RNA-Seq Profiling Shows Divergent Gene Expression Patterns in Arabidopsis Grown under Different Densities

Guo, Di; Song, Xiaoming; Yuan, Min; Wang, Zhenyi; Ge, Weina; Wang, Li; Wang, Jinpeng; Wang, Xiyin

doi:10.3389/fpls.2017.02001

Cited by 13 publications

(12 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, it was found that the vertical position had a significant effect on gene expression when comparing planting densities. Guo et al sought out 205 genes that were considered to be differentially expressed in Arabidopsis grown under different planting densities [7]. Another study found that 221 genes exhibited differential expression in response to density stress in barley [28].…”

Section: Discussionmentioning

confidence: 99%

“…Nitrate, as the main inorganic nitrogen source for plant growth and development, is not only a nutrient for plants, but can also act as a signaling molecule to regulate plant morphogenesis, physiological responses and gene expression [63–65]. Guo et al showed that nitrate availability is the main factor limiting agricultural productivity under high density conditions [7]. Bouguyon et al found that the nitrate/nitrite transporter ( NRT1 .…”

Section: Discussionmentioning

confidence: 99%

“…The density of planting has also been found to be important in acquiring a high yield in modern corn production [5,6]. Although planting density has been shown to be important for the growth of crops, vegetables, and medicinal plants [7], little is known about the molecular-level effect of planting density on plant growth.…”

Section: Introductionmentioning

confidence: 99%

“…However, to fully maximize productivity, it is important to understand the molecular mechanisms and environmental factors that affect timber yield. RNA-sequencing (RNA-Seq) of Arabidopsis thaliana grown under high and low planting densities revealed that the expression of glutaredoxin genes was influenced by the planting density the most [7]. Moreover, several genes associated with yield heterosis were found to exhibit differences in transcript accumulation in maize grown under high and low planting densities [20].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

et al. 2019

View full text Add to dashboard Cite

Certain plant genotypes can achieve optimal growth under appropriate environmental conditions. Under high planting density conditions, plants undergo competition for uptake and utilization of light and nutrients. However, the relationship between whole-genome expression patterns and the planting density in perennial woody plants remains unknown. In this study, whole-genome RNA sequencing of poplar ( Populus × euramericana ) was carried out at three different sampling heights to determine gene expression patterns under high (HD) and low (LD) planting densities. As a result, 4,004 differentially expressed genes (DEGs) were detected between HD and LD, of which 2,300, 701, and 1,003 were detected at the three positions, upper, middle and bottom, respectively. Function annotation results further revealed that a large number of the DEGs were involved in distinct biological functions. There were significant changes in the expression of metabolism-related and stimulus-related genes in response to planting density. There were 37 DEGs that were found at all three positions and were subsequently screened. Several DEGs related to plant light responses and photosynthesis were observed at different positions. Meanwhile, numbers of genes related to auxin/indole-3-acetic acid, and carbon and nitrogen metabolism were also revealed, displaying overall trends of upregulation under HD. These findings provide a basis for identifying candidate genes related to planting density and could increase our molecular understanding of the effect of planting density on gene expression.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Besides vegetative shade, high density planting also causes low R:FR light and induces SAS [ 31 ]. To further verify our results obtained from the shade experiment, we planted Arabidopsis plants under low to high densities and measured their Raman spectra.…”

Section: Resultsmentioning

confidence: 99%

Rapid metabolite response in leaf blade and petiole as a marker for shade avoidance syndrome

Sng

Singh

et al. 2020

Plant Methods

View full text Add to dashboard Cite

Background Shade avoidance syndrome (SAS) commonly occurs in plants experiencing vegetative shade, causing morphological and physiological changes that are detrimental to plant health and consequently crop yield. As the effects of SAS on plants are irreversible, early detection of SAS in plants is critical for sustainable agriculture. However, conventional methods to assess SAS are restricted to observing for morphological changes and checking the expression of shade-induced genes after homogenization of plant tissues, which makes it difficult to detect SAS early. Results Using the model plant Arabidopsis thaliana, we introduced the use of Raman spectroscopy to measure shade-induced changes of metabolites in vivo. Raman spectroscopy detected a decrease in carotenoid contents in leaf blades and petioles of plants with SAS, which were induced by low Red:Far-red light ratio or high density conditions. Moreover, by measuring the carotenoid Raman peaks, we were able to show that the reduction in carotenoid content under shade was mediated by phytochrome signaling. Carotenoid Raman peaks showed more remarkable response to SAS in petioles than leaf blades of plants, which greatly corresponded to their morphological response under shade or high plant density. Most importantly, carotenoid content decreased shortly after shade induction but before the occurrence of visible morphological changes. We demonstrated this finding to be similar in other plant species. Comprehensive testing of Brassica vegetables showed that carotenoid content decreased during SAS, in both shade and high density conditions. Likewise, carotenoid content responded quickly to shade, in a manner similar to Arabidopsis plants. Conclusions In various plant species tested in this study, quantification of carotenoid Raman peaks correlate to the severity of SAS. Moreover, short-term exposure to shade can induce the carotenoid Raman peaks to decrease. These findings highlight the carotenoid Raman peaks as a biomarker for early diagnosis of SAS in plants.

show abstract

Transcriptional analyses of maize leaves in response to high‐density planting

Cheng-hao

Chen

et al. 2022

Agronomy Journal

View full text Add to dashboard Cite

Maize (Zea mays L.) is one of the major cereal crops worldwide. Increasing planting density is an effective way to improve crop yield. However, plants grown under high‐density conditions compete for water, nutrients, and light, which often leads to changes in productivity. To date, few studies have determined the transcriptomic differences in maize leaves in response to different planting densities. This study examined the whole‐genome expression patterns in the leaves of maize planted under high and low densities to identify density‐regulated genes. Leaves at upper, ear, and lower stem nodes were collected at the grain‐filling stage of the maize hybrid Xianyu335 grown under low‐density planting and high‐density planting. In total, 72, 733, and 1,739 differentially expressed genes (DEGs) were identified in the respective upper, ear, and lower leaves under HDP. Upregulated and downregulated DEGs in the upper and lower leaves were similar in number, whereas upregulated DEGs in the ear leaves were significantly higher in number than the downregulated DEGs. Functional analysis indicated that genes responding to HDP‐related stresses were mediated by pathways involving four phytohormones responsible for metabolism and signaling, osmoprotectant biosynthesis, transcription factors, and fatty acid biosynthesis and protein kinases, which suggested that these pathways are affected by the adaptive responses of maize plants grown at high density. Research findings elucidated the molecular mechanisms underlying the physiological and biochemical responses of the leaves of maize planted at high density.

show abstract

RNA-Seq Profiling Shows Divergent Gene Expression Patterns in Arabidopsis Grown under Different Densities

Cited by 13 publications

References 28 publications

Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

Rapid metabolite response in leaf blade and petiole as a marker for shade avoidance syndrome

Transcriptional analyses of maize leaves in response to high‐density planting

Contact Info

Product

Resources

About