scholarly journals EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

2016 ◽  
Vol 28 (10) ◽  
pp. 2365-2384 ◽  
Author(s):  
Olivia Wilkins ◽  
Christoph Hafemeister ◽  
Anne Plessis ◽  
Meisha-Marika Holloway-Phillips ◽  
Gina M. Pham ◽  
...  
Keyword(s):  
High Temperature ◽  
Water Deficit ◽  
Regulatory Influence ◽  
Gene Regulatory ◽  
Influence Networks ◽  
Response To Water

scholarly journals Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments

2016 ◽  
Author(s):  
Olivia Wilkins ◽  
Christoph Hafemeister ◽  
Anne Plessis ◽  
Meisha-Marika Holloway-Phillips ◽  
Gina M. Pham ◽  
...  
Keyword(s):  
Water Deficit ◽  
Target Genes ◽  
Component Analysis ◽  
Field Conditions ◽  
Network Component Analysis ◽  
Regulatory Influence ◽  
Putative Target ◽  
Gene Regulatory ◽  
Influence Networks ◽  
Network Component

ABSTRACTEnvironmental Gene Regulatory Influence Networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental and developmental signals. EGRINs encompass many layers of regulation, which culminate in changes in the level of accumulated transcripts. Here we infer EGRINs for the response of five tropical Asian rice cultivars to high temperatures, water deficit, and agricultural field conditions, by systematically integrating time series transcriptome data (720 RNA-seq libraries), patterns of nucleosome-free chromatin (18 ATAC-seq libraries), and the occurrence of known cis-regulatory elements. First, we identify 5,447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes with known cis-regulatory motifs in nucleosome-free chromatin regions proximal to transcriptional start sites (TSS) of genes. We then use network component analysis to estimate the regulatory activity for these TFs from the expression of these putative target genes. Finally, we inferred an EGRIN using the estimated TFA as the regulator. The EGRIN included regulatory interactions between 4,052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of a large TF family, including a putative regulatory connection between abiotic stress and the circadian clock, as well as specific regulatory functions for TFs in the drought response. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference and that supplementing data from controlled experimental conditions with data from outdoor field conditions increases the resolution for EGRIN inference.

scholarly journals Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Massimiliano Trenti ◽  
Silvia Lorenzi ◽  
Pier Luigi Bianchedi ◽  
Daniele Grossi ◽  
Osvaldo Failla ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stomatal Conductance ◽  
Candidate Genes ◽  
Water Deficit ◽  
Genetic Basis ◽  
Phenotypic Diversity ◽  
Snp Array ◽  
A Genome ◽  
Raffinose Synthase ◽  
Response To Water

Abstract Background Understanding the complexity of the vine plant’s response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an ‘ad hoc’ association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit. Results In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance. Conclusions Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula

Planta ◽  
2009 ◽  
Vol 231 (3) ◽  
pp. 705-716 ◽  
Author(s):  
Inês Trindade ◽  
Cláudio Capitão ◽  
Tamas Dalmay ◽  
Manuel Pedro Fevereiro ◽  
Dulce Metelo dos Santos
Keyword(s):  
Water Deficit ◽  
Medicago Truncatula ◽  
Response To Water
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