RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies

Yang, Shaoyu; Hao, Dongli; Song, Zhizhong; Yang, Guangsheng; Wang, Li; Su, Yanhua

doi:10.1016/j.gene.2014.11.021

Cited by 85 publications

(76 citation statements)

References 48 publications

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“…The transcript GF677_11309 encodes NCED3 and it was significantly induced in roots, confirming that a water deficit enhances the synthesis of ABA (Supplementary Table S3). In agreement with previous reports, protein phosphatases PP2C, which are major ABA regulators, were also upregulated (Tang et al, 2013; Yang et al, 2015; Iovieno et al, 2016; Magalhães et al, 2016). The accumulation of ABA leads to activation of ABA-dependent TFs, such as MYB factors, as was shown in this study.…”

Section: Discussionsupporting

confidence: 93%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear. Hence, in this study, high-throughput sequencing (RNA-seq) was performed to assess the transcriptomic changes and the key genes involved in the response to drought in root tissues (GF677 rootstock) and leaf tissues (graft, var. Catherina) subjected to 16 days of drought stress. In total, 12 RNA libraries were constructed and sequenced. This generated a total of 315 M raw reads from both tissues, which allowed the assembly of 22,079 and 17,854 genes associated with the root and leaf tissues, respectively. Subsets of 500 differentially expressed genes (DEGs) in roots and 236 in leaves were identified and functionally annotated with 56 gene ontology (GO) terms and 99 metabolic pathways, which were mostly associated with aminobenzoate degradation and phenylpropanoid biosynthesis. The GO analysis highlighted the biological functions that were exclusive to the root tissue, such as “locomotion,” “hormone metabolic process,” and “detection of stimulus,” indicating the stress-buffering role of the GF677 rootstock. Furthermore, the complex regulatory network involved in the drought response was revealed, involving proteins that are associated with signaling transduction, transcription and hormone regulation, redox homeostasis, and frontline barriers. We identified two poorly characterized genes in P. persica: growth-regulating factor 5 (GRF5), which may be involved in cellular expansion, and AtHB12, which may be involved in root elongation. The reliability of the RNA-seq experiment was validated by analyzing the expression patterns of 34 DEGs potentially involved in drought tolerance using quantitative reverse transcription polymerase chain reaction. The transcriptomic resources generated in this study provide a broad characterization of the acclimation of P. persica to drought, shedding light on the major molecular responses to the most important environmental stressor.

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Section: Discussionsupporting

confidence: 93%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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“…Ammonium provision to N-starved roots predominantly up-regulates gene transcription, with only very few genes being down-regulated, whilst nitrate supply induces and represses transcription to a similar extent (Figure 1). Other studies performed in rice [40,41] and in oilseed rape (Brassica napus) [10], even if with longer treatments, showed a prevalent down-regulation of gene expression in response to ammonium, suggesting the existence of individual responses among genotypes and in dependence of the duration of the treatment.…”

Section: Discussionmentioning

confidence: 93%

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots

Ravazzolo

Trevisan

Forestan

et al. 2020

IJMS

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Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.

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“…Interestingly, possibly due to ammonium toxicity, when the N concentration increased to 15.0 mM, the axillary bud outgrowth became inhibited. Previous studies have made substantial progress in the identification of genes that respond to N [55,56] via RNA-seq. For example, to understand early responses to ammonium in rice, genes that responded to 0, 1.0, and 10.0 mM ammonium were identified in the roots and shoots that had been treated for 4 hours [55].…”

Section: Regulatory Effects Of N Treatment On Axillary Bud Growth In mentioning

confidence: 99%

Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth

Wang

Qian

Fang

et al. 2020

Preprint

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Background: N is an important macronutrient required for plant development and significantly influences axillary bud outgrowth, which affects tillering and grain yields of rice. However, how different N concentrations affect axillary bud growth at the molecular and transcriptional levels remains unclear. Results: In this study, morphological changes in the axillary bud growth of rice seedlings under different N concentrations ranging from low to high levels were systematically observed. To investigate the expression of N-induced genes involved in axillary bud growth, we used RNA-seq technology to generate mRNA transcriptomic data from two tissue types, basal parts and axillary buds, of plants grown under six different N concentrations. In total, 10,221 and 12,180 DEGs induced by LN or HN supplies were identified in the basal parts and axillary buds, respectively, via comparisons to expression levels under NN level. Analysis of the coexpression modules from the DEGs of the basal parts and axillary buds revealed an abundance of related biological processes underlying the axillary bud growth of plants under N treatments. Among these processes, the activity of cell division and expansion was positively correlated with the growth rate of axillary buds of plants grown under different N supplies. Additionally, TFs and phytohormones were shown to play crucial roles in determining the axillary bud growth of plants grown under different N concentrations. Further validation of OsGS1;2 and OsGS2 , the rice mutants of which presented altered tiller numbers, validated our transcriptomic data. Conclusion: These results indicate that different N concentrations affect the axillary bud growth rate, and our study revealed comprehensive expression profiles of genes that respond to different N concentrations, providing an important resource for future studies attempting to determine how axillary bud growth is controlled by different N supplies.

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RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies

Cited by 85 publications

References 48 publications

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots

Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth

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