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Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development.

Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK - DNA Res. (2014)

Bottom Line: Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis.Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them.The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.

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Expression profiles of OsARM superfamily genes. Reproductive development comprising six stages of panicle [P1 (0–3 cm), P2 (3–5 cm), P3 (5–10 cm), P4 (10–15 cm), P5 (15–22 cm), and P6 (22–30 cm)] and five stages of seed [S1 (0–2 DAP), S2 (3–4 DAP), S3 (4–10 DAP), S4 (11–20 DAP), and S5 (21–29 DAP)] development. Clustering of the expression profile was done with log-transformed average values taking mature leaf as baseline. Three experimental stress conditions are denoted as CS, cold stress; DS, drought stress; SS, salt stress; and S, control, 7-day-old unstressed seedling. A gene is considered differentially expressed during reproductive development if up- or down-regulated at least 2-fold, with respect to three vegetative controls (mature leaf, root, and 7-day-old seedling) and with respect to 7-day-old unstressed seedling in the case of abiotic stress. The colour scale at the bottom of the heat map is given in log2 intensity value. (A) The expression profile for OsARM genes other than U-box. (B) Expression profile of OsPUB/ARM genes.
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DST056F3: Expression profiles of OsARM superfamily genes. Reproductive development comprising six stages of panicle [P1 (0–3 cm), P2 (3–5 cm), P3 (5–10 cm), P4 (10–15 cm), P5 (15–22 cm), and P6 (22–30 cm)] and five stages of seed [S1 (0–2 DAP), S2 (3–4 DAP), S3 (4–10 DAP), S4 (11–20 DAP), and S5 (21–29 DAP)] development. Clustering of the expression profile was done with log-transformed average values taking mature leaf as baseline. Three experimental stress conditions are denoted as CS, cold stress; DS, drought stress; SS, salt stress; and S, control, 7-day-old unstressed seedling. A gene is considered differentially expressed during reproductive development if up- or down-regulated at least 2-fold, with respect to three vegetative controls (mature leaf, root, and 7-day-old seedling) and with respect to 7-day-old unstressed seedling in the case of abiotic stress. The colour scale at the bottom of the heat map is given in log2 intensity value. (A) The expression profile for OsARM genes other than U-box. (B) Expression profile of OsPUB/ARM genes.

Mentions: The microarray data for OsARM genes were generated using Affymetrix rice genome arrays for 7-day-old rice seedlings. Out of 158 genes, probe sets for 14 genes were not available on Affymetrix gene chip array. Unique probe sets were found for 105 genes, 2 for 32 genes, 3 for 6 genes, and 4 for 1 gene. In the case of multiple probe sets, one with the highest baseline expression in the array was chosen for the analysis. Expression profile of 144 OsARM genes was analysed under three abiotic stress conditions (salt, cold, and drought) (FigsΒ 3 and 4 and Supplementary Table S5). After defining a criterion of fold change value of β‰₯2 (either up- or down-regulated) for experimental samples in comparison to control untreated 7-day-old seedlings, 36 OsARM genes showed differential expression, with 26 of them being up-regulated and 10 were found to be down-regulated in any of the above given conditions. Four genes (OsPUB33, OsPUB41, OsPUB2, and OsPUB39) were found to be up-regulated and a single gene OsARM14 was found to be down-regulated in all three stress conditions together. Notably, out of 26 up-regulated genes, 7 (OsPUB8, OsARM82, OsPUB22, OsARM54, OsARM11, OsPUB43, and OsPUB28) exhibited higher expression under drought stress, whereas 5 genes (OsARM1, OsPUB38, OsPUB40, OsPUB3, and OsPUB46) were up-regulated under salt stress, specifically. Eight genes (OsARM7, OsPUB30, OsPUB32, Oryzadillo, OsARM8, OsARM92, OsPUB5, and OsPUB6) were up-regulated under salt and drought stresses together. Whereas, only a single gene (OsARM13) was found to be up-regulated under cold and drought stresses together. Interestingly, one gene (OsPUB28) was found to be up-regulated in drought and down-regulated under cold stress simultaneously.FigureΒ 3.


Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development.

Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK - DNA Res. (2014)

Expression profiles of OsARM superfamily genes. Reproductive development comprising six stages of panicle [P1 (0–3 cm), P2 (3–5 cm), P3 (5–10 cm), P4 (10–15 cm), P5 (15–22 cm), and P6 (22–30 cm)] and five stages of seed [S1 (0–2 DAP), S2 (3–4 DAP), S3 (4–10 DAP), S4 (11–20 DAP), and S5 (21–29 DAP)] development. Clustering of the expression profile was done with log-transformed average values taking mature leaf as baseline. Three experimental stress conditions are denoted as CS, cold stress; DS, drought stress; SS, salt stress; and S, control, 7-day-old unstressed seedling. A gene is considered differentially expressed during reproductive development if up- or down-regulated at least 2-fold, with respect to three vegetative controls (mature leaf, root, and 7-day-old seedling) and with respect to 7-day-old unstressed seedling in the case of abiotic stress. The colour scale at the bottom of the heat map is given in log2 intensity value. (A) The expression profile for OsARM genes other than U-box. (B) Expression profile of OsPUB/ARM genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4060948&req=5

DST056F3: Expression profiles of OsARM superfamily genes. Reproductive development comprising six stages of panicle [P1 (0–3 cm), P2 (3–5 cm), P3 (5–10 cm), P4 (10–15 cm), P5 (15–22 cm), and P6 (22–30 cm)] and five stages of seed [S1 (0–2 DAP), S2 (3–4 DAP), S3 (4–10 DAP), S4 (11–20 DAP), and S5 (21–29 DAP)] development. Clustering of the expression profile was done with log-transformed average values taking mature leaf as baseline. Three experimental stress conditions are denoted as CS, cold stress; DS, drought stress; SS, salt stress; and S, control, 7-day-old unstressed seedling. A gene is considered differentially expressed during reproductive development if up- or down-regulated at least 2-fold, with respect to three vegetative controls (mature leaf, root, and 7-day-old seedling) and with respect to 7-day-old unstressed seedling in the case of abiotic stress. The colour scale at the bottom of the heat map is given in log2 intensity value. (A) The expression profile for OsARM genes other than U-box. (B) Expression profile of OsPUB/ARM genes.
Mentions: The microarray data for OsARM genes were generated using Affymetrix rice genome arrays for 7-day-old rice seedlings. Out of 158 genes, probe sets for 14 genes were not available on Affymetrix gene chip array. Unique probe sets were found for 105 genes, 2 for 32 genes, 3 for 6 genes, and 4 for 1 gene. In the case of multiple probe sets, one with the highest baseline expression in the array was chosen for the analysis. Expression profile of 144 OsARM genes was analysed under three abiotic stress conditions (salt, cold, and drought) (FigsΒ 3 and 4 and Supplementary Table S5). After defining a criterion of fold change value of β‰₯2 (either up- or down-regulated) for experimental samples in comparison to control untreated 7-day-old seedlings, 36 OsARM genes showed differential expression, with 26 of them being up-regulated and 10 were found to be down-regulated in any of the above given conditions. Four genes (OsPUB33, OsPUB41, OsPUB2, and OsPUB39) were found to be up-regulated and a single gene OsARM14 was found to be down-regulated in all three stress conditions together. Notably, out of 26 up-regulated genes, 7 (OsPUB8, OsARM82, OsPUB22, OsARM54, OsARM11, OsPUB43, and OsPUB28) exhibited higher expression under drought stress, whereas 5 genes (OsARM1, OsPUB38, OsPUB40, OsPUB3, and OsPUB46) were up-regulated under salt stress, specifically. Eight genes (OsARM7, OsPUB30, OsPUB32, Oryzadillo, OsARM8, OsARM92, OsPUB5, and OsPUB6) were up-regulated under salt and drought stresses together. Whereas, only a single gene (OsARM13) was found to be up-regulated under cold and drought stresses together. Interestingly, one gene (OsPUB28) was found to be up-regulated in drought and down-regulated under cold stress simultaneously.FigureΒ 3.

Bottom Line: Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis.Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them.The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.

Show MeSH
Related in: MedlinePlus