scholarly journals In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control

2009 ◽  
Vol 25 (11) ◽  
pp. 1345-1348 ◽  
Author(s):  
Angelica Lindlöf ◽  
Marcus Bräutigam ◽  
Aakash Chawade ◽  
Olof Olsson ◽  
Björn Olsson
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
In Silico ◽  
Oryza Sativa L ◽  
In Silico Analysis ◽  
Promoter Regions ◽  
Combinatorial Control ◽  
Induced Genes ◽  
Silico Analysis

In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia

2009 ◽  
Vol 5 (5) ◽  
pp. 525 ◽  
Author(s):  
Ashutosh Kumar ◽  
Shuchi Smita ◽  
Neeti Sahu ◽  
Vivekanand Sharma ◽  
N.A. Shankaracharya ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Differentially Expressed Genes ◽  
In Silico ◽  
Oryza Sativa L ◽  
In Silico Analysis ◽  
Differentially Expressed ◽  
Silico Analysis

scholarly journals Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10053
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Libia Iris Trejo-Téllez ◽  
Atonaltzin García-Jiménez ◽  
Hugo Fernando Escobar-Sepúlveda ◽  
Sara Monzerrat Ramírez-Olvera
Keyword(s):  
Plant Growth ◽  
Plant Species ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Plant Tissues ◽  
Promoter Regions ◽  
Root Cells ◽  
Physiological Processes ◽  
Silico Analysis

Background Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data. Methods We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis. Results Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors. Conclusion Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

Appraisal of H2S metabolism in Arabidopsis thaliana: In silico analysis at the subcellular level

2020 ◽  
Vol 155 ◽  
pp. 579-588
Author(s):  
Salvador González-Gordo ◽  
José M. Palma ◽  
Francisco J. Corpas
Keyword(s):  
Arabidopsis Thaliana ◽  
In Silico ◽  
In Silico Analysis ◽  
Subcellular Level ◽  
Silico Analysis

scholarly journals In silico analysis of the fragrance gene (badh2) in Asian rice (Oryza sativa L.) germplasm and validation of allele specific markers

2020 ◽  
Vol 18 (2) ◽  
pp. 71-80
Author(s):  
Withanage Vidyani Erandika Withana ◽  
Rathanyaka Maudiyanselage Ramesha Eshani Kularathna ◽  
Nisha Sualri Kottearachchi ◽  
Deepthika S. Kekulandara ◽  
Jagath Weerasena ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
In Silico ◽  
Oryza Sativa L ◽  
Major Gene ◽  
In Silico Analysis ◽  
Betaine Aldehyde Dehydrogenase ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Asian Rice ◽  
Allele Specific

AbstractBadh2 of rice is considered to be the major gene responsible for the fragrance in rice. The wild type badh2 allele encodes betaine aldehyde dehydrogenase 2 (BADH2) enzyme while the mutated version of badh2 gene encodes non-functional BADH2 enzyme that leads to the accumulation of 2-acetyl-1-pyrroline (2AP), the principal fragrant compound in rice. There are many mutated recessive alleles causing fragrance in global rice germplasm, although the badh2.1 allele present in Basmati type rice is the most well-known among breeders. In this study, we attempted to reveal potential fragrance causing mutations, and the respective varieties carrying them, through in silico analysis based on the sequences available in the Rice SNP-Seek-Database of International Rice Research Institute. The sequences of 1878 rice accessions from 22 countries were analysed to identify mutations in each exon of badh2 comparatively with the non-fragrant ‘wildtype’ GenBank sequence in Nanjing11, Oryza sativa indica (EU770319.1). Results revealed that 63 varieties from 12 countries possessed the most prevalent allele, badh2.1 having an 8 bp deletion and three single nucleotide polymorphisms in the 7th exon. The second most prevalent allele in genotypes from Asia was badh2.7 having a ‘G’ insertion in the 14th exon. A novel allele with a T deletion in 9th exon was detected in a Thai rice accession. Rice varieties containing either badh2.1 or badh2.7 alleles could be identified with DNA markers for badh2.1 (frg) and badh2.7 (Bad2.7CAPS). The marker, Bad2.7CAPS, co-segregated with the fragrance phenotype in two crosses, confirming the possibility of employing it in marker assisted breeding.

Sign in / Sign up

Export Citation Format

Share Document