scholarly journals Transcriptome and mebabolomic profiling: the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

2020 ◽  
Author(s):  
Dejin Xie ◽  
Lingyan Chen ◽  
Chengcheng Zhou ◽  
Muhammad Waqqas Khan Tarin ◽  
Deming Yang ◽  
...  
Keyword(s):  
Leaf Area ◽  
Molecular Mechanism ◽  
Red Light ◽  
Chinese Herb ◽  
Leaf Tissue ◽  
Transcriptome Profiling ◽  
Accumulation Pattern ◽  
Phenylpropanoid Biosynthesis ◽  
Myb Proteins ◽  
Almost All

Abstract Background Sarcandra glabra is an evergreen and traditional Chinese herb, having medicinal significance as anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor. Recently, China has initiated to establish cultivation of this plant in greenhouse under artificial light-emitting diodes (LED). However, little is known regarding the effects of the different LED lights on plant growth, accumulation pattern of secondary metabolites, and the molecular mechanism of Sarcandra glabra. Results Compared to white light (WL), the red light (RL) increased the height and decreased the stem diameter and leaf area, while blue light (BL) suppressed the height and leaf area. According to our transcriptome profiling, some differentially expressed genes (DEGs) were enriched in the phenylpropanoid biosynthesis. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, while the expression level of RNA-seq and qPCR were largely consistent. Meanwhile, we found 53 unigenes encoding R2R3-MYB proteins and 53 unigenes encoding bHLH proteins that several of them were related to flavonoids biosynthesis. Based on metabolomic profiling, a total of 454 metabolites were detected and the distribution of chemicals varied significantly. While flavonoids, phenolic acids, and tannins were mainly located in leaves; Organic acids, lignans and coumarins, and terpenoids were much more abundant in WG (root tissue under WL). Meanwhile, the yields of most flavonoids from BY (leaf tissue under BL) and the synthesis of primarily targeted compounds was lower than in WY (leaf tissue under WL) and RY (leaf tissue under RL). Instead, the leaves grown under RL exhibited a greater production of bioactive phytochemicals such as esculetin, fraxetin, esculin, and scopoletin. Conclusion These results provide further insight into the molecular mechanism of metabolites accumulation patterns in S. glabra under different light conditions, enabling the development of optimum breeding conditions for this plant.

scholarly journals Transcriptomic and metabolomic profiling reveals  the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds  accumulation in Sarcandra glabra seedlings

2020 ◽  
Author(s):  
Dejin Xie ◽  
Lingyan Chen ◽  
Chengcheng Zhou ◽  
Muhammad Waqqas Khan Tarin ◽  
Deming Yang ◽  
...  
Keyword(s):  
Leaf Area ◽  
Regulatory Mechanism ◽  
Chinese Herb ◽  
Leaf Tissue ◽  
Led Light ◽  
Metabolomic Profiling ◽  
Coa Ligase ◽  
Red Led ◽  
Myb Proteins ◽  
Almost All

Abstract Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Recently, artificial light-emitting diodes (LEDs) have been widely used as energy for plants in greenhouse. However, little is known regarding the effects of the different LED lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds accumulation patterns in S. glabra. Results: Compared to white LED light (WL), the red LED light (RL) significantly increased the plant height and decreased the stem diameter and leaf area, whereas blue LED light (BL) significantly suppressed the height and leaf area of S. glabra. According to the results of transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs leaf tissue under RL (RY), BY vs leaf tissue under WL (WY), RY vs WY, root tissue under WL (WG) vs WY, stem tissue under WL (WJ) vs WG, and WJ vs WY, respectively. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), 4-coumaroyl CoA ligase (4CL), chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), and flavonol synthase (FLS). We found 53 unigenes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. Based on metabolomic profiling, a total of 454 metabolites were identified, of which 44, 87, and 296 compounds were differentially produced in WY vs RY, WY vs BY, and WY vs WG, respectively. In BY, the production of esculetin, caffeic acid, isofraxidin, and fraxidin were significantly reduced, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol were significantly decreased. In addition, the production of metabolites (e.g., chlorogenic acid, cryptochlorogenic acid, and scopolin) were significantly reduced, whereas the yields of metabolites (e.g., esculetin, fraxetin, isofraxidin, and fraxidin) were significantly promoted in WG. Conclusion: These results provide further insight into the regulatory mechanism of phenylpropanoid-derived compounds accumulation patterns in S. glabra under different light conditions, enabling the development of optimum breeding conditions for this plant.

scholarly journals Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Xueqiang Cui ◽  
Jieling Deng ◽  
Changyan Huang ◽  
Xuan Tang ◽  
Xianmin Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Transcriptome Profiling ◽  
Flower Color ◽  
Flower Bud ◽  
Color Formation ◽  
Color Development ◽  
Purple Coloration ◽  
Purple Color

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

scholarly journals Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Meat Quality ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Protein Protein Interaction ◽  
Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Transcriptome-Based Analysis of Phosphite-Induced Resistance against Pathogens in Rice

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1334
Author(s):  
Yuqing Huang ◽  
Shengguan Cai ◽  
Guoping Zhang ◽  
Songlin Ruan
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanism ◽  
Differentially Expressed Genes ◽  
Induced Resistance ◽  
Plant Hormone ◽  
Xanthomonas Oryzae ◽  
Pyricularia Grisea ◽  
Protection Effect ◽  
Phenylpropanoid Biosynthesis ◽  
Xanthomonas Oryzae Pv.Oryzae

Phosphite (PHI) has been used in the management of Phytophthora diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of Xanthomonas oryzae pv.oryzae and Pyricularia grisea. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.

Red-light effect on tracer distribution in etiolated leaf tissue

Planta ◽  
1967 ◽  
Vol 76 (2) ◽  
pp. 190-196 ◽  
Author(s):  
K. Mitrakos ◽  
L. Price ◽  
W. H. Klein ◽  
A. Steiner
Keyword(s):  
Red Light ◽  
Leaf Tissue ◽  
Light Effect ◽  
Tracer Distribution

Transcriptomic and metabolomic profiling reveals the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

2020 ◽  
Author(s):  
Dejin Xie ◽  
Lingyan Chen ◽  
Chengcheng Zhou ◽  
Muhammad Waqqas Khan Tarin ◽  
Deming Yang ◽  
...  
Keyword(s):  
Leaf Area ◽  
Regulatory Mechanism ◽  
Substantial Reduction ◽  
Leaf Tissue ◽  
Influential Factor ◽  
Led Light ◽  
Metabolomic Profiling ◽  
Red Led ◽  
Genes Encoding ◽  
The Impact

Abstract Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. Results: The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin).Conclusion: These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.

Carbon Dioxide Assimilation by Pineapple Plants, Ananas comosus (L.) Merr. I. Effects of Daily Irradiance

1980 ◽  
Vol 7 (4) ◽  
pp. 363 ◽  
Author(s):  
PJM Sale ◽  
TF Neales
Keyword(s):  
Leaf Area ◽  
Leaf Tissue ◽  
Extended Period ◽  
Titratable Acidity ◽  
Dry Weight ◽  
Co2 Assimilation ◽  
Co2 Exchange ◽  
Ananas Comosus ◽  
Molar Ratio ◽  
Weight Changes

Net carbon exchange over 24-h cycles was measured in well watered pineapple plants, using a 'minicrop' in field assimilation chambers and single leaves in a growth cabinet. Whole plants under natural light and a standard 30°C day/15°C night regime showed crassulacean acid metabolism, nearly all assimilation occurring in the dark period, with a net efflux of CO2 in the day. Assimilation, as measured by both CO2 exchange and changes in titratable acidity in the leaf tissue, was markedly dependent on the total photosynthetically active radiation incident in the previous photoperiod. The molar ratio of the maximum acidity change to maximum net nocturnal CO2 influx was 1.8 : 1. The rate of deacidification depended on the irradiance in the current photoperiod. Efflux in the photoperiod was largely independent of irradiance, but was greater at very low irradiances. Maximum rates of CO2 assimilation in the minicrop were about 15 ng cm-2 (leaf area) s-1 in the dark at the standard temperature regime, and 22 ng-2 s-1 when photoperiod assimilation was induced by a 20°C day/30°C night regime. Similar rates were recorded in the single-leaf experiments, and are higher than those previously found for pineapple. Over a 24-h period, mean rates of about 6 ng cm-2 (leaf area) s-1 were recorded, in good agreement with measured dry weight changes over an extended period. These data help to explain earlier discrepancies in the literature between measured rates of CO2 assimilation and of crop growth rates in pineapples.

scholarly journals Convergence in leaf size versus twig leaf area scaling: do plants optimize leaf area partitioning?

2016 ◽  
Vol 119 (3) ◽  
pp. 447-456 ◽  
Author(s):  
Duncan D. Smith ◽  
John S. Sperry ◽  
Frederick R. Adler
Keyword(s):  
Leaf Area ◽  
Leaf Tissue ◽  
Leaf Size ◽  
Similar Species ◽  
Exact Nature ◽  
Canopy Opening ◽  
Scaling Relationship ◽  
Cornus Sericea ◽  
Tentative Explanation ◽  
The Cost

Background and Aims Corner’s rule states that thicker twigs bear larger leaves. The exact nature of this relationship and why it should occur has been the subject of numerous studies. It is obvious that thicker twigs should support greater total leaf area (Atwig) for hydraulical and mechanical reasons. But it is not obvious why mean leaf size (A-) should scale positively with Atwig. We asked what this scaling relationship is within species and how variable it is across species. We then developed a model to explain why these relationships exist. Methods To minimize potential sources of variability, we compared twig properties from six co-occurring and functionally similar species: Acer grandidentatum, Amelanchier alnifolia, Betula occidentalis, Cornus sericea, Populus fremontii and Symphoricarpos oreophilus. We modelled the economics of leaf display, weighing the benefit from light absorption against the cost of leaf tissue, to predict the optimal A- :Atwig combinations under different canopy openings. Key Results We observed a common A- by Atwig exponent of 0.6, meaning that A -and leaf number on twigs increased in a specific coordination. Common scaling exponents were not supported for relationships between any other measured twig properties. The model consistently predicted positive A- by Atwig scaling when twigs optimally filled canopy openings. The observed 0·6 exponent was predicted when self-shading decreased with larger canopy opening. Conclusions Our results suggest Corner’s rule may be better understood when recast as positive A- by Atwig scaling. Our model provides a tentative explanation of observed A- by Atwig scaling and suggests different scaling may exist in different environments.

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