Research Paper
Proteomics
Maryam Jamshidnia; Sayed Kamal Kazemitabar; Christian Lindermayr; Hamid Najafi Zarini
Volume 6, Issue 16 , March 2017, Pages 1-12
Abstract
Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in ...
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Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in two species of tobacco plants (Nicotiana tabacum and Nicotiana bentamiana) by means of transient transformation. Specific primers were designed and used for PCR amplification and cloning of HDA19 gene in the plant expression vector pB2GW7. The recombinant construct was transferred into Agrobacterium tumefaciens strain GV3101, and was used for Agrobacterium mediated transformation of tobacco plants. The presence of the desired gene in transgenic lines was confirmed through colony PCR. The expression of the protein in transgenic lines was confirmed by immune-dot blot assay and ELISA. Although the transformation of the two species was confirmed by immune-dot blot assay and SDS-PAGE, recombinant protein production in Nicotiana tabacum plants was confirmed by ELISA and it was estimated 400 µg per gram wet weight of tobacco leaves. According to the results, this species is the appropriate host for the production of recombinant HDA19, one of the histone deacetylases, rather than Nicotiana bentamiana.
Research Paper
Bioinformatics
Amin Abedi; Reza Shirzadian-Khorramabad; Mohamad mehdi Sohani
Volume 6, Issue 16 , March 2017, Pages 13-29
Abstract
Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice ...
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Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice genome sequence completed, SSL genes were also identified in these plants. However, little is known about evolutionary path, gene structure, expansion and function of SSL family in rice. In this study, through bioinformatic analysis, a total of 23 SSL genes were identified in rice genome. A phylogenetic analysis of the SSL genes in rice and Arabidopsis clarified that these genes could be divided into four different groups and the evolutionary paths are different in rice and Arabidopsis. The OsSSL genes contained zero to five introns and were distributed across 10 out of 12 chromosomes at different densities and tandem duplication was a major cause in expanding this family. Promoter analysis showed the presence of several cis-regulatory elements related to stress and hormone response in regulatory region, indicating probable their role in stress response. Microarray-based expression analysis of OsSSL genes indicated that a few number of these genes were widely expressed in various tissues and also in response to some abiotic stresses. This study is the first report about SSL gene family in rice and provides a framework for further analysis of the biological functions of SSL genes in either rice or other crops.
Research Paper
Proteomics
Marouf Khalili; Mohammad Reza Naghavi
Volume 6, Issue 16 , March 2017, Pages 31-44
Abstract
In this research, proteome analysis was done by two-dimensional electrophoresis and stainig by Commassie brilliant blue method for two cultivars of Kavir as tolerant and Bahar as susceptible was done. After of be quantitative spots with Same spot progenesis software, 10 common protein spots with significant ...
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In this research, proteome analysis was done by two-dimensional electrophoresis and stainig by Commassie brilliant blue method for two cultivars of Kavir as tolerant and Bahar as susceptible was done. After of be quantitative spots with Same spot progenesis software, 10 common protein spots with significant difference between control and drought stress conditions in the Kavir and Bahar was diagnosed. Using MALDI-TOF/TOF mass spectrometry of common proteins, nine common protein spots were identified and the type of activity and mode of action of these proteins in the cells was determined. Based on the results, proteins involved in light reactions of photosynthesis (three protein spots Chlorophyll ab binding protein 8, chloroplastic, Cytochrome b6-f complex iron-sulfur subunit, chloroplasti and Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic) and Calvin cycle (two protein spots include Fructose-1,6-bisphosphatase, chloroplastic and ribulose-bisphosphate carboxylase small chain precursor) in both cultivars were the greatest functional groups and in other words, the most important common proteins for maintain of efficiency under drought stress were. Since these proteins in both tolerant and susceptible cultivars showed changes in expression, seems to be the most sensitive proteins in response to drought stress in wheat. In other words, these results show that it is important to maintain the efficiency of photosynthesis under drought stress.
Research Paper
Genomics
Atena Shadmehr; Hossein Ramshini; Mehrshad Zinalabedini; Masoud Parvizi Almani; MohammadReza Ghaffari; Aali Izadi darbandi; Maryam Farsi
Volume 6, Issue 16 , March 2017, Pages 45-59
Abstract
Considering the potential of sugarcane in terms of energy and sugar production the study of genetic diversity is the best way to use available genetic germplasm for breeding programs in this plant. Thirty microsatellite primer pairs were used to screen 160 varieties. In total 169 alleles were recorded ...
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Considering the potential of sugarcane in terms of energy and sugar production the study of genetic diversity is the best way to use available genetic germplasm for breeding programs in this plant. Thirty microsatellite primer pairs were used to screen 160 varieties. In total 169 alleles were recorded with an average of 5.6 alleles per locus. The number of effective alleles per locus was ranged from 1.06 (locus AP-SSR03) to 1.921 (locus SMC119CG) with an average of 1.508. The PIC value was variable ranging from 0.06 (for AP-SSR03) to 0.5 (for SMC851MS). The principal coordinate analysis (PCoA) revealed six groups, so that the first three axes explained 15.20% of cumulative variation altogether. Clustering analysis was done using Neihbour-Joining algorithm and population structure analysis was performed using Bayesian method. The best number of sub-populations was identified as six. The grouping of genotypes in the sub-populations was not in consistent with their geographic origins. The grouping obtained from Bayesian method, phylogenetic relatedness analysis results and principal coordinates analysis grouping showed good agreement with each other. Analysis of molecular variance revealed that variation within subgroups was significantly higher than that of among subgroups. So it will be better to do selection within populations in order to select suitable parents in sugarcane breeding programs. The knowledge obtained in this study would be useful for breeding programs to improve the conservation and management of this valuable genetic resource to meet the demand of sugarcane cultivation for sugar and bioenergy production.
Research Paper
Biotic and Abiotic stress
Amin Azadi; Mohsen Mardi; Eslam Majidi Harvan; Seyed Abolghasem Mohammadi; Foad Moradi
Volume 6, Issue 16 , March 2017, Pages 61-73
Abstract
So far, many quantitative trait loci (QTLs) have been detected for yield and its components in wheat under normal conditions. In order to identify QTLs associated with concentrations of sodium and potassium in bread wheat under salt stress conditions, a population consisted of 186 recombinant inbred ...
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So far, many quantitative trait loci (QTLs) have been detected for yield and its components in wheat under normal conditions. In order to identify QTLs associated with concentrations of sodium and potassium in bread wheat under salt stress conditions, a population consisted of 186 recombinant inbred lines from a cross between Roshan ×SuperHead#2 were evaluated. Salinity treatments were performed using a hydroponic system in a greenhouse. Normal conditions (10 mM NaCl) and salinity (150 mM NaCl) were considered and stress was conducted in stages. The molecular genetic map of the population consisted of 23 simple sequence repeat (SSR) and 428 diversity arrays technology (DArT) markers. Three QTLs for each of sodium and potassium concentration traits and a QTL for potassium to sodium ratio were detected on chromosomes 4A, 2B, 3B, 7B and 2D using composite interval mapping approach. The QNa.abrii-3B, with a LOD score of 5.9, explained 8.3 % of the phenotypic variation for sodium concentration under salt stress conditions and gwm247 marker showed a strong linkage with this QTL. In addition, two novel QTLs for sodium concentration were detected on chromosomes 2B and 2D and QNa.abrii-2D explained 9.2 % of the phenotypic variation for this trait under salt stress conditions. Proceed with future researches, there is probability of identifying QNa.abrii-2B and QNa.abrii-2D as two homoeologous group in wheat, beside Nax1 gene.
Research Paper
Molecular Plant Breeding
Ashkboos Amini; Habibollah Gazvini; Reza Amirnia
Volume 6, Issue 16 , March 2017, Pages 75-89
Abstract
In order to evaluate allelic diversity of microsatellite markers in QTL regions associated with salinity tolerance and to assess relatedness of these markers with yield performance of Iranian wheats under normal and salt stress conditions, twenty-five wheat genotypes (comprising tolerant and sensitive ...
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In order to evaluate allelic diversity of microsatellite markers in QTL regions associated with salinity tolerance and to assess relatedness of these markers with yield performance of Iranian wheats under normal and salt stress conditions, twenty-five wheat genotypes (comprising tolerant and sensitive Iranian landraces, commercial cultivars and breeding lines), were studied using 45 microsatellite primers. Results of yield mean comparison showed that there were significant differences among genotypes in both environmental conditions. Under stress conditions, genotypes no 25 (Pishtaz/Karchia) and 16 (Sissons/3/Alvd//Aldan/Ias58) had the highest and lowest grain yields, respectively. Based on grain yield mean under both stress and non-stress conditions as well as tolerance and susceptibility indices, the genotypes were classified into tolerant, moderately tolerant and sensitive groups. From 45 microsatellite primer pairs used, 27 markers were polymorphic. In total, these markers generated 95 alleles, from which 89 alleles were polymorphic, possessing 2-7 alleles with the average of 3.52 alleles per locus. The polymorphic information content (PIC) varied from 0.077 to 0.454 with the average of 0.258 and the Marker Index (MI) ranged from 0.151 to 1.19 with the average of 0.79 for different primers. Cluster analysis based on molecular data, could completely separate sensitive and tolerant genotypes and relatively was concordant with grouping of genotypes based on field results. Principal coordinate analysis (PCOA), mostly confirmed the results of cluster analysis. Results of molecular data demonstrated that SSR markers: gwm291, gpw345, wmc249, barc353.1, cfa2170.2, gwm339 and wmc326 had higher PIC & MI values and can be considered as suitable microsatellite markers to assess the genetic diversity among the wheat genotypes in salinity stress breeding programs.
