scholarly journals Genome-wide expression analysis identifies core components during iron starvation in hexaploid wheat

2019 ◽  
Author(s):  
Gazaldeep Kaur ◽  
Vishnu Shukla ◽  
Anil Kumar ◽  
Mandeep Kaur ◽  
Parul Goel ◽  
...  
Keyword(s):  
Hexaploid Wheat ◽  
Design Strategies ◽  
Glutathione S Transferase ◽  
Iron Starvation ◽  
Wheat Roots ◽  
Metal Transporters ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Yellow Stripe

AbstractIron is one of essential micronutrient for all organisms. Its deficiency causes a severe loss in crops yield. Nevertheless, our current understanding on major crops response to Fe deficiency remains limited. Herein, we investigated the effect of Fe deprivation at both transcriptomic and metabolic levels in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent, analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc-induced facilitator-like protein was noticed. Our transcriptomic data were in agreement with the GC-MS analysis that showed an enhancement of accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be linked for enhancing Fe-mobilization. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase both at transcriptional and enzymatic activity, which indicate the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops.

scholarly journals Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation

2019 ◽  
Vol 70 (21) ◽  
pp. 6141-6161 ◽  
Author(s):  
Gazaldeep Kaur ◽  
Vishnu Shukla ◽  
Anil Kumar ◽  
Mandeep Kaur ◽  
Parul Goel ◽  
...  
Keyword(s):  
Hexaploid Wheat ◽  
Activity Level ◽  
Fe Deficiency ◽  
Transcriptional Level ◽  
Glutathione S Transferase ◽  
Iron Starvation ◽  
Wheat Roots ◽  
Metal Transporters ◽  
Expression Of Genes ◽  
Yellow Stripe

Abstract Iron (Fe) is an essential micronutrient for all organisms. In crop plants, Fe deficiency can decrease crop yield significantly; however, our current understanding of how major crops respond to Fe deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic level in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differentially expressed. Homoeologue and subgenome-specific analysis unveiled the induction-biased contribution from the A and B genomes. In general, the predominance of genes coding for nicotianamine synthase, yellow stripe-like transporters, metal transporters, ABC transporters, and zinc-induced facilitator-like protein was noted. Expression of genes related to the Strategy II mode of Fe uptake was also predominant. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate, and xylofuranose, which could be contributing to Fe mobilization. Interestingly, Fe starvation leads to a significant temporal increase of glutathione S-transferase at both the transcriptional level and enzymatic activity level, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at the molecular level and lays the foundation to design new strategies for the improvement of Fe nutrition in crops.

Abstract 5340: Cardiac Resynchronization Therapy Corrects Dyssynchrony-induced Regional Gene Expression Changes on a Genomic Level

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Andreas S Barth ◽  
Takeshi Aiba ◽  
Victoria Halperin ◽  
Deborah DiSilvestre ◽  
Chakir Khalid ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cardiac Resynchronization Therapy ◽  
Cardiac Resynchronization ◽  
Functional Improvement ◽  
Large Animal ◽  
Atrial Pacing ◽  
Resynchronization Therapy ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding

Purpose: Cardiac Resynchronization Therapy (CRT) improves symptoms and reduces mortality in patients with heart failure (HF). To characterize the molecular processes associated with functional improvement in CRT, we used a genomic approach in a large animal HF model. Methods: After creation of a left bundle branch block (LBBB), dogs in the HF group were subjected to either rapid atrial pacing with 200 bpm for 6 weeks (dyssynchronous HF, DHF, n=10), or 3 weeks of atrial pacing followed by 3 weeks of biventricular stimulation at 200bpm (CRT, n=9). Control animals without LBBB were not paced (NF, n=11). After 6 weeks, RNA from anterior and lateral regions of the LV was hybridized onto canine 44K arrays. Statistical Analysis of Microarrays (SAM) was used for data analysis. Results: Echocardiographically, CRT led to a significant increase in stroke volume (+27%, p=0.03) which translated into a non-significant increase in EF (DHF 25±4%; CRT 31±3% (p=0.15); NF 67±3%). A multiclass analysis of NF, DHF and CRT animals identified 1050 differentially expressed transcripts between anterior and lateral walls with a false discovery rate of 5%. For all these transcripts, dyssynchrony-induced expression changes were reversed by CRT to levels of NF hearts. As a result, CRT samples clustered with NF rather than DHF samples. Of particular interest were genes encoding for signal transduction pathways and contractile processes. Conclusions: By using a whole genome approach, we demonstrate a profound effect of electrical activation on the regional cardiac transcriptome. This is the first study showing that dyssynchrony-induced gene expression changes can be corrected by CRT on a genome-wide level.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast

2008 ◽  
Vol 7 (3) ◽  
pp. 493-508 ◽  
Author(s):  
Alexandre Mercier ◽  
Stephen Watt ◽  
Jürg Bähler ◽  
Simon Labbé
Keyword(s):  
Iron Deficiency ◽  
Fission Yeast ◽  
Tricarboxylic Acid Cycle ◽  
Transcriptional Level ◽  
Mrna Levels ◽  
Gata Factor ◽  
Iron Starvation ◽  
A Genome ◽  
Binding Factor ◽  
Genes Encoding

ABSTRACT The fission yeast Schizosaccharomyces pombe responds to the deprivation of iron by inducing the expression of the php4 + gene, which encodes a negative regulatory subunit of the heteromeric CCAAT-binding factor. Once formed, the Php2/3/4/5 transcription complex is required to inactivate a subset of genes encoding iron-using proteins. Here, we used a pan-S. pombe microarray to study the transcriptional response to iron starvation and identified 86 genes that exhibit php4 + -dependent changes on a genome-wide scale. One of these genes encodes the iron-responsive transcriptional repressor Fep1, whose mRNA levels were decreased after treatment with the permeant iron chelator 2,2′-dipyridyl. In addition, several genes encoding the components of iron-dependent biochemical pathways, including the tricarboxylic acid cycle, mitochondrial respiration, amino acid biosynthesis, and oxidative stress defense, were downregulated in response to iron deficiency. Furthermore, Php4 repressed transcription when brought to a promoter using a yeast DNA-binding domain, and iron deprivation was required for this repression. On the other hand, Php4 was constitutively active when glutathione levels were depleted within the cell. Based on these and previous results, we propose that iron-dependent inactivation of Php4 is regulated at two distinct levels: first, at the transcriptional level by the iron-responsive GATA factor Fep1 and second, at the posttranscriptional level by a mechanism yet to be identified, which inhibits Php4-mediated repressive function when iron is abundant.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

2020 ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background: The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results: A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear ( Pyrus bretschneideri ) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions: This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals A genome-wide survey of DNA methylation in hexaploid wheat

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Laura-Jayne Gardiner ◽  
Mark Quinton-Tulloch ◽  
Lisa Olohan ◽  
Jonathan Price ◽  
Neil Hall ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Hexaploid Wheat ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

A Genome-Wide Survey of Genes Encoding Transcription Factors in Japanese Pearl Oyster Pinctada fucata: II. Tbx, Fox, Ets, HMG, NFκ;B, bZIP, and C2H2 Zinc Fingers

2013 ◽  
Vol 30 (10) ◽  
pp. 858 ◽  
Author(s):  
Hiroyuki Koga ◽  
Naoki Hashimoto ◽  
Daichi G. Suzuki ◽  
Hiroki Ono ◽  
Miho Yoshimura ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Fingers ◽  
Pearl Oyster ◽  
Pinctada Fucata ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Genome-wide analysis of oligopeptide transporters and detailed characterization of yellow stripe transporter genes in hexaploid wheat

2018 ◽  
Vol 19 (1) ◽  
pp. 75-90 ◽  
Author(s):  
Anil Kumar ◽  
Gazaldeep Kaur ◽  
Parul Goel ◽  
Kaushal Kumar Bhati ◽  
Mandeep Kaur ◽  
...  
Keyword(s):  
Hexaploid Wheat ◽  
Detailed Characterization ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Yellow Stripe

scholarly journals Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using GWAS

2020 ◽  
Author(s):  
Lingqiang Wang ◽  
Ali Muhammad ◽  
Weicheng Hu ◽  
Jinsheng Yu ◽  
Shahid Ullah Khan ◽  
...  
Keyword(s):  
Plant Height ◽  
Hexaploid Wheat ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Significant Snps ◽  
Leaf Length ◽  
Genome Wide ◽  
A Genome ◽  
Multiple Environments ◽  
Architectural Traits

Abstract Background: Wheat is a staple food crop worldwide. Plant height is a key factor in plant architecture as it plays a crucial role in lodging and thus affects yield and quality. Genome-wide studies are mostly applied in crop plants, due to its advanced genotyping technologies, identification of novel loci, and improved statistical approaches. Results: In this study, the population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by four ML-GWAS and three SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were commonly detected, including seven across multiple environments and thirty-six across multiple methods. Interestingly, five most stable SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, possibly played a role in modulating plant height and flag leaf length. When comparing ML-GWAS methods, pLARmEB was the most powerful and accountable for the detection of 49 significant SNPs that mostly contributed to plant height (36 SNPs). However, in SL-GWAS the FarmCPU model detected most of the significant SNPs. Moreover, a total of 152 candidate genes were found that are likely to be involved in plant growth and development which may provide insightful information related to plant architectural traits.Conclusion: Altogether, our results reveal 174 and 97 significant SNPs controlling plant architectural traits using four ML-GWAS and three SL-GWAS methods, respectively. The detection of the stable loci across multiple environments and methods, possibly play a role in modulating plant architectural traits in hexaploid wheat, and finally will contribute to the discovery of valuable SNP loci for marker-assisted selection (MAS) in wheat molecular breeding.

scholarly journals Complete Metamorphosis in Manduca sexta Involves Specific Changes in DNA Methylation Patterns

2021 ◽  
Vol 9 ◽  
Author(s):  
Jasmin Gegner ◽  
Heiko Vogel ◽  
André Billion ◽  
Frank Förster ◽  
Andreas Vilcinskas
Keyword(s):  
Dna Methylation ◽  
Manduca Sexta ◽  
Histone Deacetylases ◽  
Transcriptional Reprogramming ◽  
Evolution And Development ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Methylation Patterns ◽  
Complete Metamorphosis

The transition between morphologically distinct phenotypes during complete metamorphosis in holometabolous insects is accompanied by fundamental transcriptional reprogramming. Using the tobacco hornworm (Manduca sexta), a powerful model for the analysis of insect evolution and development, we conducted a genome-wide comparative analysis of gene expression and DNA methylation in caterpillars and adults to determine whether complete metamorphosis has an epigenetic basis in this species. Bisulfite sequencing indicated a generally low level of DNA methylation with a unimodal CpGO/E distribution. Expression analysis revealed that 24 % of all known M. sexta genes (3.729) were upregulated in last-instar larvae relative to the adult moth, whereas 26 % (4.077) were downregulated. We also identified 4.946 loci and 4.960 regions showing stage-specific differential methylation. Interestingly, genes encoding histone acetyltransferases and histone deacetylases were differentially methylated in the larvae and adults, indicating there is crosstalk between different epigenetic mechanisms. The distinct sets of methylated genes in M. sexta larvae and adults suggest that complete metamorphosis involves epigenetic modifications associated with profound transcriptional reprogramming, involving approximately half of all the genes in this species.

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