scholarly journals Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

2019 ◽  
Vol 20 (17) ◽  
pp. 4303 ◽  
Author(s):  
Hongyou Li ◽  
Qiuyu Lv ◽  
Jiao Deng ◽  
Juan Huang ◽  
Fang Cai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Development ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fagopyrum Esculentum ◽  
Rna Seq ◽  
Common Buckwheat ◽  
Size Change ◽  
Key Genes

Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

Detection of a Major QTL and Development of KASP Markers for Seed Weight by Combining QTL-seq, QTL-mapping and RNA-seq in Peanut

2021 ◽  
Author(s):  
Zhihui Wang ◽  
Liying Yan ◽  
Yuning Chen ◽  
Xin Wang ◽  
Dongxin Huai ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Seed Development ◽  
Seed Weight ◽  
Molecular Mechanisms ◽  
Large Contribution ◽  
Phenotypic Variance ◽  
Rna Seq ◽  
Late Stages ◽  
Kasp Markers

Abstract Seed weight is a major target of peanut breeding as an important component of seed yield. However, relatively little is known about QTLs and candidate genes associated with seed weight in peanut. In this study, three major QTLs on chromosomes A05, B02 and B06 were determined by applying NGS-based QTL-seq approach for a RIL population. These three QTL regions have been successfully narrowed down through newly developed SNP and SSR markers based on traditional QTL mapping. Among these three QTL regions, qSWB06.3 exhibited stable expression with large contribution to phenotypic variance across all environments. Furthermore, RNA-seq were applied for early, middle and late stages of seed development, and differentially expression genes (DEGs) were identified in ubiquitin-proteasome pathway, serine/threonine protein pathway and signal transduction of hormones and transcription factors. Notably, DEGs at early stage were majorly related to regulating cell division, whereas DEGs at middle and late stages were mainly associated with cell expansion during seed development. Through integrating SNP variation, gene expression and functional annotation, candidate genes related to seed weight in qSWB06.3 were predicted and distinct expression pattern of those genes were exhibited using qRT-PCR. In addition, KASP-markers in qSWB06.3 were successfully validated in diverse peanut varieties and the alleles of parent Zhonghua16 in qSWB06.3 was associated with high seed weight. This suggested that qSWB06.3 was reliable and the markers in qSWB06.3 could be deployed in marker-assisted breeding to enhance seed weight. This study provided insights into the understanding of genetic and molecular mechanisms of seed weight in peanut.

scholarly journals Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb.

2020 ◽  
Author(s):  
Zhiheng Huang ◽  
Ke Bao ◽  
Zonghui Jin ◽  
Qian Wang ◽  
Huifang Duan ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Potential Role ◽  
Growth Stages ◽  
Transduction Pathway ◽  
Rna Seq ◽  
Market Growth ◽  
Euryale Ferox ◽  
Indole 3 Acetic Acid

Abstract Background: Aquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Unveiling the control of seed size is of remarkable importance in improvement of crops. Here, we generated a new hybrid line (HL) with larger seeds by crossing South Gordon Euryale and North Gordon Euryale (WT) which hasn’t been reported before. However, the functional genes and molecular mechanisms controlling the seed size in Euryale ferox Salisb. remain unclear. In this study, we focused on the exploration of candidate regulatory genes participated in regulating seed size by investigating the new hybrid generation. Results: Both concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism and to seek the key genes underlying this difference, RNA-seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis. Conclusion: Hybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs (SAURs) -mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.

scholarly journals De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.)

2019 ◽  
Vol 69 (3) ◽  
pp. 487-497 ◽  
Author(s):  
Xiaomei Fang ◽  
Yuanli Zhang ◽  
Yuke Zhang ◽  
Kehui Huang ◽  
Wenjuan Yang ◽  
...  
Keyword(s):  
Seed Size ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Fagopyrum Esculentum ◽  
Common Buckwheat

scholarly journals Genes involved in brassinosteroids's metabolism and signal transduction pathways

2007 ◽  
Vol 50 (4) ◽  
pp. 605-618 ◽  
Author(s):  
Adaucto Bellarmino Pereira-Netto
Keyword(s):  
Signal Transduction ◽  
Biosynthetic Pathway ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Normal Growth ◽  
The Past ◽  
C 23 ◽  
Pathway Regulation ◽  
Regulation Of Cell Cycle

Brassinosteroids (BRs) are plant steroids essential for the normal growth and development, which carry an oxygen moiety at C-3 and additional ones at one or more of the C-2, C-6, C-22 and C-23 carbon atoms. In the past few years, application of molecular genetics allowed significant progress on the understanding of the BRs biosynthetic pathway regulation and on the identification of several components of their signal transduction pathway, as well. Search in eletronic databases show dozens of records for brassinosteroid-related genes for the last twelve months, demonstrating the big efforts being carried out in this field. This review highlights the recent advances on the characterization of genes and mutations that are helping to unravel the molecular mechanisms involved in the BRs synthesis/metabolism, perception and response, with especial emphasis on their role in plant cell elongation. Aspects of the involvement of BRs on the regulation of cell cycle-controlling proteins are discussed as well.

scholarly journals Regulation of AMPA receptor subunit GluA1 surface expression by PAK3 phosphorylation

2015 ◽  
Vol 112 (43) ◽  
pp. E5883-E5890 ◽  
Author(s):  
Natasha K. Hussain ◽  
Gareth M. Thomas ◽  
Junjie Luo ◽  
Richard L. Huganir
Keyword(s):  
Signal Transduction ◽  
Synaptic Plasticity ◽  
Ampa Receptors ◽  
Cortical Neurons ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Cognitive Disorders ◽  
Surface Expression ◽  
Nucleotide Exchange

AMPA receptors (AMPARs) are the major excitatory receptors of the brain and are fundamental to synaptic plasticity, memory, and cognition. Dynamic recycling of AMPARs in neurons is regulated through several types of posttranslational modification, including phosphorylation. Here, we identify a previously unidentified signal transduction cascade that modulates phosphorylation of serine residue 863 (S863) in the GluA1 AMPAR subunit and controls surface trafficking of GluA1 in neurons. Activation of the EphR–Ephrin signal transduction pathway enhances S863 phosphorylation. Further, EphB2 can interact with Zizimin1, a guanine–nucleotide exchange factor that activates Cdc42 and stimulates S863 phosphorylation in neurons. Among the numerous targets downstream of Cdc42, we determined that the p21-activated kinase-3 (PAK3) phosphorylates S863 in vitro. Moreover, specific loss of PAK3 expression and pharmacological inhibition of PAK both disrupt activity-dependent phosphorylation of S863 in cortical neurons. EphB2, Cdc42, and PAKs are broadly capable of controlling dendritic spine formation and synaptic plasticity and are implicated in multiple cognitive disorders. Collectively, these data delineate a novel signal cascade regulating AMPAR trafficking that may contribute to the molecular mechanisms that govern learning and cognition.

scholarly journals An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments

2009 ◽  
Vol 3 ◽  
pp. BBI.S3485
Author(s):  
Haiyan Hu
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Efficient Method ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Signal Transduction Pathway ◽  
Protein Interaction Data ◽  
Transduction Pathway ◽  
Binding Data ◽  
Microarray Datasets

A signal transduction pathway (STP) is a cascade composed of a series of signal transferring steps, which often activate one or more transcription factors (TFs) to control the transcription of target genes. Understanding signaling pathways is important to our understanding of the molecular mechanisms of disease. Many condition-annotated pathways have been deposited in public databases. However, condition-annotated pathways are far from complete, considering the large number of possible conditions. Computational methods to assist in the identification of conditionally activated pathways are greatly needed. In this paper, we propose an efficient method to identify conditionally activated pathway segments starting from the identification of conditionally activated TFs, by incorporating protein-DNA binding data, gene expression data and protein interaction data. Applying our methods on several microarray datasets, we have discovered many significantly activated TFs and their corresponding pathway segments, which are supported by evidence in the literature.

scholarly journals Key Cannabis Salt-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Varieties

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2338
Author(s):  
Jiangjiang Zhang ◽  
Cuiping Zhang ◽  
Siqi Huang ◽  
Li Chang ◽  
Jianjun Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Mapk Signaling ◽  
Molecular Networks ◽  
Molecular Response ◽  
Rna Seq ◽  
Physiological Diversity ◽  
Phenylpropanoid Biosynthesis

For the dissection and identification of the molecular response mechanisms to salt stress in cannabis, an experiment was conducted surveying the diversity of physiological characteristics. RNA-seq profiling was carried out to identify differential expression genes and pathway which respond to salt stress in different cannabis materials. The result of physiological diversity analyses showed that it is more sensitive to proline contents in K94 than in W20; 6 h was needed to reach the maximum in K94, compared to 12 h in W20. For profiling 0–72 h after treatment, a total of 10,149 differentially expressed genes were identified, and 249 genes exhibited significantly diverse expression levels in K94, which were clustered in plant hormone signal transduction and the MAPK signaling pathway. A total of 371 genes showed significant diversity expression variations in W20, which were clustered in the phenylpropanoid biosynthesis and plant hormone signal transduction pathway. The pathway enrichment by genes which were identified in K94 and W20 showed a similar trend to those clustered in plant hormone signal transduction pathways and MAPK signaling. Otherwise, there were 85 genes which identified overlaps between the two materials, indicating that these may be underlying genes related to salt stress in cannabis. The 86.67% agreement of the RNA-seq and qRT-PCR indicated the accuracy and reliability of the RNA-seq technique. Additionally, the result of physiological diversity was consistent with the predicted RNA-seq-based findings. This research may offer new insights into the molecular networks mediating cannabis to respond to salt stress.

scholarly journals Genome-wide characterization of Rice Black Streaked Dwarf Virus-responsive genes in rice

2020 ◽  
Vol 5 (2) ◽  
pp. 66-82
Author(s):  
Wei Liu ◽  
◽  
Zhen Li ◽  
Qingguo Wang ◽  
Jiaowen Pan ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Cell Structure ◽  
Brown Planthopper ◽  
Digital Gene Expression ◽  
Dwarf Virus ◽  
Rna Seq ◽  
Digital Gene Expression Profile ◽  
Dark Green

Background: Rice black streaked dwarf virus (RBSDV) is an important pathogen disease in rice and gramineous planting regions all over the world. The major phenotypes of RBSDV infected rice were dwarf with dark green leaves, which generally resulted in seriously loss of yield. The RBSDV known so far is preoperatively transmitted to rice in a persistent manner by small brown planthopper (SBPH), instead of transmitting to offspring through ovary. Results: To identify RBSDV responsive genes and to explore and clarify the molecular mechanisms involved in plant-virus interaction, digital gene expression profile (DGE) analysis was performed by high-throughput sequencing using wild-type (WT) and RBSDV infected rice leaves (IRL) as materials. A total of 165,975 and 165,940 unique tags were obtained in IRL and WT libraries, respectively. In comparison with the control, 896 differentially expressed genes (DEGs) were obtained, of which 500 DEGs were up regulated and 396 DEGs were down regulated. Functional analysis showed that DEGs mainly classified into10 groups, including metabolism, stress pathogen and defense, signal transduction, Transporter, transcription and post-transcription, cell structure and division etc. To further validate reliability and authenticity of the data, 10 DEGs were randomly picked and Real-time RT-PCR was carried out, and the expression trends of 7 genes were in line with the RNA-seq results. By searching the RBSDV related miRNA database of rice, 10 targeted genes of 6 significantly changed miRNAs were also identified in these DEGs. Conclusions: The data derived from RNA-seq were valid and credible. Through this research, a series of candidate RBSDV-responsive genes were obtained, and special signal transduction and metabolism pathways were built and pulled out in rice. This study provided further insight into the molecular mechanisms during compatible and incompatible interactions between viruses and their host plants.

scholarly journals Comparative Transcriptomic Analysis Revealed Complex Molecular Mechanisms Underlying Pests, Pathogens Resistance and Seed Development in Wild and Cultivated Blackgram

2020 ◽  
Author(s):  
Avi Raizada ◽  
Souframanien Jegadeesan
Keyword(s):  
Seed Development ◽  
Molecular Mechanisms ◽  
Callosobruchus Maculatus ◽  
Transmembrane Protein ◽  
Mosaic Disease ◽  
Molecular Networks ◽  
Wild Accession ◽  
Rna Seq ◽  
Legume Production ◽  
Related Proteins

AbstractBlackgram is a widely cultivated pulse crop in Asia. Bruchid pests and yellow mosaic disease (YMD) causes huge loss in legume production including blackgram. Blackgram wild accession (Vigna mungo var. silvestris), Trombay wild urd (INGR10133) conferred resistance to bruchids especially Callosobruchus maculatus, through antibiosis. However, the mechanisms still remains uncharacterized. We performed the comparative transcriptome analysis of the developing seeds of wild and cultivated blackgram with contrasting phenotypes for 3 traits, bruchids infestation, YMD and seed size. In this study,715differentially expressed genes(DEGs) were re-annotated with reference to NCBI nr database. RNA-Seq was validated by quantitative real-time PCR for 22 DEGs. In Trombay wild, defense related components such as acid phosphatase, vicilins, trypsin inhibitor, brassinosteroid signalling components were found up-regulated. While in cultivar, transcripts for LEA, cysteine protease, autophagy related proteins(ATG3, ATG5, ATG8C and ATG1t), DnaJ, tobamovirus multiplication protein, downy mildew resistance protein, LRR/F-box proteins were found up-regulated. In TW, three transcripts were found common for both bruchids pest and geminivirus resistance (LRR receptor kinase, transmembrane protein 87b and thaumatin like protein).Our study is the first report on transcriptomic differences between wild and cultivated blackgram with new insights into the molecular networks underlying seed development, resistance to pests and pathogens.

scholarly journals Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

2020 ◽  
Vol 21 (13) ◽  
pp. 4615 ◽  
Author(s):  
Weilong Kong ◽  
Chenhao Zhang ◽  
Yalin Qiang ◽  
Hua Zhong ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Stress Response ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Growth And Yield ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Stress Related Genes ◽  
Qtls Mapping

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

Sign in / Sign up

Export Citation Format

Share Document