scholarly journals Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

2017 ◽  
Vol 7 ◽  
Author(s):  
Abhishek Bhandawat ◽  
Gagandeep Singh ◽  
Romit Seth ◽  
Pradeep Singh ◽  
Ram K. Sharma
Keyword(s):  
Transcriptional Profiling ◽  
Bud Burst ◽  
Dendrocalamus Hamiltonii ◽  
Genome Wide

scholarly journals Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts

2014 ◽  
Vol 5 ◽  
Author(s):  
Barbara Blanco-Ulate ◽  
Abraham Morales-Cruz ◽  
Katherine C. H. Amrine ◽  
John M. Labavitch ◽  
Ann L. T. Powell ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Plant Cell ◽  
Cell Walls ◽  
Transcriptional Profiling ◽  
Plant Cell Walls ◽  
Genome Wide

scholarly journals A description of large-scale metabolomics studies: increasing value by combining metabolomics with genome-wide SNP genotyping and transcriptional profiling

2012 ◽  
Vol 215 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Georg Homuth ◽  
Alexander Teumer ◽  
Uwe Völker ◽  
Matthias Nauck
Keyword(s):  
Blood Cells ◽  
Large Scale ◽  
Genetic Factors ◽  
Association Studies ◽  
Transcriptional Profiling ◽  
Genome Wide Association Studies ◽  
Protein Levels ◽  
Future Developments ◽  
Genome Wide ◽  
Metabolome Data

The metabolome, defined as the reflection of metabolic dynamics derived from parameters measured primarily in easily accessible body fluids such as serum, plasma, and urine, can be considered as the omics data pool that is closest to the phenotype because it integrates genetic influences as well as nongenetic factors. Metabolic traits can be related to genetic polymorphisms in genome-wide association studies, enabling the identification of underlying genetic factors, as well as to specific phenotypes, resulting in the identification of metabolome signatures primarily caused by nongenetic factors. Similarly, correlation of metabolome data with transcriptional or/and proteome profiles of blood cells also produces valuable data, by revealing associations between metabolic changes and mRNA and protein levels. In the last years, the progress in correlating genetic variation and metabolome profiles was most impressive. This review will therefore try to summarize the most important of these studies and give an outlook on future developments.

scholarly journals Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex

2017 ◽  
Author(s):  
Abraham Morales-Cruz ◽  
Gabrielle Allenbeck ◽  
Rosa Figueroa-Balderas ◽  
Vanessa E. Ashworth ◽  
Daniel P. Lawrence ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Transcriptional Profiling ◽  
Underlying Disease ◽  
In Planta ◽  
Dna And Rna ◽  
Trunk Disease ◽  
Specificity And Sensitivity ◽  
Genome Wide ◽  
Field Samples ◽  
Trunk Diseases

SummaryGrapevines, like other perennial crops, are affected by so-called ‘trunk diseases’, which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e., metatranscriptomics) approach that can monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for mapping and quantifying DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally-infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.

scholarly journals Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

2021 ◽  
Author(s):  
Caijing Li ◽  
Jindong Liu ◽  
Jianxin Bian ◽  
Tao Jin ◽  
Baoli Zou ◽  
...  
Keyword(s):  
Low Temperature ◽  
Association Study ◽  
Cold Tolerance ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

scholarly journals Genome-wide identification and transcriptional analyses of MATE transporter genes in root tips of wild Cicer spp. under aluminium stress

2020 ◽  
Author(s):  
Xia Zhang ◽  
Brayden Weir ◽  
Hongru Wei ◽  
Zhiwei Deng ◽  
Xiaoqi Zhang ◽  
...  
Keyword(s):  
Root Growth ◽  
Root Elongation ◽  
Transcriptional Profiling ◽  
Functional Characterization ◽  
Relative Reduction ◽  
Root Tips ◽  
Al Tolerance ◽  
Genome Wide ◽  
Encoding Genes ◽  
Al Treatment

AbstractChickpea is an economically important legume crop with high nutritional value in human diets. Aluminium-toxicity poses a significant challenge for the yield improvement of this increasingly popular crop in acidic soils. The wild progenitors of chickpea may provide a more diverse gene pool for Al-tolerance in chickpea breeding. However, the genetic basis of Al-tolerance in chickpea and its wild relatives remains largely unknown. Here, we assessed the Al-tolerance of six selected wild Cicer accessions by measuring the root elongation in solution culture under control (0 µM Al3+) and Al-treatment (30 µM Al3+) conditions. Al-treatment significantly reduced the root elongation in all target lines compared to the control condition after 2-day’s growth. However, the relative reduction of root elongation in different lines varied greatly: 3 lines still retained significant root growth under Al-treatment, whilst another 2 lines displayed no root growth at all. We performed genome-wide identification of multidrug and toxic compound extrusion (MATE) encoding genes in the Cicer genome. A total of 56 annotated MATE genes were identified, which divided into 4 major phylogeny groups (G1-4). Four homologues to lupin LaMATE (> 50% aa identity; named CaMATE1-4) were clustered with previously characterised MATEs related to Al-tolerance in various other plants. qRT-PCR showed that CaMATE2 transcription in root tips was significantly up-regulated upon Al-treatment in all target lines, whilst CaMATE1 was up-regulated in all lines except Bari2_074 and Deste_064, which coincided with the lines displaying no root growth under Al-treatment. Transcriptional profiling in five Cicer tissues revealed that CaMATE1 is specifically transcribed in the root tissue, further supporting its role in Al-detoxification in roots. This first identification of MATE-encoding genes associated with Al-tolerance in Cicer paves the ways for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.

scholarly journals Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dan Wang ◽  
Zhuo Liu ◽  
Yinghui Xiao ◽  
Xionglun Liu ◽  
Yue Chen ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Gene Knockout ◽  
Micro Rna ◽  
Negative Regulator ◽  
Bud Burst ◽  
Rab Protein ◽  
Genome Wide ◽  
Direct Seeded

AbstractCold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.

scholarly journals Post-trauma behavioral phenotype predicts vulnerability to fear relapse after extinction

2021 ◽  
Author(s):  
Fanny Demars ◽  
Ralitsa Todorova ◽  
Gabriel Makdah ◽  
Antonin Forestier ◽  
Marie-Odile Krebs ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Psychiatric Patients ◽  
Transcriptional Profiling ◽  
Behavioral Assessment ◽  
Trauma Recovery ◽  
Genome Wide ◽  
Differential Vulnerability ◽  
Response Profiles ◽  
Automated Pipeline ◽  
Post Therapy

Current treatments for trauma-related disorders remain ineffective for many patients. Here, we modeled interindividual differences in post-therapy fear relapse with a novel ethologically relevant trauma recovery paradigm. After traumatic fear conditioning, rats underwent fear extinction while foraging in a large enriched arena, permitting the expression of a wide spectrum of behaviors, assessed by an automated pipeline. This multidimensional behavioral assessment revealed that post-conditioning fear response profiles clustered into two groups, respectively characterized by active vs. passive fear responses. After trauma, some animals expressed fear by freezing, while others darted, as if fleeing from danger. Remarkably, belonging to the darters or freezers group predicted differential vulnerability to fear relapse after extinction. Moreover, genome-wide transcriptional profiling revealed that these groups differentially regulated specific sets of genes, some of which have previously been implicated in anxiety and trauma-related disorders. Our results suggest that post-trauma behavioral phenotypes and the associated epigenetic landscapes can serve as markers of fear relapse susceptibility, and thus may be instrumental for future development of more effective treatments for psychiatric patients.

scholarly journals Molecular patterning of the embryonic cranial mesenchyme revealed by genome-wide transcriptional profiling

2019 ◽  
Vol 455 (2) ◽  
pp. 434-448 ◽  
Author(s):  
Krishnakali Dasgupta ◽  
Jong Uk Chung ◽  
Kesava Asam ◽  
Juhee Jeong
Keyword(s):  
Transcriptional Profiling ◽  
Molecular Patterning ◽  
Genome Wide
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