Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq of 6 day old shoots of 6 rice accessions under WL or WL + supplemental FR (far-red) light

ABSTRACT: This experiment was designed to uncover the transcriptomic changes that would occur in rice after 24 h of supplemental FR treatment, in an accession dependant manner. To do so, 6 different varieties of rice (IR64, Nipponbare, Luk Takhar, M Blatec, Mudgo, Sabharaj and Zhenshan) were grown in the greenhouse facilities of the Botanical Gardens, Utrecht University, in The Netherlands, in summer and autumn of 2021. After five days in WL (400 µmol m-2 s-1 of combined sunlight and artificial light), the treatment group was exposed to supplemental FR (500 µmol m-2 s-1 FR, R:FR of 0.2) light for 24 hours. The whole shoot was sampled, with four plants pooled in one sample. The experiment was repeated four times, resulting in 48 samples (6 varieties x 2 treatments x 4 replicates). Same samples were run on two individual lanes.

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Oryza sativa

SUBMITTER: Andres Romanowski

PROVIDER: E-MTAB-13023 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Plants grown under a canopy recognize changes in light quality and modify their growth patterns; this modification is known as shade avoidance syndrome. In leaves, leaf blade expansion is suppressed, whereas petiole elongation is promoted under the shade. However, the mechanisms that control these responses are largely unclear. Here, we demonstrated that both auxin and brassinosteroid (BR) are required for the normal leaf responses to shade. The microarray analysis of leaf blades and petioles treated with end-of-day far-red light (EODFR) revealed that almost half of the genes induced by the treatment in both parts were previously identified as auxin-responsive genes. Likewise, BR-responsive genes were overrepresented in the EODFR-induced genes. Hence, the auxin and BR responses were elevated by EODFR treatment in both leaf blades and petioles, although opposing growth responses were observed in these two parts. The analysis of the auxin-deficient doc1/big mutant and BR-deficient rot3/cyp90c1 mutant further indicates that auxin and BR were equally required for the normal petiole elongation response to the shade stimulus. In addition, the spotlight irradiation experiment revealed that phytochrome in leaf blades but not that in petioles regulated petiole elongation, which was probably mediated through regulation of the auxin/BR responses in petioles. On the basis of these findings, we conclude that auxin and BR cooperatively promote petiole elongation in response to the shade stimulus under the control of phytochrome in the leaf blade. The WT seedlings were grown for 19 days under continuous white light condition before experimental treatment with three light conditions. Seedlings were either maintained in white light for 2 h (WL), incubated in the dark condition for 2 h (D), or experienced a pulse irradiation of FR light before incubated in the dark condition for 2 h (FRD). Total RNAs were separately prepared from leaf blades and petioles after each light treatment. Three independent biological replicates were used.

Dataset Information

RNAseq of 6 day old shoots of 6 rice accessions under WL or WL + supplemental FR (far-red) light

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