scholarly journals Transcriptome Profiling Reveals Effects of Drought Stress on Gene Expression in Diploid Potato Genotype P3-198

2019 ◽  
Vol 20 (4) ◽  
pp. 852 ◽  
Author(s):  
Xiaohui Yang ◽  
Jie Liu ◽  
Jianfei Xu ◽  
Shaoguang Duan ◽  
Qianru Wang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Signaling Pathway ◽  
Drought Resistance ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Solanum Tuberosum L ◽  
Differentially Expressed ◽  
Protein Kinase Activity ◽  
Diploid Potato ◽  
Potato Genotype

Potato (Solanum tuberosum L.) is one of the three most important food crops worldwide; however, it is strongly affected by drought stress. The precise molecular mechanisms of drought stress response in potato are not very well understood. The diploid potato genotype P3-198 has been verified to be highly resistant to drought stress. Here, a time-course experiment was performed to identify drought resistance response genes in P3-198 under polyethylene glycol (PEG)-induced stress using RNA-sequencing. A total of 1665 differentially expressed genes (DEGs) were specifically identified, and based on gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the transcription factor activity, protein kinase activity, and the plant hormone signal transduction process were significantly enriched. Annotation revealed that these DEGs mainly encode transcription factors, protein kinases, and proteins related to redox regulation, carbohydrate metabolism, and osmotic adjustment. In particular, genes encoding abscisic acid (ABA)-dependent signaling molecules were significantly differentially expressed, which revealed the important roles of the ABA-dependent signaling pathway in the early response of P3-198 to drought stress. Quantitative real-time PCR experimental verification confirmed the differential expression of genes in the drought resistance signaling pathway. Our results provide valuable information for understanding potato drought-resistance mechanisms, and also enrich the gene resources available for drought-resistant potato breeding.

scholarly journals Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress

2022 ◽  
Vol 23 (1) ◽  
pp. 569
Author(s):  
Peiting Li ◽  
Pingping Lin ◽  
Zhenli Zhao ◽  
Zihong Li ◽  
Yanming Liu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Signaling Pathway ◽  
High Performance ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Future Research ◽  
Sugarcane Varieties ◽  
Significant Enrichment ◽  
Drought Resistant

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.

scholarly journals Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon)

2017 ◽  
Vol 37 (3) ◽  
Author(s):  
Fantao Zhang ◽  
Yi Zhou ◽  
Meng Zhang ◽  
Xiangdong Luo ◽  
Jiankun Xie
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Wild Rice ◽  
Molecular Mechanisms ◽  
Oryza Rufipogon ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Regulatory Pathways ◽  
Drought Resistant ◽  
Dongxiang Wild Rice

Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice (Oryza rufipogon, DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars.

scholarly journals Arabidopsis MADS-box factor AGL16 negatively regulates drought resistance via stomatal density and stomatal movement

2020 ◽  
Vol 71 (19) ◽  
pp. 6092-6106 ◽  
Author(s):  
Ping-Xia Zhao ◽  
Zi-Qing Miao ◽  
Jing Zhang ◽  
Si-Yan Chen ◽  
Qian-Qian Liu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Stomatal Density ◽  
Stomatal Closure ◽  
Negative Regulator ◽  
Stomatal Development ◽  
Mads Box ◽  
Mobility Shift ◽  
Aba Metabolism

Abstract Drought is one of the most important environmental factors limiting plant growth and productivity. The molecular mechanisms underlying plant drought resistance are complex and not yet fully understood. Here, we show that the Arabidopsis MADS-box transcription factor AGL16 acts as a negative regulator in drought resistance by regulating stomatal density and movement. Loss-of-AGL16 mutants were more resistant to drought stress and had higher relative water content, which was attributed to lower leaf stomatal density and more sensitive stomatal closure due to higher leaf ABA levels compared with the wild type. AGL16-overexpressing lines displayed the opposite phenotypes. AGL16 is preferentially expressed in guard cells and down-regulated in response to drought stress. The expression of CYP707A3 and AAO3 in ABA metabolism and SDD1 in stomatal development was altered in agl16 and overexpression lines, making them potential targets of AGL16. Using chromatin immunoprecipitation, transient transactivation, yeast one-hybrid, and electrophoretic mobility shift assays, we demonstrated that AGL16 was able to bind the CArG motifs in the promoters of the CYP707A3, AAO3, and SDD1 and regulate their transcription, leading to altered leaf stomatal density and ABA levels. Taking our findings together, AGL16 acts as a negative regulator of drought resistance by modulating leaf stomatal density and ABA accumulation.

An ABA-flavonoid relationship contributes to the differences in drought resistance between different sea buckthorn subspecies

2020 ◽  
Author(s):  
Guori Gao ◽  
Zhongrui Lv ◽  
Guoyun Zhang ◽  
Jiayi Li ◽  
Jianguo Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Normal Growth ◽  
Carotenoid Biosynthesis ◽  
Sea Buckthorn ◽  
Mutual Regulation ◽  
The Difference

Abstract Drought is the most severe abiotic stress and hinders the normal growth and development of plants. Sea buckthorn (Hippophae rhamnoides Linn.) is a typical drought-resistant tree species. In this study, the leaves of the H. rhamnoides ssp. sinensis (“FN”) and H. rhamnoides ssp. mongolica (“XY”) were selected during drought-recovery cycles for RNA sequencing, and physiological and biochemical analyses. The results revealed that drought stress significantly decreased leaf water potential, net photosynthetic rate, and stomatal conductance in both sea buckthorn subspecies. Similarly, the contents of flavone, flavonol, isoflavone and flavanone significantly decreased under drought stress in “XY.” Conversely, in “FN,” the flavone and abscisic acid (ABA) contents were significantly higher under drought stress and recovered after rehydration. Meanwhile, 4,618 and 6,100 differentially expressed genes (DEGs) were identified under drought stress in “FN” and “XY,” respectively. In total, 5,164 DEGs were observed in the comparison between “FN” and “XY” under drought stress. This was more than the 3,821 and 3,387 DEGs found when comparing the subspecies under control and rehydration conditions, respectively. These DEGs were mainly associated with carotenoid biosynthesis, flavonoid biosynthesis, photosynthesis, and plant hormone signal transduction. Six hub DEGs (ABCG5, ABCG22, ABCG32, ABCG36, ABF2 and PYL4) were identified to respond to drought stress based on WGCNA and BLAST analysis using DroughtDB. These six DEGs were annotated to play roles in the ABA-dependent signaling pathway. Sixteen RNA sequencing results involving eight genes and similar expression patterns (12/16) were validated using quantitative real-time PCR. The biochemical and molecular mechanisms underlying the regulation of drought responses by ABA and flavonoids in sea buckthorn were clarified. In this study, gene co-expression networks were constructed, and the results suggested that the mutual regulation of ABA and flavonoid signaling contributed to the difference in drought resistance between the different sea buckthorn subspecies.

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

scholarly journals Identification of Differentially Expressed Kinase and Screening Potential Anticancer Drugs in Papillary Thyroid Carcinoma

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Huairong Zhang ◽  
Bo Gao ◽  
Bingyin Shi
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Signaling Pathway ◽  
Protein Kinases ◽  
Molecular Mechanisms ◽  
Kinase Inhibitors ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Papillary Thyroid

Aim. We aim to identify protein kinases involved in the pathophysiology of papillary thyroid carcinoma (PTC) in order to provide potential therapeutic targets for kinase inhibitors and unfold possible molecular mechanisms.Materials and Methods. The gene expression profile of GSE27155 was analyzed to identify differentially expressed genes and mapped onto human protein kinases database. Correlation of kinases with PTC was addressed by systematic literature search, GO and KEGG pathway analysis.Results. The functional enrichment analysis indicated that “mitogen-activated protein kinases pathway” expression was extremely enriched, followed by “neurotrophin signaling pathway,” “focal adhesion,” and “GnRH signaling pathway.” MAPK, SRC, PDGFRa, ErbB, and EGFR were significantly regulated to correct these pathways. Kinases investigated by the literature on carcinoma were considered to be potential novel molecular therapeutic target in PTC and application of corresponding kinase inhibitors could be possible therapeutic tool.Conclusion. SRC, MAPK, and EGFR were the most important differentially expressed kinases in PTC. Combined inhibitors may have high efficacy in PTC treatment by targeting these kinases.

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 Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Shi ◽  
Wei Jiao ◽  
Lan Yun ◽  
Zhiqiang Zhang ◽  
Xiujuan Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Small Rna ◽  
Mirna Target ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Limiting Factor ◽  
Degradome Sequencing ◽  
Medicago Ruthenica

Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

scholarly journals Genome-Wide Regulation of Acupuncture and Moxibustion on Ulcerative Colitis Rats

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Zhaoqin Wang ◽  
Yan Huang ◽  
Di Wang ◽  
Rumeng Wang ◽  
Kunshan Li ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Wnt Signaling Pathway ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Clinical Effects ◽  
Sprague Dawley ◽  
Acupuncture And Moxibustion

Acupuncture and moxibustion have definite clinical effects on treating ulcerative colitis (UC), but their mechanism is still unclear. To investigate the molecular mechanisms, we applied herb-partitioned moxibustion or electroacupuncture at the Tianshu (ST25) points on UC rats and used RNA sequencing to identify molecular consequences. Male Sprague Dawley (SD) rats were divided into 6 groups randomly: the normal control (NC) group, the control + herb-partitioned moxibustion (NCHM) group, the control + electroacupuncture (NCEA) group, the model (UC) group, the model + herb-partitioned moxibustion (UCHM) group, and the model + electroacupuncture (UCEA) group. Compared to the UC group, HE staining in the UCHM group and UCEA group indicated that colitis was relieved, the histopathological score and MPO were both significantly reduced, and the serum hs-CRP concentration was decreased significantly. The results of RNA-seq suggested that, compared to the NC group, 206 upregulated genes and 167 downregulated genes were identified in colon tissues from the UC group; compared to the UC group, the expression levels of some genes were both affected in the UCHM group and the UCEA group (684 differentially expressed genes were identified in the UCHM group, and 1182 differentially expressed genes were identified in the UCEA group). KEGG signal pathway analysis indicated that the differentially expressed genes in the UCHM group were associated with the JAK-STAT signaling pathway and cell adhesion molecule (CAM); the differentially expressed genes in the UCEA group were associated with the NF-κB signaling pathway, the toll-like receptor signaling pathways, the PI3K-Akt signaling pathway, the MAPK signaling pathway, and the Wnt signaling pathway. This is the first study to reveal the gene expression characteristics of the anti-inflammatory effect of UC rats from the perspective of acupuncture and moxibustion control, which provide a clue for further investigation into the molecular mechanisms of UC treatment by acupuncture and moxibustion.

scholarly journals Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Kejun Wang ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

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