scholarly journals Unique transcriptome and gene expression analysis of rice seedling reveals different cadmium response regulatory mechanisms between indica and japonica rice

2020 ◽  
Author(s):  
Shan Tong ◽  
Xin Luo ◽  
Hira Khanzada ◽  
Ghulam Mustafa Wassan ◽  
Licao Cui ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Rice Seedling ◽  
Resistant Variety ◽  
Japonica Rice ◽  
Biological Processes ◽  
Cd Stress ◽  
Metabolic Pathway Analysis ◽  
Improvement Programs ◽  
Rice Improvement ◽  
Different Response

Abstract Background: In general, the Cd content in indica rice is higher than that in japonica. However, the mechanism underlying this discrepancy has not been elucidated. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is highly important for rice improvement programs.Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd, and seedlings of the two varieties at two critical stages (the 3rd and 5th day) were selected for dynamic gene analysis by the transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differentially expressed genes (DEGs) associated with Cd stress were detected on the 3rd day and 5th day, respectively. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathway analysis of DEGs preferentially expressed in a stage-specific and cultivar-specific manner showed that secondary metabolic processes were enriched in SCR, while protein metabolism and plant hormones were enriched in RCR. The diverted metabolic pathways might be the major reason for the different response mechanisms of Cd in indica and japonica rice.Conclusion: These results provide novel insights regarding the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might help to elucidate the mechanisms of the indica and japonica rice Cd response differences.

scholarly journals Unique Transcriptome and Gene Expression Analysis of Rice Seedling Reveals Different Cadmium Response Regulatory Mechanisms Between Indica and Japonica Rice

2020 ◽  
Author(s):  
Shan Tong ◽  
Xin Luo ◽  
Hira Khanzada ◽  
Ghulam Mustafa Wassan ◽  
Licao Cui ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Rice Seedling ◽  
Resistant Variety ◽  
Japonica Rice ◽  
Response Mechanism ◽  
Cd Stress ◽  
Pathways Analysis ◽  
Improvement Programs ◽  
Rice Improvement ◽  
Different Response

Abstract Background: In general, the Cd content in indica rice is usually higher than that in japonica. However, the mechanism for this discrepancy is unclear. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is extremely important for rice improvement programs.Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd and seedlings of the two varieties at two critical stages (3rd and 5th day) were selected for the dynamic genes analysis by transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differently expressed genes (DEGs) associated with Cd stress were detected at 3rd day and 5th day. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathways analysis of DEGs preferentially expressed in a stage-specific and cultivars-specific manner, and secondary metabolic processes were enriched in SCR while protein metabolism and plant hormone were enriched in RCR. The diverted metabolic pathways might be the major cause for different response mechanism of Cd in indica and japonica rice. Conclusion: These results provide a novel insight into the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might provide a novel insight over indica and japonica rice Cd response mechanism difference.

scholarly journals Combining Targeted Metabolite Analyses and Transcriptomics to Reveal Specific Chemical Composition and Associated Genes in Resistant Soybean Infected with Soybean Cyst Nematode

2020 ◽  
Author(s):  
Xue Shi ◽  
Qiansi Chen ◽  
Shiming Liu ◽  
Jiajun Wang ◽  
Deliang Peng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Cyst Nematode ◽  
Sphingolipid Metabolism ◽  
Resistant Variety ◽  
Biological Processes ◽  
Specific Chemical ◽  
Kegg Pathways ◽  
Before And After

Abstract Background: Soybean cyst nematode Heterodera glycines is one of the most devastating pathogens on soybean and causes severe annual yield loss worldwide. Different soybean varieties exhibit different responses to soybean cyst nematode infection at various levels, such as genomic, transcriptional, proteomic, and metabolomic levels. However, there were not yet any reports on the differential responses of resistant and susceptible soybeans infected with soybean cyst nematode by combining the metabolomic analyses and transcriptomics.Results: In this study, a highly-resistant variety PI 437654 and three susceptible varieties Williams 82, Zhonghuang 13 and Hefeng 47 were used as the test materials to clarify the differences in metabolites and transcriptomics between resistant and susceptible soybeans before and after SCN infection. A local metabolite-calibrated database was used to identify potential differential metabolites, and the differences of metabolites and metabolic pathways were compared between the resistant and susceptible soybean varieties after inoculation with SCN. Totally, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories including the metabolites/pathways overlapped among resistant and susceptible soybeans, specific in susceptible or resistant soybeans, respectively. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specifically differential metabolites such as significantly up-regulated nicotine and down-regulated D-aspartic acid, and their involved KEGG pathways such as tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolisms, sphingolipid metabolism and arginine biosynthesis were significantly changed and abundantly enriched in the resistant soybean, and likely played pivotal roles in defensing against SCN infection. Three key metabolites including N-acetyltranexamic acid, nicotine, and D, L-typotophan, which were found to be significantly up-regulated in the resistant soybean PI437654 infected by SCN, classified into two types and used for combination analyses with the transcriptomic expression profiling. Associated genes were predicted, and suggested their likely biological processes, cellular component, molecular function and involved pathways. Conclusions: Our results not only found out the potential novel metabolites and associated genes in the resistant response of soybean to soybean cyst nematode, but also provided new insights into the interactions between soybean and soybean cyst nematode.

scholarly journals Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 14 (1) ◽  
pp. 1
Author(s):  
Joko Prasetiyono ◽  
Nurul Hidayatun ◽  
Tasliah Tasliah
Keyword(s):  
Genetic Diversity ◽  
Morphological Characters ◽  
Snp Markers ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Rice Chromosomes ◽  
Improvement Programs ◽  
Rice Genotypes ◽  
Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

scholarly journals Redox Homeostasis and Metabolism in Cancer: A Complex Mechanism and Potential Targeted Therapeutics

2020 ◽  
Vol 21 (9) ◽  
pp. 3100 ◽  
Author(s):  
Alia Ghoneum ◽  
Ammar Yasser Abdulfattah ◽  
Bailey Olivia Warren ◽  
Junjun Shu ◽  
Neveen Said
Keyword(s):  
Cancer Cells ◽  
Cancer Progression ◽  
Metabolic Pathways ◽  
Redox Homeostasis ◽  
Ros Production ◽  
Biological Processes ◽  
Survival Pathways ◽  
Oncogenic Mutations ◽  
And Oxidative Stress ◽  
Shed Light

Reactive Oxygen Species or “ROS” encompass several molecules derived from oxygen that can oxidize other molecules and subsequently transition rapidly between species. The key roles of ROS in biological processes are cell signaling, biosynthetic processes, and host defense. In cancer cells, increased ROS production and oxidative stress are instigated by carcinogens, oncogenic mutations, and importantly, metabolic reprograming of the rapidly proliferating cancer cells. Increased ROS production activates myriad downstream survival pathways that further cancer progression and metastasis. In this review, we highlight the relation between ROS, the metabolic programing of cancer, and stromal and immune cells with emphasis on and the transcription machinery involved in redox homeostasis, metabolic programing and malignant phenotype. We also shed light on the therapeutic targeting of metabolic pathways generating ROS as we investigate: Orlistat, Biguandes, AICAR, 2 Deoxyglucose, CPI-613, and Etomoxir.

scholarly journals Transcriptome Reveals the Specificity of Phyllostachys edulis ‘Pachyloen’ Shoots at Different Developmental Stages

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 861 ◽  
Author(s):  
Yaping Hu ◽  
Ying Zhang ◽  
Jie Zhou ◽  
Guibing Wang ◽  
Qirong Guo
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Moso Bamboo ◽  
Biological Processes ◽  
Phyllostachys Edulis ◽  
Monthly Basis ◽  
Bamboo Shoots ◽  
Tyrosine Metabolism ◽  
Culm Wall ◽  
Cellular Components

Phyllostachys edulis ‘Pachyloen’ can have a stalk wall thickness of up to 2.5 cm at a height of 1.3 m, which is 1.8 times that of normal Moso bamboo (Phyllostachys edulis); this serves as an excellent cultivar, comprising both wood and bamboo shoots. We collected bamboo shoot samples of Phyllostachys edulis ‘Pachyloen’ and Moso bamboo on a monthly basis from September to April and used transcriptome sequencing to explore the differences in their development. The results showed that there were 666–1839 Phyllostachys edulis ‘Pachyloen’-specific genes at different developmental stages enriched in 20 biological processes, 15 cellular components, 12 molecular functions, and 137 metabolic pathways, 52 of which were significant. Among these, 27 metabolic pathways such as tyrosine metabolism and their uniquely expressed genes were found to play important roles in the thickening of Phyllostachys edulis ‘Pachyloen’. This study provides insights into the mechanisms underlying the thickening of the culm wall of Phyllostachys edulis ‘Pachyloen’.

Different response to Cd stress in domesticated and wild safflower (Carthamus spp.)

2019 ◽  
Vol 171 ◽  
pp. 321-328 ◽  
Author(s):  
Nasibeh Pourghasemian ◽  
Tommy Landberg ◽  
Parviz Ehsanzadeh ◽  
Maria Greger
Keyword(s):  
Cd Stress ◽  
Different Response ◽  
Wild Safflower

scholarly journals Characterization and potential of plant growth-promoting rhizobacteria on rice seedling growth and the effect on Xanthomonas oryzae pv. oryzae

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Haliatur Rahma ◽  
NURBAILIS ◽  
NILA KRISTINA
Keyword(s):  
Plant Growth ◽  
Seedling Growth ◽  
Plant Growth Promoting Rhizobacteria ◽  
Rice Seedling ◽  
Xanthomonas Oryzae ◽  
Resistant Variety ◽  
Dual Culture ◽  
Rice Seedlings ◽  
Plant Growth Promoting ◽  
Growth Promoting

Abstract. Rahma H, Nurbailis, Kristina N. 2019. Characterization and potential of plant growth-promoting rhizobacteria on rice seedling growth and the effect on Xanthomonas oryzae pv. oryzae. Biodiversitas 20: 3654-3661. Xanthomonas oryzae pv. oryzae (Xoo), a major limiting factor in rice production, and the use of resistant Xoo varieties have failed to control the bacterial pathogens as well as increased yield. It is due to the diversity in pathotypes, caused by environmental factors, the nature of resistant variety used, and gene mutation. The aims of this study were to select rhizobacterial strains with the potential of suppressing Xoo growth and promoting the growth of rice seedlings. This experiment was conducted in a completely randomized design (CRD) using seven rhizobacterial isolates selected through a dual culture test, with four replications. There were four isolates that potential in inhibiting the growth of Xoo, namely KJKB5.4, LMTSA5.4, Bacillus cereus AJ34, and Alcaligenes faecalis AJ14, with inhibition diameters greater than 11.50 mm. Rhizobacterial supernatant of 4 potential isolates has a zone of inhibition ranging from 12.25 to 24.00 mm. Four potential isolates were also able to solubilize phosphate, produce indole acetic acid (IAA) growth hormone, and siderophore, as well as enhance the growth of rice seedlings. Based on the nucleic acid sequencing of LMTSA5.4, KJKB5.4, and RK12 isolates were identified as Stenotrophomonas malthopilia strain LMG 958 (99.13%) accession NR 119220.1, Stenotrophomonas pavanii strain LMG 25348 (95.84%) accession NR 118008.1 and Ochrobactrum ciceri strain ca-34 (92.91%) accession NR115819.1.

scholarly journals Molecular characterization of metabolic subtypes of gastric cancer based on metabolism-related lncRNA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lingdi Li ◽  
Jianfei Ma
Keyword(s):  
Gastric Cancer ◽  
Metabolic Pathways ◽  
Metabolic Regulation ◽  
Protective Factor ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Underlying Mechanism ◽  
Functional Enrichment ◽  
Biological Processes

AbstractIncreasing evidence has demonstrated that lncRNAs are critical regulators in diverse biological processes, but the function of lncRNA in metabolic regulation remains largely unexplored. In this study, we evaluated the association between lncRNA and metabolic pathways and identified metabolism-related lncRNAs. Gastric cancer can be mainly subdivided into 2 clusters based on these metabolism-related lncRNA regulators. Comparative analysis shows that these subtypes are found to be highly consistent with previously identified subtypes based on other omics data. Functional enrichment analysis shows that they are enriched in distinct biological processes. Mutation analysis shows that ABCA13 is a protective factor in subtype C1 but a risk factor in C2. Analysis of chemotherapeutic and immunotherapeutic sensitivity shows that these subtypes tend to display distinct sensitivity to the same chemical drugs. In conclusion, these findings demonstrated the significance of lncRNA in metabolic regulation. These metabolism-related lncRNA regulators can improve our understanding of the underlying mechanism of lncRNAs and advance the research of immunotherapies in the clinical management of gastric cancer.

scholarly journals Metabolomic Interactions: An Insight into Health and Disease

2021 ◽  
pp. 61-67
Author(s):  
Maheswara Reddy Mallu ◽  
Shaik Mohammad Anjum ◽  
Sai Sri Samyutha Katravulapalli ◽  
Sri Sai Priya Avuthu ◽  
Koteswara Reddy Gujjula ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Human Body ◽  
Metabolic Pathways ◽  
Biological Processes ◽  
Therapeutic Treatment ◽  
The Past ◽  
Metabolic Functions ◽  
Health And Disease ◽  
Metabolic Reactions ◽  
Insight Into

Over the past decade, metabolic engineering has emerged as an active and distinct discipline characterized by its over-arching emphasis on integration. In practice, metabolic engineering is the directed improvement of cellular properties through the application of modern genetic methods. The concept of metabolic regulations deals with the varied and innumerable metabolic pathways that are present in the human body. A combination of such metabolic reactions paves the way to the proper functioning of different physiological and biological processes. Dealing with the adversities of a disease, engineering of novel metabolic pathways showcases the potential of metabolic engineering and its application in the therapeutic treatment of diseases. A proper and deeper understanding of the metabolic functions in the human body can be known from simulated yeast models. This review gives a brief understanding about the interactions between the molecular set of metabolome and its complexity.

scholarly journals Multifarious Roles of GRAS Transcription Factors in Plants

2021 ◽  
Author(s):  
Priya Kumari ◽  
Mrinalini Kakkar ◽  
Vijay Gahlaut ◽  
Vandana Jaiswal ◽  
Sanjay Kumar
Keyword(s):  
Stress Responses ◽  
Crop Improvement ◽  
Structural Features ◽  
Biological Processes ◽  
Interacting Proteins ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Conserved Domain ◽  
Improvement Programs ◽  
Transcription Factor Gene Family

The GAI‐RGA ‐ and ‐SCR (GRAS) proteins belong to the plant-specific transcription factor gene family and involved in several developmental processes, phytohormone and phytochrome signaling, symbiosis, stress responses etc. GRAS proteins have a conserved GRAS domain at C-terminal and hypervariable N-terminal. The C-terminal conserved domain directly affects the function of the GRAS proteins. For instance, in Arabidopsis, mutations in this domain in Slender rice 1 (SLR1) and Repressor of GA (RGA) proteins cause significant phenotypic changes. GRAS proteins have been reported in more than 30 plant species and till now it has been divided into 17 subfamilies. This review highlighted GRAS protein's importance during several biological processes in plants, structural features of GRAS proteins, their expansion and diversification in the plants, GRAS-interacting proteins complexes and their role in biological processes. We also summarized available recent research that utilized CRISPR-Cas9 technology to manipulate GRAS genes in a plant for different traits. Further, the exploitation of GRAS genes in crop improvement programs has also been discussed

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