Molecular Genetics and Genetic Engineering
Seyede mehri Javadi; Zahra-Sadat Shobbar; Asa Ebrahimi; Maryam Shahbazi
Abstract
Drought is the most important environmental stress that reduces crop yield. Therefore, research toward developing tolerant varieties is of great importance. In this study, microarray data analysis was used for identification of drought stress responsive genes and relevant hub genes in the reproductive ...
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Drought is the most important environmental stress that reduces crop yield. Therefore, research toward developing tolerant varieties is of great importance. In this study, microarray data analysis was used for identification of drought stress responsive genes and relevant hub genes in the reproductive stage of barley, and then their promoter analysis was performed. To achieve the goal, all the differentially expressed genes (DEGs) at drought conditions with fold changes ≥+2.5 and ≤-2.5 were identified between two microarray data-series in barley using FlexArray software. Bioinformatics analysis indicated that 559 genes were drought responsive at reproductive stage. The hub genes were distinguished using three Cyto-Hubba computational algorithms by Cytoscape software. Based on the hub analysis results, 10 unique (non-redundant) genes were identified as the most effective genes in response to drought stress. According to the gene ontology analysis of DEGs and hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) at drought tolerance mechanism. Amongst the hubs, several TFs such as HvCBF6, HvDRF1.3, LFL1, VP1, ABI5 and WRKY71 genes (belonged to AP2, WRKY and bZIP families) were observed. Promoter analysis was also revealed that some TF families including AP2, AT-hook family, bHLH, NAC, bZIP and MYB had binding site in 85% of promoters of the drought responsive genes and the hub genes in barley. Studying these transcription factors can help in better identification of drought tolerance mechanism in barley.
Bioinformatics
Khazar Edrisi Maryan; Habibollah Samizadeh Lahiji; Hassan Hasani Komeleh; Naser Farrokhi
Abstract
Low temperature is an important abiotic stress limiting the production and geographical dispersion of many crops, including rapeseed, as an important oil crop. In this study, known cis-elements regulating molecular responses of plant to cold stress were used to identify genes involved in cold tolerance. ...
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Low temperature is an important abiotic stress limiting the production and geographical dispersion of many crops, including rapeseed, as an important oil crop. In this study, known cis-elements regulating molecular responses of plant to cold stress were used to identify genes involved in cold tolerance. From 62,384 Unigenes from Brassica Genome Gateway, 56 cold responsive genes were identified. Promoter analysis, gene ontology enrichment, co-occurrence, protein- protein interaction and in silico gene expression analysis were performed to validate the results of gene identification. The results showed known cis-element appearance in promoter region of all identified genes which involved in different biological pathways such as Calvin cycle, respiration and signal transduction in different cell parts. Co-occurrence study of identified genes illustrated mutual connections of genes with correlations above 0.64. Promoter analysis, PPI network and investigating transcription factors involved in transcription regulation of 56 identified genes and 98 co-expressed genes indicated the molecular mechanisms and similar pathways of plant response to cold and introduce candidate genes to be used in breeding and genetic engineering programs.
Biotic and Abiotic stress
Marjan Bahrabadi; Farhad Shokouhifar; Mohammad Ali Ebrahimi
Volume 4, Issue 6 , October 2014, , Pages 11-20
Abstract
Synthetic pathogen-inducible promoters are suitable alternatives for native promoters in plant genetic manipulation to the purpose of resistant crop production. An ideal pathogen-inducible promoter would only be activated in response to target pathogens. Furthermore, it should express the transgene locally ...
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Synthetic pathogen-inducible promoters are suitable alternatives for native promoters in plant genetic manipulation to the purpose of resistant crop production. An ideal pathogen-inducible promoter would only be activated in response to target pathogens. Furthermore, it should express the transgene locally and temporarily. The absence of these characteristics in native promoters have drawn the attentions toward design and construction of synthetic promoters. Some components like cis-regulatory elements are used in construction of synthetic promoters and this provides high flexibility in determining the expression quantity and the inducibility type. One of the most common methods for a synthetic inducible promoter analysis is using Agrobacterium-mediated transient expression system. With this method, Functional analysis of the promoter can be performed in a short time by application of biotic and abiotic treatments and assaying the transgene expression. In this study, the SP-DD synthetic pathogen inducible promoter (containing of two copies of Box D cis-element derived from parsley PR2 promoter) fused with an intron-containing ß-glucuronidase reporter gene was transferred to tobacco leaves (Nicotiana benthamiana) by agroinjection. The promoter function was evaluated in response to salicylic acid treatment and environmental stresses like heat, cold and UV radiation. The results showed that the SP-DD synthetic promoter induced the ß-glucuronidase gene expression in response to salicylic acid and the expression amount increased over time from 2 hours to 24 hours post applicaion. Besides, the promoter showed slight sensitivity in response to heat and cold stresses but the ultraviolet radiation stress had no effect on the promoter induction.
