Research Paper
Bioinformatics
Manzar Heidari; Zahra-Sadat Shobbar; Parisa Koobaz; Mohammad javad Heydari
Volume 6, Issue 14 , August 2016, Pages 1-15
Abstract
Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. ...
Read More
Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. EST libraries data under normal and drought stress conditions were downloaded from NCBI databank. Preprocessing, clustering and assembly of the EST sequences were done using EGassembler software. Generated contig and singleton sequences were used as template for BLASTx analysis against rice protein database and functional category assignment using CLC Protein Workbench software and AgriGO. The identified proteins in the normal and drought libraries were allocated to 70 and 82 functional categories, respectively. IDEG6 were used to identify significant differences between functional categories in control and drought stress libraries. Gene ontology analysis, revealed significant differences in 20 groups of molecular function, 35 groups of biological processes and 12 groups of the intracellular components. In order to find the significant differential expression between the two libraries, 4012 ESTs with unigene accession numbers were implemented through applying an algorithm by MATLAB software and were analyzed by IDEG6 software, where 42 genes were found to be differentially expressed between drought and normal conditions (31 up-regulated and 11 down-regulated genes). The up-regulated genes were involved in environmental and oxidative stress response, homestasis, proteolysis and glycolysis, while photosynthesis related genes were down-regulated.
Research Paper
Biotic and Abiotic stress
Parviz Heidari
Volume 6, Issue 14 , August 2016, Pages 17-25
Abstract
Auxin is a central hormone that exerts pleiotropic effects on plant growth including the development of shoots, roots, and other organs under normal condition or stress. In this study, the transcripts change of AUX/IAA, ARF, BRX and PIN4 which involve in auxin transporter and signaling were evaluated ...
Read More
Auxin is a central hormone that exerts pleiotropic effects on plant growth including the development of shoots, roots, and other organs under normal condition or stress. In this study, the transcripts change of AUX/IAA, ARF, BRX and PIN4 which involve in auxin transporter and signaling were evaluated in root of tolerant and sensitive tomato genotypes under 15°C. AUX/IAA4 which is a negative regulator of auxin response genes was strongly up regulated in tolerant genotype at 15°C however, the transcript level of this gene was decreased in sensitive genotype. ARF and PIN4 were highly up regulated by suboptimal temperature in sensitive genotype whereas they were down regulated in tolerant genotype in recovery time (2 hours). The expression pattern of BREVIS RADIX (BRX) gene as a common point of interaction of auxin and brassinosteroids suggested that the BRX gene under sub optimal temperature in sensitive genotype was up regulated and reached the maximum level after 2h transfer to 23°C. The results of this study show that auxin concentration is increased in sensitive genotype and it induced the ARF, PIN4 and BRX whereas AUX/IAA4 was repressed. The results of common motifs in 1500 bp of upstream revealed that the AATAT motif of PRISM algorithm was frequency observed in all genes.
Research Paper
Molecular Plant Breeding
Habibollah Ghazvini; Mohsen Mohsen
Volume 6, Issue 14 , August 2016, Pages 27-42
Abstract
Stem rust of wheat caused by Puccinia graminis is known as one of the most important and prevalent diseases of wheat worldwide. Deployment of stem rust resistance genes such as Sr24, Sr26, Sr31, Sr36 and Sr38 in wheat cultivars in the last decades of 20th century dramatically reduced damaged caused by ...
Read More
Stem rust of wheat caused by Puccinia graminis is known as one of the most important and prevalent diseases of wheat worldwide. Deployment of stem rust resistance genes such as Sr24, Sr26, Sr31, Sr36 and Sr38 in wheat cultivars in the last decades of 20th century dramatically reduced damaged caused by this disease. One of the durable resistance genes that controlled stem rust during this period was Sr2 which has been transferred to bread wheat from Triticum turgidum. Sr2 is a non-race specific resistance gene with slow rusting effect which confers resistance at the adult plant stage. In recent years, molecular markers which are tightly linked to Sr2 have been identified and are widely used in many countries. In this study, presence/absence of Sr2 in some of the Iranian varieties and elite wheat lines was tested using a SSR marker gwm533, and a CAPS marker. Results indicated that from 188 studied genotypes, only 16 genotypes had linked alleles to Sr2 genes. Results of this study also showed that the newly identified CAPS marker is more precise marker compared to SSR marker gwm533 to detect Sr2 gene.
Research Paper
Molecular Plant Breeding
Khosro Mafakheri; Mohammad Reza Bihamta; Ali Reza Abbasi
Volume 6, Issue 14 , August 2016, Pages 43-60
Abstract
In the current investigation, 22 SSR primer pairs were used to identify molecular markers associated with morphological traits in cowpea (Vigna unguiculata L.) based association analysis, markers produced 186 locations in 32 cowpea genotypes. 22 SSR primers pair amplified 8.45 for each primer location ...
Read More
In the current investigation, 22 SSR primer pairs were used to identify molecular markers associated with morphological traits in cowpea (Vigna unguiculata L.) based association analysis, markers produced 186 locations in 32 cowpea genotypes. 22 SSR primers pair amplified 8.45 for each primer location and the average polymorphism information content (PIC) ranged from 0.445 to 0.25 (Vm25) and 0.625 (Vm5) were varied, respectively. Cluster analysis based on Dice, Jaccard and Simple Maching similarity coefficients based on molecular traits revealed primarily two major groups. Stepwise regression analysis between molecular data as independent variables, and morphological data as dependent variables was performed to identify informative markers associated with the studied traits. SSR loci associated with economic and biological yield, in normal conditions and in drought stress condition were Vm70 and Vm33, and Vm3 and Vm26 respectively. In drought stress condition the maximum variation of number of days to 50% flowering, days to 50% maturity of pods and pod length (99.9%, respectively) was accounted by Vm22, Vm31 and Vm26 markers. While in the normal condition the maximum variation of traits sheath thickness, width of pod and days to 50% flowering (99.9%) was accounted by Vm14, Vm34 and Vm34 markers. In both normal and drought conditions most of the used SSR primers showed significant association with the studied traits, so we can use these markers along with morphological traits in breeding cowpea genotypes to identify drought tolerant and hardy cultivars suitable for the preparation and use mapping populations.
Research Paper
Genomics
Faramarz Hoshyardel; Reza Darvishzadeh
Volume 6, Issue 14 , August 2016, Pages 61-72
Abstract
Tobacco (Nicotiana tabacum L.) is an industrial plant that play important role in economy of most countries. Oriental tobacco is a sun-cured, small-leafed, highly aromatic type of tobacco with limited information about its agronomic and chemical characteristics and their genetic control. This research ...
Read More
Tobacco (Nicotiana tabacum L.) is an industrial plant that play important role in economy of most countries. Oriental tobacco is a sun-cured, small-leafed, highly aromatic type of tobacco with limited information about its agronomic and chemical characteristics and their genetic control. This research was conducted to prepare the genetic linkage map of oriental type tobacco in a recombinant inbred line population (103 lines) produced from the cross between SPT406 (male parent) and Basma seres 31 (female parent) and identification of genomic locations controlling some agronomic characteristics accompanied with chlorine content under field conditions. Markers including SSR, ISSR, REMAP and IRAP were utilized in construction of genetic linkage map. Linkage map comprising 46 markers was developed which covered 586.1 cM of tobacco genome and the average distance between two markers was 12.74 cM. Number of markers per linkage groups varied between 2 to 13. In this study, 19 QTLs with phenotypic variation between 13.2 to 40.1 were identified for characteristics including leaf length, leaf width, leaf number, plant height, internode distance, stem girth, dry leaf yield, photosynthesis value and leaf chlorine content using composite interval mapping. Co-localized QTLs were recognized in linkage groups 1, 3 and 5. Highest values of phenotypic variation achieved in the present study manifest the possibility for using identified retrotransposon and microsatellite markers in marker assisted selection programs of oriental type tobacco.
Research Paper
Plant Disease and Biotechnology
Mohammad Amin Almasi
Volume 6, Issue 14 , August 2016, Pages 73-84
Abstract
Alfalfa mosaic virus (AMV) causing a disease in Alfalfa (Medicago sativa) crop in Iran has been identified on the basis of determination of symptom expression and morphological properties. There are several techniques to detect the virus including serological test and molecular methods. Reverse transcription ...
Read More
Alfalfa mosaic virus (AMV) causing a disease in Alfalfa (Medicago sativa) crop in Iran has been identified on the basis of determination of symptom expression and morphological properties. There are several techniques to detect the virus including serological test and molecular methods. Reverse transcription Loop-mediated isothermal amplification (RT-LAMP) assay is a novel technique for amplifying RNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency that is used in this study for detection of Alfalfa mosaic virus. Leaf samples (100 samples) with symptoms similar to AMV were collected from Hamedan and Kurdestan provinces and were subjected to a serological test. All four RT-LAMP reaction primers (i.e. F3, B3, FIP and BIP) together with RT-PCR reaction primers were designed on the basis of the highly conserved sequence of coat protein (CP) gene. Total RNA was extracted and molecular reactions were carried out and finally was detected six positive sampled The advantages of this new method in compare to other methods include the high specificity, high sensitivity, high rapidity, high efficiency, safety, fascinatingly, no requirement of expensive and tools for amplification, no post-amplification treatment of the amplicons, visual detection and user friendly.
