB online).

Bottom Line: In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified.The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets.To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China.

ABSTRACT
Bamboo (Phyllostachys praecox) is one of the largest members of the grass family Poaceae, and is one of the most economically important crops in Asia. However, complete knowledge of bamboo development and its molecular mechanisms is still lacking. In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified. The rice cross-species microarray hybridization showed a total of 318 up-regulated and 339 down-regulated genes, including those involved in regulation and signalling, metabolism, and stress, and also cell wall-related genes, in the bamboo rhizome buds versus the leaves. By referring to the functional dissection of the homologous genes from Arabidopsis and rice, the putative functions of the 52 up-regulated genes in the bamboo rhizome bud were described. Six genes related to the development of the bamboo rhizome bud were further cloned and sequenced. These show 66-90% nucleotide identity and 68-98% amino acid identity with the homologous rice genes. The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets. Furthermore, in situ hybridization showed that the PpRLK1 gene is expressed in the procambium and is closely related to meristem development of bamboo shoots. The PpHB1 gene is expressed at the tips of bamboo shoots and procambium, and is closely related to rhizome bud formation and procambial development. To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development.

Show MeSH