Identification of ABA-responsive genes in rice shoots via cDNA macroarray

Lin, Fang; Xu, Shan-Mei; Ni, Wei; Chu, Zhao; Xu, Zhihong; Xue, Hong

doi:10.1038/sj.cr.7290151

Cited by 33 publications

(27 citation statements)

References 56 publications

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“…For 2-week-old rice seedlings, 43 of 1,700 cDNAs were induced by ABA (Rabbani et al, 2003). For rice shoots, 29 of 4,000 cDNAs were up with GA and 42 were down with GA 24 h after hormone treatment (Yang et al, 2004), and 30 of 6,144 cDNAs were up with ABA and seven down with ABA within 12 h of hormone treatment (Lin et al, 2003). Accounting for these differences is difficult, but with the exception of experiments with rice callus, the larger number of hormone-responsive genes may reflect the greater number of cell types involved.…”

Section: Discussionmentioning

confidence: 99%

“…In particular, it is now possible to compare the responses of selected, individual genes to the responses of large groups of genes that have not been identified in advance. Global or large-scale changes in transcription have been determined for cereals on a few occasions (Potokina et al, 2002;Lin et al, 2003;Rabbani et al, 2003;Close et al, 2004;Schnable et al, 2004;Yang et al, 2004;Yazaki et al, 2004). In most cases, however, RNA was isolated from complex tissues or after relatively long treatment times.…”

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confidence: 99%

“…In most cases, however, RNA was isolated from complex tissues or after relatively long treatment times. For example, RNA for hybridization with cDNA or oligonucleotide-based microarrays has been extracted from developing rice seedlings (Lin et al, 2003;Rabbani et al, 2003); rice shoots, leaves, or roots (Kawasaki et al, 2001;Ozturk et al, 2002;Yang et al, 2004); barley leaves (Close et al, 2004); or maize (Zea mays) embryos (Lee et al, 2002). Interpretation of the data for these experiments is complicated because different tissues and cell types are expected to show distinct, yet overlapping, patterns of gene expression.…”

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Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice

et al. 2005

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The cereal aleurone layer is a model system for studying the regulation of transcription by gibberellin (GA) and abscisic acid (ABA). GA stimulates and ABA prevents the transcription of genes for a-amylases and other secreted hydrolytic enzymes, but how GA and ABA affect the transcription of other genes is largely unknown. We characterized gene expression in rice (Oryza sativa) aleurone using a half-genome rice microarray. Of the 23,000 probe sets on the chip, approximately 11,000 hybridized with RNA from rice aleurone treated with ABA, GA, or no hormone. As expected, GA regulated the expression of many genes, and 3 times as many genes were up-regulated by GA at 8 h than were down-regulated. Changes in gene expression resulting from ABA treatment were not consistent with the hypothesis that the role of ABA in this tissue is primarily to repress gene expression, and 10 times more genes were up-regulated by ABA at 8 h than were down-regulated by ABA. We also measured transcript abundance in aleurone of dwarf1 (d1) mutant rice. The d1 protein is the sole a-subunit of heterotrimeric G-proteins in rice. Genes up-regulated by GA or ABA had higher expression in wild type than in d1 aleurone, and genes down-regulated by GA had lower expression in wild type relative to d1 aleurone. The d1 mutation did not result in a decrease in sensitivity to GA at the level of transcription. Rather, changes in transcript abundance were smaller in the d1 mutant than in wild type.

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Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice

et al. 2005

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“…Transient gene induction was also found following abiotic stress treatment, such as cold, osmotic, or drought (Bray, 2002;Reddy et al, 2002), and by addition of the phytohormone ABA (AtGenExpress; Lin et al, 2003). Another link with plant hormones is also suggested by remorin AtREM1.3 (Alliotte et al, 1989), which was copurified with the cytokinin-induced response regulator AtARR4 (Yamada et al, 1998).…”

Section: The Remorin Family Consists Of Six Different Groupsmentioning

confidence: 99%

Genome-Wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

et al. 2007

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“…The completed sequencing of the A. thaliana genome allowed the first genome-wide screens for relevant genes [28], and the recent development of cDNA chip technology made possible the large-scale analysis of light control-related genes [29], specific gene expression in developing seeds [30], drought-and wound-related genes [31,32], rice ABA-responsive genes [33], and the relative effects of mutant vs. wild-type gene expression [34].…”

Section: Introductionmentioning

confidence: 99%

DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

Lin

Rui

et al. 2004

Cell Res

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The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses. Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK), phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms. In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf, stem and flower tissues, and leaves from plants treated with various hormones (auxin, cytokinin, gibberellin, abscisic acid and brassinosteroid) or environmental factors (temperature, calcium, sodium, drought, salicylic acid and jasmonic acid). Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions. In particular, the different isoforms of each family were specifically expressed in many cases, suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses.

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Identification of ABA-responsive genes in rice shoots via cDNA macroarray

Cited by 33 publications

References 56 publications

Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice

Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice

Genome-Wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

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