scholarly journals Genes, pathways and networks responding to drought stress in oil palm roots

2020 ◽  
Author(s):  
Le Wang ◽  
May Lee ◽  
baoqing Ye ◽  
Gen Hua Yue
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Ion Transport ◽  
Palm Oil ◽  
Stress Responses ◽  
Oil Palm ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Hormone Regulation ◽  
Transcriptomic Responses

Abstract Background: Palm oil is an important feedstock for biofuel. Palm oil yield is seriously affected by drought stress. However, not much is known about the molecular responses of oil palm to drought stress.Results: We studied the root transcriptomic responses of oil palm seedlings under normal culture and 14-day drought stress using RNA-seq and bioinformatics analysis. We identified 1293 differentially expressed genes (DEGs), involved in several molecular processes, such as cell wall biogenesis and functions, phenylpropanoid biosynthesis and metabolisms, ion transport and homeostasis and cellular ketone metabolic process, as well as small molecule biosynthetic process. We observed that DEGs were significantly enriched into the two categories: hormone regulation and metabolism, as well as ABC transporters. In addition, we identified three protein-protein interaction networks involved in the response to drought stress, including ion transport, reactive nitrogen species metabolic process and nitrate assimilation. Finally, 96 differentially expressed transcription factors were detected to be associated with drought stress response, which were classified into 28 families.Conclusions : The transcriptomic responses of oil palm seedlings to drought stress were systematically analysed, revealing important genes, pathways, networks and transcription factors involved in drought stress responses. These results provide new insights into the mechanisms of drought stress responses in economic crops. The genes and pathways identified in this study provide valuable genomic resources to improve drought tolerance of oil palm by both genetic modification and selective breeding.

scholarly journals Genes, pathways and networks responding to drought stress in oil palm roots

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Le Wang ◽  
May Lee ◽  
Baoqing Ye ◽  
Gen Hua Yue
Keyword(s):  
Drought Stress ◽  
Ion Transport ◽  
Stress Responses ◽  
Oil Palm ◽  
Nitrate Assimilation ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Oilseed Crop ◽  
Hormone Regulation ◽  
Protein Protein Interaction

AbstractOil palm is the most productive oilseed crop and its oil yield is seriously affected by frequent drought stress. However, little is known about the molecular responses of oil palm to drought stress. We studied the root transcriptomic responses of oil palm seedlings under 14-day drought stress. We identified 1293 differentially expressed genes (DEGs), involved in several molecular processes, including cell wall biogenesis and functions, phenylpropanoid biosynthesis and metabolisms, ion transport and homeostasis and cellular ketone metabolic process, as well as small molecule biosynthetic process. DEGs were significantly enriched into two categories: hormone regulation and metabolism, as well as ABC transporters. In addition, three protein–protein interaction networks: ion transport, reactive nitrogen species metabolic process and nitrate assimilation, were identified to be involved in drought stress responses. Finally, 96 differentially expressed transcription factors were detected to be associated with drought stress responses, which were classified into 28 families. These results provide not only novel insights into drought stress responses, but also valuable genomic resources to improve drought tolerance of oil palm by both genetic modification and selective breeding.

scholarly journals HARA STATUS OF POTASSIUM Absorption IN PRODUCING PALM OIL PLANT IN PERLABIAN VILLAGE, KAMPUNG RAKYAT DISTRICT, LABUHANBATU SELATAN DISTRICT

2021 ◽  
Vol 46 (2) ◽  
pp. 193
Author(s):  
Artisa Ainun ◽  
Hilwa Walida ◽  
Badrul Ainy Dalimunthe ◽  
Khairul Rizal
Keyword(s):  
Drought Stress ◽  
Nutrient Uptake ◽  
Palm Oil ◽  
Oil Palm ◽  
Survey Method ◽  
Grid Survey ◽  
The Status ◽  
Oil Plant ◽  
Potassium Absorption ◽  
Plastic Sample

Potassium is a macro nutrient that can affect the quality and quantity of oil palm bunches as well as resistance to disease and drought stress. So far, testing the status of potassium nutrient uptake in people's plantations in Perlabian Village, Kampung Rakyat Labuhanbatu Selatan District has never been carried out. Fertilization and maintenance are carried out through knowledge from generation to generation, so it is important to have a study on the nutrient uptake status of potassium in oil palm leaves. This research was conducted using a free grid survey method at the semi-detailed survey level with a density of 100 meters. A total of 6 leaf samples were taken on the 17th leaf midrib and then rubbed with 70% alcohol and then put into the plastic sample for further testing in the laboratory of PT. Socfindo. The results showed that the potassium in leaf samples 1, 3 and 4 experienced deficiency and leaf samples 2, 5 and 6 were at the optimum. In oil palm plantations in smallholder plantations in Perlabian Village, Kampung Rakyat Subdistrict, it shows that the total K content of leaves is included in the optimum category. 

scholarly journals Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Liang ◽  
Kunhua Wei ◽  
Fan Wei ◽  
Shuangshuang Qin ◽  
Chuanhua Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Small Rna ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Severe Drought ◽  
A Genome ◽  
Sophora Tonkinensis

Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

scholarly journals Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat

2020 ◽  
Author(s):  
Xiangchi Zhang ◽  
Weidan Lu ◽  
Xiaoli Wang ◽  
Bin Ma ◽  
Kaiyong Fu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Winter Wheat ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Phosphorus Level ◽  
Root Tips ◽  
Percentage Content ◽  
Low Phosphorus

Abstract Phosphorus stress and drought stress are common abiotic stresses. In this study, two winter wheat “Xindong20” and “Xindong23” were solution cultured and then treated with drought stress under conventional phosphorus level (CP: 1.0 mmol/L) and low phosphorus level (LP: 0.05 mmol /L), respectively. The results showed that with the increase of drought stress, the LP application was more conducive to the growth of root tips, length, forks, surfarea and root vitality of wheat. Under the LP treatment, the total phosphorus content of root at rewatered 3d was increased by 94.2% in Xindong20 wheat and decreased by 48.9% in Xindong23 wheat, compared with their respective samples at drought 0d. The LP treatment increased the percentage content of K and decreased the P and Ca percentage content. However, under CP treatment, the percentage content of Zn after rewatered 3 days were increased, compared with drought 7d. Based on the GeneChip analysis of root samples from drought 7d, the microarray results showed that 4577 and 202 differentially expressed genes were detected from Xindong20 and Xindong23, respectively. Among them, 89.9% of differentially expressed genes were involved in organelles and vesicles in Xindong20, and 69.8% were involved in genes encoding root anatomical structure, respiratory chain, electron transport chain, ion transport and enzyme activity in Xindong23. Therefore, the supply of low phosphorus has more effects on the drought tolerance of wheat, and the wheat with different drought tolerance has different regulatory genes. The higher drought-tolerant wheat has more genes up-regulation in response to drought stress.

scholarly journals Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton

2021 ◽  
Vol 22 (2) ◽  
pp. 898
Author(s):  
Muhammad Sajjad ◽  
Xi Wei ◽  
Lisen Liu ◽  
Fuguang Li ◽  
Xiaoyang Ge
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Plant Growth ◽  
Growth And Development ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Regulatory Pathways ◽  
Vascular Growth

Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.

scholarly journals Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress inBrassica rapaL. (Inbred Line “Chiifu”)

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Soon-Wook Kwon ◽  
Mijeong Kim ◽  
Hijin Kim ◽  
Joohyun Lee
Keyword(s):  
Drought Stress ◽  
Inbred Line ◽  
Stress Responses ◽  
Target Genes ◽  
Antioxidant Activities ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Family Protein

Through a comparative shotgun quantitative proteomics analysis inBrassica rapa(inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein.

scholarly journals Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fernanda Ferreira Salgado ◽  
Letícia Rios Vieira ◽  
Vivianny Nayse Belo Silva ◽  
André Pereira Leão ◽  
Priscila Grynberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Salinity Stress ◽  
Oil Palm ◽  
Functional Annotation ◽  
Target Genes ◽  
Early Response ◽  
Differentially Expressed ◽  
Putative Target

Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

scholarly journals Genome-wide analysis of AP2/ERF Transcription Factors in sugarcane Saccharum spontaneum L. Reveals Functional Divergence During Drought, Salt Stress and Plant Hormones Treatment

2020 ◽  
Author(s):  
Piting Li ◽  
Zhe Chai ◽  
Pingping Lin ◽  
Chaohua Huang ◽  
Guoqiang Huang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Drought Stress ◽  
Stress Responses ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Structure Evolution ◽  
Saccharum Spontaneum ◽  
Erf Transcription Factors

Abstract Background: APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play important roles in plant growth, development, metabolism, as well as in biotic and abiotic stress responses. However, there are few studies concerning AP2/ERF genes in sugarcane, which is the most critical sugar and energy crop worldwide. Results: A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs, and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV) and 4 Soloist genes. These genes were unevenly distributed on 32 chromosomes. Analysis of the structural of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum have a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflects their similarity. Multiple cis-regulatory elements (CREs) are present in the SsAP2/ERF promoter, and many are related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to the adaptation of sugarcane crops to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different stages of development. In 10 sugarcane samples, 39 SsAP2/ERFs were not expressed at all, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under drought stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 hours of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in ABA and GA-associated drought stress response mechanisms. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes play an important role in drought and salt stress responses of S. spontaneum. Conclusions: In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

scholarly journals VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

2020 ◽  
Author(s):  
Haley S. Toups ◽  
Noé Cochetel ◽  
Dennis Gray ◽  
Grant R. Cramer
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Berry Development ◽  
Rna Seq ◽  
Abiotic And Biotic Stresses ◽  
Vitis Species ◽  
Biotic Stresses ◽  
Similar Expression

Abstract Background: VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq. Results: A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions: VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

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