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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.

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Rice cross-species microarray analysis of the bamboo rhizome bud versus leaves. (A) The distribution of the average normalized hybridization intensity (Cy5, rhizome bud; Cy3, leaf) of three measurements. Grey points indicate data with a ratio >0.5 and <2, while black points indicate data that are out of the range (>2.0 for up-regulated genes and <0.5 for down-regulated genes). (B) The putative functions of 318 up-regulated genes (U, unknown genes; N, not found in Arabidopsis; H, housekeeping genes; R, regulation and signalling-related genes; M, metabolism-related genes; S, stress-related genes; C, cell wall-related genes). The number of genes is indicated.
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fig2: Rice cross-species microarray analysis of the bamboo rhizome bud versus leaves. (A) The distribution of the average normalized hybridization intensity (Cy5, rhizome bud; Cy3, leaf) of three measurements. Grey points indicate data with a ratio >0.5 and <2, while black points indicate data that are out of the range (>2.0 for up-regulated genes and <0.5 for down-regulated genes). (B) The putative functions of 318 up-regulated genes (U, unknown genes; N, not found in Arabidopsis; H, housekeeping genes; R, regulation and signalling-related genes; M, metabolism-related genes; S, stress-related genes; C, cell wall-related genes). The number of genes is indicated.

Mentions: To investigate gene expression in the bamboo rhizome buds versus leaves, rice cross-species microarray analyses were carried out. Cy5-labelled cDNA from rhizome buds was hybridized against Cy3-labelled cDNA from the leaves on the same rice gene chip with 10 369 spots. The distribution of the average normalized hybridization intensity of the three measurements showed that a total of 8795 spots were effective (Fig. 2A). The average hybridization efficiency is 84.82%. According to the criterion of the Cy5/Cy3 ratio being >2.0 or <0.5 for genes to be up- or down-regulated, respectively, a total of 318 up- and 339 down-regulated genes were identified. The reproducibility of the replicated hybridizations is 95%. By comparing the homologous genes from Arabidopsis and rice, the putative functions of these 318 up-regulated genes in the rhizome bud were classified into seven groups (Fig. 2B). Furthermore, except for the housekeeping genes, 52 of the 318 up-regulated genes with known functions in the rhizome bud are listed and described in Table 3.


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)

Rice cross-species microarray analysis of the bamboo rhizome bud versus leaves. (A) The distribution of the average normalized hybridization intensity (Cy5, rhizome bud; Cy3, leaf) of three measurements. Grey points indicate data with a ratio >0.5 and <2, while black points indicate data that are out of the range (>2.0 for up-regulated genes and <0.5 for down-regulated genes). (B) The putative functions of 318 up-regulated genes (U, unknown genes; N, not found in Arabidopsis; H, housekeeping genes; R, regulation and signalling-related genes; M, metabolism-related genes; S, stress-related genes; C, cell wall-related genes). The number of genes is indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Rice cross-species microarray analysis of the bamboo rhizome bud versus leaves. (A) The distribution of the average normalized hybridization intensity (Cy5, rhizome bud; Cy3, leaf) of three measurements. Grey points indicate data with a ratio >0.5 and <2, while black points indicate data that are out of the range (>2.0 for up-regulated genes and <0.5 for down-regulated genes). (B) The putative functions of 318 up-regulated genes (U, unknown genes; N, not found in Arabidopsis; H, housekeeping genes; R, regulation and signalling-related genes; M, metabolism-related genes; S, stress-related genes; C, cell wall-related genes). The number of genes is indicated.
Mentions: To investigate gene expression in the bamboo rhizome buds versus leaves, rice cross-species microarray analyses were carried out. Cy5-labelled cDNA from rhizome buds was hybridized against Cy3-labelled cDNA from the leaves on the same rice gene chip with 10 369 spots. The distribution of the average normalized hybridization intensity of the three measurements showed that a total of 8795 spots were effective (Fig. 2A). The average hybridization efficiency is 84.82%. According to the criterion of the Cy5/Cy3 ratio being >2.0 or <0.5 for genes to be up- or down-regulated, respectively, a total of 318 up- and 339 down-regulated genes were identified. The reproducibility of the replicated hybridizations is 95%. By comparing the homologous genes from Arabidopsis and rice, the putative functions of these 318 up-regulated genes in the rhizome bud were classified into seven groups (Fig. 2B). Furthermore, except for the housekeeping genes, 52 of the 318 up-regulated genes with known functions in the rhizome bud are listed and described in Table 3.

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